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A

a - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
a - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
a - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
a - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
a - Variable in class org.jmol.jvxl.readers.MapFileReader
 
a - Variable in class org.jmol.minimize.forcefield.Calculation
 
a - Variable in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
a - Variable in class org.jmol.util.SimpleUnitCell
 
A0 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
a1 - Variable in class org.jmol.g3d.Hermite3D
 
a2 - Variable in class org.jmol.g3d.Hermite3D
 
a_ - Variable in class org.jmol.util.SimpleUnitCell
 
a_count - Variable in class org.jmol.export.image.GifEncoder
 
aa - Variable in class org.jmol.modelset.Measurement
 
aa - Variable in class org.jmol.shapebio.BioShapeRenderer
 
AANscale(double[], int[], int) - Static method in class org.jmol.util.DCT
 
AANscaleFactor - Static variable in class org.jmol.util.DCT
 
aaPlus - Static variable in class org.jmol.viewer.JmolConstants
 
aaRet - Variable in class org.jmol.modelset.AtomCollection
 
aaSp2 - Static variable in class org.jmol.viewer.JmolConstants
 
aaStep - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
aaStepCenter - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
aaStepNavCenter - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
aaT - Variable in class org.jmol.shape.MeasuresRenderer
 
aaTest1 - Variable in class org.jmol.viewer.TransformManager
 
aatoken - Variable in class org.jmol.script.ScriptContext
 
aatoken - Variable in class org.jmol.script.ScriptEvaluator
 
aatoken - Variable in class org.jmol.script.ScriptFunction
 
aatokenCompiled - Variable in class org.jmol.script.ScriptCompiler
 
aaTotal - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
abc - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
abNo - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
aboutComputedMenuBaseCount - Variable in class org.jmol.popup.JmolPopup
 
AboutDialog - Class in org.openscience.jmol.app.jmolpanel
 
AboutDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
 
AboutDialog.PageLoader - Class in org.openscience.jmol.app.jmolpanel
temporary class that loads synchronously (although later than the request so that a cursor change can be done).
AboutDialog.PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog.PageLoader
 
abs - Static variable in class org.jmol.script.Token
 
absolute - Static variable in class org.jmol.script.Token
 
ABSOLUTE_MIN_MESH_SIZE - Static variable in class org.jmol.shapebio.BioShapeRenderer
 
absoluteButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
abYes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
AC_matrix - Variable in class org.jmol.util.Huffman
 
AC_matrix0 - Variable in class org.jmol.util.Huffman
 
AC_matrix1 - Variable in class org.jmol.util.Huffman
 
acc - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
accept(File, String) - Method in class org.jmol.console.JmolConsole.FileChecker
 
accept(File) - Method in class org.jmol.export.dialog.Dialog.TypeFilter
 
acceptsStringParameter(String) - Static method in class org.jmol.viewer.PropertyManager
 
accum - Variable in class org.jmol.export.image.GifEncoder
 
accumulate - Variable in class org.jmol.export.image.ImageEncoder
 
accumulator - Variable in class org.jmol.export.image.ImageEncoder
 
acos - Static variable in class org.jmol.script.Token
 
ACtableNumber - Variable in class org.jmol.util.JpegInfo
 
action - Variable in class org.jmol.viewer.ActionManager.Gesture
 
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
ACTION_assignNew - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_center - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_clickFrank - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_connectAtoms - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_count - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_deleteAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_deleteBond - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_depth - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragDrawObject - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragDrawPoint - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragLabel - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragMinimize - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragMinimizeMolecule - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragSelected - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragZ - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_multiTouchSimulation - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_navTranslate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickIsosurface - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickLabel - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickMeasure - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickNavigate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickPoint - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_popupMenu - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_reset - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateBranch - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateSelected - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateZ - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateZorZoom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_select - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectAndDrag - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectAndNot - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectNone - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectOr - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectToggle - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectToggleExtended - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_setMeasure - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slab - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slabAndDepth - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slideZoom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_spinDrawObjectCCW - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_spinDrawObjectCW - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_stopMotion - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_swipe - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_translate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_wheelZoom - Static variable in class org.jmol.viewer.ActionManager
 
actionInfo - Static variable in class org.jmol.viewer.ActionManager
 
actionManager - Variable in class org.jmol.awt.Mouse
 
actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
ActionManager - Class in org.jmol.viewer
 
ActionManager() - Constructor for class org.jmol.viewer.ActionManager
 
actionManager - Variable in class org.jmol.viewer.Viewer
 
ActionManager.Gesture - Class in org.jmol.viewer
 
ActionManager.Gesture(int) - Constructor for class org.jmol.viewer.ActionManager.Gesture
 
ActionManager.HoverWatcher - Class in org.jmol.viewer
 
ActionManager.HoverWatcher() - Constructor for class org.jmol.viewer.ActionManager.HoverWatcher
 
ActionManager.MotionPoint - Class in org.jmol.viewer
 
ActionManager.MotionPoint() - Constructor for class org.jmol.viewer.ActionManager.MotionPoint
 
ActionManager.Mouse - Class in org.jmol.viewer
 
ActionManager.Mouse(int) - Constructor for class org.jmol.viewer.ActionManager.Mouse
 
ActionManager.TimeoutThread - Class in org.jmol.viewer
 
ActionManager.TimeoutThread(String, int, String) - Constructor for class org.jmol.viewer.ActionManager.TimeoutThread
 
ActionManagerMT - Class in org.jmol.multitouch
 
ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
 
actionNames - Static variable in class org.jmol.viewer.ActionManager
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
 
actionPerformed(ActionEvent) - Method in class org.jmol.popup.SimplePopup.MenuItemListener
 
actionPerformed(ActionEvent) - Method in class org.openscience.chimetojmol.ChimePanel
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Molecules
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Orbitals
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Test
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
actionRotateBond(int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
actionStates - Variable in class org.jmol.viewer.Viewer
 
actionStatesRedo - Variable in class org.jmol.viewer.Viewer
 
activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
active - Variable in class org.jmol.export.dialog.FilePreview
 
actualID - Variable in class org.jmol.shapesurface.Isosurface
 
adapter - Variable in class org.jmol.multitouch.ActionManagerMT
 
adapterModelCount - Variable in class org.jmol.modelset.ModelLoader
 
adapterName - Variable in class org.jmol.api.JmolAdapter
 
adapterTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
 
add - Static variable in class org.jmol.script.Token
 
add(float) - Method in class org.jmol.util.Quaternion
 
add(int, int, int, long) - Method in class org.jmol.viewer.ActionManager.Gesture
 
ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JmolConstants
 
addAllPixels - Variable in class org.jmol.g3d.Graphics3D
 
addAllPixels - Variable in class org.jmol.g3d.Sphere3D
 
addAllTriangles() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addAtom(Atom) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
addAtom() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtom(int, Group, short, String, int, int, float, float, float) - Method in class org.jmol.modelset.ModelCollection
 
addAtom(int, Group, short, String, int, int, float, float, float, float, float, float, float, int, float, int, float, Object[], boolean, char, byte, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
addAtom(boolean, BitSet, int, Object, short, String, int, float, Object[], int, float, float, float, float, boolean, int, String, float, float, float, char, float) - Method in class org.jmol.modelset.ModelLoader
 
addAtom() - Method in class org.jmol.smiles.SmilesSearch
 
addAtomOr() - Method in class org.jmol.smiles.SmilesAtom
 
addAtoms(BitSet) - Method in interface org.jmol.api.AtomIndexIterator
 
addAtoms(BitSet) - Method in class org.jmol.modelset.AtomIteratorWithinModel
turns this into a SPHERICAL iterator for "within Distance" measures
addAtoms(int) - Method in class org.jmol.modelset.Group
 
addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAttr() - Method in class org.jmol.export._MayaExporter
 
addAttrib(List<String[]>, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
addAxis(int, Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
addBinding(String, Object) - Method in class org.jmol.viewer.binding.Binding
 
addBioPolymerToModel(Polymer, Model) - Method in class org.jmol.modelset.ModelCollection
 
addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addBond(SmilesBond) - Method in class org.jmol.smiles.SmilesAtom
Add a bond to the atom.
addBondOr() - Method in class org.jmol.smiles.SmilesBond
 
addBonds(String, int) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
addBondToAtom(Atom, Bond) - Method in class org.jmol.modelset.BondCollection
 
addBoundBoxPoint(Point3f) - Method in class org.jmol.util.BoxInfo
 
addBracketedBioName(StringBuffer, JmolNode, String) - Method in class org.jmol.smiles.SmilesGenerator
 
addBridge(AminoPolymer.Bridge, Map<int[][], Boolean>) - Method in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
addBs(StringBuffer, String, BitSet) - Static method in class org.jmol.viewer.SelectionManager
 
addBundle(String, String) - Method in class org.jmol.i18n.GT
 
addBundles(String, String, String, String) - Method in class org.jmol.i18n.GT
 
addBytes(byte[], int, int) - Method in class org.jmol.util.ZipUtil.GZipData
 
addCheckboxMenuItem(Object, String, String, String, boolean) - Method in class org.jmol.popup.SimplePopup
 
addCheckboxMenuItem(Object, String, String, String, boolean, boolean) - Method in class org.jmol.popup.SimplePopup
 
addColix(short, boolean) - Method in class org.jmol.export._IdtfExporter
 
addColorToMap(Map<String, BitSet>, String, BitSet) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
adds a set of specifically-colored vertices to the map, ensuring that no vertex is in two maps.
addCommand(String) - Method in class org.jmol.util.CommandHistory
Adds any number of lines to the command history
addCommand(String) - Method in class org.jmol.viewer.Viewer
Adds one or more commands to the command history
addCommandLine(String) - Method in class org.jmol.util.CommandHistory
Adds a single line to the bottom of the list, resets list position.
addConnect() - Method in class org.jmol.export._MayaExporter
 
addConnection(int[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addConstraint(Object[]) - Method in class org.jmol.minimize.Minimizer
 
addContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
 
addContextVariable(Map<String, ScriptVariable>, String) - Static method in class org.jmol.script.ScriptCompiler
 
addContourPoints(List<Object>, BitSet, int, StringBuffer, Point3f[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
addContourVertex(Point3f, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addCount - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
addCurrentItem(StringBuffer, char, int, String, String, String, String) - Static method in class org.jmol.popup.SimplePopup
 
addData10F() - Method in class org.jmol.quantum.MOCalculation
 
addData5D() - Method in class org.jmol.quantum.MOCalculation
 
addData6D() - Method in class org.jmol.quantum.MOCalculation
 
addData7F() - Method in class org.jmol.quantum.MOCalculation
 
addDataP() - Method in class org.jmol.quantum.MOCalculation
 
addDataS() - Method in class org.jmol.quantum.MOCalculation
 
addDataSP() - Method in class org.jmol.quantum.MOCalculation
 
addDirectory(String, String) - Static method in class org.jmol.viewer.FileManager
 
addDisplayedBackbone(int, boolean) - Method in class org.jmol.modelset.Atom
 
addDisplayedBond(int, boolean) - Method in class org.jmol.modelset.Atom
 
addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addFace(IsoSolventReader.Face) - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
addFile(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
Adds this file to the history.
addForce(Vector3d, int, double) - Method in class org.jmol.minimize.forcefield.Calculations
 
addFunction(ScriptFunction) - Method in class org.jmol.viewer.StateManager
 
addFunction(ScriptFunction) - Method in class org.jmol.viewer.Viewer
 
addGroup(Chain, Group) - Method in class org.jmol.modelset.ModelLoader
 
addGroup3Name(String) - Static method in class org.jmol.modelset.Group
 
addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
 
addHbond(List<Bond>, Monomer, Monomer, int, int, Map<String, Boolean>) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
addHelpItems(JMenu, String, String) - Method in class org.jmol.console.AppletConsole
 
addHelpMenuBar(JMenuBar) - Method in class org.jmol.console.AppletConsole
 
addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addHetero(String, String) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
addHydrogenBond(List<Bond>, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
 
addHydrogens - Variable in class org.jmol.jvxl.readers.Parameters
 
addHydrogens(List<Atom>, Point3f[]) - Method in class org.jmol.modelset.ModelSet
these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW
addhydrogens - Static variable in class org.jmol.script.Token
 
addHydrogens(BitSet, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
addHydrogensInline(BitSet, List<Atom>, Point3f[]) - Method in class org.jmol.viewer.Viewer
 
addImplicitHydrogenAtoms(JmolAdapter, int) - Method in interface org.jmol.api.JmolBioResolver
 
addImplicitHydrogenAtoms(JmolAdapter, int) - Method in class org.jmol.modelsetbio.Resolver
 
addIncompleteFaces(FastBitSet) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
addIndex - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
addInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
addIntersectionVertex(Point3f, float, int, Map<String, Integer>, int, int) - Method in class org.jmol.util.MeshSurface
 
addItems(String[][]) - Method in class org.jmol.popup.PopupResource
 
addJmolFiles(String) - Method in class org.openscience.chimetojmol.ChimePanel
 
addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addJsonTuple(StringBuilder, Tuple3f) - Static method in class org.jmol.util.Escape
 
addKeyBuffer(char) - Method in class org.jmol.awt.Mouse
 
addLadder(Map<int[][], Boolean>) - Method in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
addListener(JmolSelectionListener) - Method in class org.jmol.viewer.SelectionManager
 
addMacrosMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addMenuItem(Object, String) - Method in class org.jmol.popup.SimplePopup
 
addMenuItem(Object, String, String, String) - Method in class org.jmol.popup.SimplePopup
 
addMenuItems(String, String, Object, PopupResource) - Method in class org.jmol.popup.SimplePopup
 
addMenuSeparator(Object) - Method in class org.jmol.popup.SimplePopup
 
addMenuSubMenu(Object, Object) - Method in class org.jmol.popup.SimplePopup
 
addMesh(String, MeshSurface, Matrix4f, Matrix4f, short, Point, BitSet) - Method in class org.jmol.export._ObjExporter
Adds a new mesh using the given data (faces, vertices, and normals) and colix after transforming it via the given affine transform matrix.
addMeshData(String, int, int, int, int, StringBuffer, StringBuffer, StringBuffer, StringBuffer, StringBuffer, StringBuffer) - Method in class org.jmol.export._IdtfExporter
 
addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Contact
 
addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Isosurface
 
addMo(AdfReader.SymmetryData, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
addMOData(int, List<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
addMolecule(JmolMolecule[], int, JmolNode[], int, BitSet, int, int, BitSet) - Static method in class org.jmol.util.JmolMolecule
 
addMolFile(StringBuffer, BitSet, BitSet, boolean, Quaternion) - Method in class org.jmol.modelset.ModelCollection
 
addMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
Note that this method does not check to see that there are no overlapping protein structures.
addName(String) - Method in class org.jmol.script.ContextToken
 
addNeighboringVertexes(short[], short, short) - Static method in class org.jmol.geodesic.Geodesic
 
addNested(String) - Method in class org.jmol.smiles.SmilesSearch
 
addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(int, int) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
add the bond and mark it for molecular processing
addNewBond(String, String, int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
addNewBond(int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBondWithMappedSerialNumbers(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNextToken() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
addNextTokenIf(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
addNormal(Vector3f, Vector3f, float) - Static method in class org.jmol.smiles.SmilesAromatic
 
addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addOp(Token) - Method in class org.jmol.script.ScriptMathProcessor
addOp The primary driver of the Reverse Polish Notation evaluation engine.
addOp(Token, boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
addOperation(String, int) - Method in class org.jmol.symmetry.SpaceGroup
 
addPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
addPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D.Pixel
 
addPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D.ShadePixel
 
addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
 
addPoint(Point3f, int) - Method in class org.jmol.shapespecial.Draw
 
addPoint(int) - Method in class org.jmol.smiles.SmilesMeasure
 
addPoint(Point3f, Point3f, Point3f, float) - Static method in class org.jmol.util.BoxInfo
 
addPolygon(int, int, int, int, int, int, BitSet) - Method in class org.jmol.util.MeshSurface
 
addPolygon(int[], int, BitSet) - Method in class org.jmol.util.MeshSurface
 
addPolygon(int[], BitSet) - Method in class org.jmol.util.MeshSurface
 
addPrimitive() - Method in class org.jmol.smiles.SmilesAtom
 
addPrimitive() - Method in class org.jmol.smiles.SmilesBond
 
addPrimitiveLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addProcess(String, ScriptContext) - Method in class org.jmol.script.ParallelProcessor
 
addProcess(int, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
addProperties(Properties) - Method in class org.jmol.export.history.HistoryFile
Adds the given properties to the history.
addProperty(String, String) - Method in class org.jmol.export.history.HistoryFile
Adds the given property to the history.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.export.JmolFileDropper
 
addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
 
addRequiredFile(String) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
addRequiredFile(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
addRequiredFile(String) - Method in class org.jmol.shapesurface.Isosurface
 
addResidueHydrogenBond(Atom, Atom, int, int, float, List<Bond>) - Method in class org.jmol.modelsetbio.AminoPolymer
 
addRgb(int, int) - Method in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
addScript(String) - Method in class org.jmol.viewer.ScriptManager
 
addScript(String, boolean, boolean) - Method in class org.jmol.viewer.ScriptManager
 
addScript(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.ScriptManager
 
addSecondaryStructure(EnumStructure, String, int, int, char, int, char, int) - Method in class org.jmol.modelset.Model
 
addSecondaryStructure(EnumStructure, String, int, int, char, int, char, int) - Method in class org.jmol.modelset.Polymer
 
addSecondaryStructure(EnumStructure, String, int, int, char, int, char, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addSecondaryStructure(EnumStructure, String, int, int, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
 
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
 
addShader(String, short) - Method in class org.jmol.export._IdtfExporter
 
addShapeProperty(List<Object[]>, String, Object) - Method in class org.jmol.script.ScriptEvaluator
 
addSites(Map<String, Map<String, Object>>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addSiteScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addSlabInfo(Object[]) - Method in class org.jmol.jvxl.readers.Parameters
 
addSlater(int, int, int, int, int, double, float) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
 
addSpaceGroupOperation(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
 
addSpaceGroupOperation(Matrix4f) - Method in interface org.jmol.api.SymmetryInterface
 
addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
 
addSpaceGroupOperation(Matrix4f) - Method in class org.jmol.symmetry.Symmetry
 
addStateScript(String, BitSet, BitSet, BitSet, String, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
 
addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
addStateScript(String, BitSet, BitSet, BitSet, String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
addStereoCheck(int, JmolNode[], int, String) - Method in class org.jmol.smiles.SmilesGenerator
checks a group and either adds a new group to the growing check string or returns null
addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addStructuresFromTags(EnumStructure[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addSubstituteTokenIf(int, Token) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
addSymmetry(String, int) - Method in class org.jmol.symmetry.SpaceGroup
 
addSymmetry(String, Matrix4f) - Method in class org.jmol.symmetry.SpaceGroup
 
addTexture(short, String) - Method in class org.jmol.export._ObjExporter
Adds a texture to the .mtl file if it is a new texture.
addTickInfo(StringBuffer, TickInfo, boolean) - Static method in class org.jmol.shape.FontLineShape
 
addTo(StringBuffer) - Method in class org.jmol.util.ZipUtil.GZipData
 
addToBonds(Bond, Bond[]) - Method in class org.jmol.modelset.BondCollection
 
addToken(String, Token) - Static method in class org.jmol.script.Token
 
addTokenToPostfix(int, Object) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
addTokenToPostfix(int, int, Object) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
addTokenToPostfix(Token) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
addTokenToPrefix(Token) - Method in class org.jmol.script.ScriptCompiler
 
addToMeasurement(int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
 
addToMenu(Object, JComponent) - Method in class org.jmol.popup.SimplePopup
 
addTrajectoryStep() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
 
addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.PmeshReader
 
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.shapesurface.Isosurface
 
addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
 
addTuple(int, Point3f) - Method in class org.jmol.bspt.Bspf
 
addTuple(Point3f) - Method in class org.jmol.bspt.Bspt
Iterate through all of your data points, calling addTuple
addTuple(int, Point3f) - Method in class org.jmol.bspt.Element
 
addTuple(int, Point3f) - Method in class org.jmol.bspt.Leaf
 
addTuple(int, Point3f) - Method in class org.jmol.bspt.Node
 
addUnitCellOffset(Point3f) - Method in class org.jmol.viewer.Viewer
 
addVariable(String, boolean) - Method in class org.jmol.script.ScriptFunction
 
addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addVertexCopy(Point3f, float, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
addVertexCopy(Point3f, float, int) - Method in class org.jmol.jvxl.data.MeshData
 
addVertexCopy(Point3f, float, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
addVertexCopy(Point3f, float, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
addVertexCopy(Point3f, float, int) - Method in class org.jmol.shapesurface.Isosurface
 
addVertexCopy(Point3f, float, int, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
addVertexCopy(Point3f) - Method in class org.jmol.util.MeshSurface
 
addVertexCopy(Point3f, float) - Method in class org.jmol.util.MeshSurface
 
addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addVibrationVector(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
addWindowBorder(String, Point) - Method in class org.jmol.export.history.HistoryFile
Adds the window border to the history.
addWindowInfo(String, Component, Point) - Method in class org.jmol.export.history.HistoryFile
Adds the window informations to the history.
addWindowListener() - Method in class org.jmol.console.JmolConsole
 
addWindowPosition(String, Point) - Method in class org.jmol.export.history.HistoryFile
Adds the window position to the history.
addWindowSize(String, Dimension) - Method in class org.jmol.export.history.HistoryFile
Adds the window size to the history.
addWindowVisibility(String, boolean) - Method in class org.jmol.export.history.HistoryFile
Adds the window visibility to the history.
addX(ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
 
addX(Object) - Method in class org.jmol.script.ScriptMathProcessor
 
addX(BitSet) - Method in class org.jmol.script.ScriptMathProcessor
 
addX(Point3f) - Method in class org.jmol.script.ScriptMathProcessor
 
addX(boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
addX(int) - Method in class org.jmol.script.ScriptMathProcessor
 
addX(float) - Method in class org.jmol.script.ScriptMathProcessor
 
addXNum(ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
 
addZoomTranslationNavigationText(StringBuffer) - Method in class org.jmol.viewer.TransformManager
 
adfContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
AdfReader - Class in org.jmol.adapter.readers.quantum
TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
AdfReader() - Constructor for class org.jmol.adapter.readers.quantum.AdfReader
 
AdfReader.SymmetryData - Class in org.jmol.adapter.readers.quantum
 
AdfReader.SymmetryData(int, String) - Constructor for class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
adjust - Static variable in class org.jmol.script.Token
 
adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelCollection
 
adjustForWindow - Variable in class org.jmol.shape.Object2d
 
adjustment - Variable in class org.jmol.jvxl.readers.MapFileReader
 
adjustTemporaryScreenPoint() - Method in class org.jmol.viewer.TransformManager
adjusts the temporary point for perspective and offsets
adjustTemporaryScreenPoint() - Method in class org.jmol.viewer.TransformManager10
 
adjustTemporaryScreenPoint() - Method in class org.jmol.viewer.TransformManager11
 
adjustVertex(int[], float) - Method in class org.jmol.g3d.Triangle3D
 
aDOMNode - Variable in class org.jmol.viewer.FileManager.DOMReader
 
ADP_TYPE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
adpmax - Static variable in class org.jmol.script.Token
 
adpmin - Static variable in class org.jmol.script.Token
 
adpMode - Variable in class org.jmol.atomdata.AtomData
 
aEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
Ah - Variable in class org.jmol.util.JpegInfo
 
AimsReader - Class in org.jmol.adapter.readers.xtal
FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).
AimsReader() - Constructor for class org.jmol.adapter.readers.xtal.AimsReader
 
Al - Variable in class org.jmol.util.JpegInfo
 
AlchemyReader - Class in org.jmol.adapter.readers.simple
TRIPOS simple Alchemy reader.
AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
 
align - Static variable in class org.jmol.script.Token
 
align - Variable in class org.jmol.shape.Object2d
 
align1 - Variable in class org.jmol.shapespecial.Polyhedra
 
align2 - Variable in class org.jmol.shapespecial.Polyhedra
 
ALIGN_CENTER - Static variable in class org.jmol.shape.Object2d
 
ALIGN_FLAGS - Static variable in class org.jmol.shape.Labels
 
ALIGN_LEFT - Static variable in class org.jmol.shape.Object2d
 
ALIGN_NONE - Static variable in class org.jmol.shape.Object2d
 
ALIGN_RIGHT - Static variable in class org.jmol.shape.Object2d
 
alignLeft - Variable in class org.jmol.modelset.LabelToken
 
alignZX(Point3f, Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager11
brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane
all - Static variable in class org.jmol.script.Token
 
ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
allCarbohydrates - Static variable in class org.jmol.viewer.JmolConstants
 
allconnected - Static variable in class org.jmol.script.Token
 
allData - Variable in class org.jmol.util.CifDataReader
 
allfloat - Static variable in class org.jmol.script.Token
 
allFractionalRelative - Variable in class org.jmol.symmetry.UnitCell
 
allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
allInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
allocateArray(JmolMolecule[], int) - Static method in class org.jmol.util.JmolMolecule
 
allocateBioPolymer(Group[], int, boolean) - Static method in class org.jmol.modelsetbio.BioPolymer
 
allocateBitmap(int) - Static method in class org.jmol.util.FastBitSet
 
allocateBuffers(int, int, boolean) - Method in class org.jmol.g3d.Platform3D
 
allocateColix(int) - Static method in class org.jmol.g3d.Colix3D
 
allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
 
allocateImage() - Method in class org.jmol.g3d.Platform3D
 
allocateOffscreenImage(int, int) - Method in class org.jmol.g3d.Platform3D
 
allocateRenderer(int, Graphics3D) - Method in class org.jmol.viewer.RepaintManager
 
allocateRgbImage(int, int, int[], int, boolean) - Method in interface org.jmol.api.ApiPlatform
 
allocateRgbImage(int, int, int[], int, boolean) - Static method in class org.jmol.awt.Image
 
allocateRgbImage(int, int, int[], int, boolean) - Method in class org.jmol.awt.Platform
 
allocateShape(int) - Method in class org.jmol.viewer.ShapeManager
 
allocateSimpleViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolSimpleViewer
This is the main access point for creating an application or applet viewer.
allocateTBuffers(boolean) - Method in class org.jmol.g3d.Platform3D
 
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
This is the main access point for creating an application or applet viewer.
allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
default null htmlName, URL bases, comandOptions, and statusListener.
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.viewer.Viewer
NOTE: for APPLICATION AND APPLET call setModeMouse(JmolConstants.MOUSE_NONE); before setting viewer=null in order to remove references to display window in listeners and hoverWatcher This is the main access point for creating an application or applet viewer.
allocateXmlReader14() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
allocateXmlReaderAelfred2() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
allocDipole(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
allocDotsConvexMaps(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
allocMesh(String, Mesh) - Method in class org.jmol.shape.MeshCollection
 
allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
 
allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
 
allocRaster(boolean) - Method in class org.jmol.g3d.Cylinder3D
 
allocTempEnum(int) - Method in class org.jmol.util.TempArray
 
allocTempEnum(int) - Method in class org.jmol.viewer.Viewer
 
allocTempPoints(int) - Method in class org.jmol.util.TempArray
 
allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
 
allocTempScreens(int) - Method in class org.jmol.util.TempArray
 
allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
 
allocVertexColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
allowedQuaternionFrames - Static variable in class org.jmol.viewer.JmolConstants
 
allowembeddedscripts - Static variable in class org.jmol.script.Token
 
allowEmbeddedScripts - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowgestures - Static variable in class org.jmol.script.Token
 
allowGestures - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowkeystrokes - Static variable in class org.jmol.script.Token
 
allowKeyStrokes - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowMapData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
allowMesh - Variable in class org.jmol.shapesurface.Isosurface
 
allowmodelkit - Static variable in class org.jmol.script.Token
 
allowModelkit - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowmoveatoms - Static variable in class org.jmol.script.Token
 
allowMoveAtoms - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
allowmultitouch - Static variable in class org.jmol.script.Token
 
allowMultiTouch - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowMultiTouch() - Method in class org.jmol.viewer.Viewer
 
allowNegative - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
allowrotateselected - Static variable in class org.jmol.script.Token
 
allowRotateSelected - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowRotateSelected() - Method in class org.jmol.viewer.Viewer
 
allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
allowSignedFeatures - Variable in class org.jmol.popup.SimplePopup
 
allowSmilesUnbracketed(String) - Static method in class org.jmol.smiles.SmilesAtom
 
allowSpecAtom() - Method in class org.jmol.modelset.ModelSet
 
allowSpecAtom() - Method in class org.jmol.viewer.Viewer
 
allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
 
allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
 
allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
 
allPositive - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
allSelectedWidgets() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
almost180 - Static variable in class org.jmol.modelset.AtomCollection
 
alpha - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
alpha - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
alpha - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
alpha - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
alpha - Variable in class org.jmol.jvxl.readers.MapFileReader
 
alpha - Variable in class org.jmol.util.SimpleUnitCell
 
ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.shapebio.BioShape
 
ALPHA_SHIFT - Static variable in class org.jmol.g3d.Graphics3D
 
alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
AlphaMonomer - Class in org.jmol.modelsetbio
 
AlphaMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.AlphaMonomer
 
alphaOffsets - Static variable in class org.jmol.modelsetbio.AlphaMonomer
 
alphaOffsets - Static variable in class org.jmol.modelsetbio.CarbohydrateMonomer
 
AlphaPolymer - Class in org.jmol.modelsetbio
 
AlphaPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.AlphaPolymer
 
alphaPolymer - Variable in class org.jmol.modelsetbio.Sheet
 
AlphaPolymer.Code - Enum in org.jmol.modelsetbio
 
AlphaPolymer.Code() - Constructor for enum org.jmol.modelsetbio.AlphaPolymer.Code
 
alphas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
ALT - Static variable in class org.jmol.util.ColorEncoder
 
ALT - Static variable in class org.jmol.viewer.binding.Binding
 
ALT_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ALT_MASK - Static variable in class org.jmol.api.Event
 
altArgbsCpk - Variable in class org.jmol.viewer.ColorManager
 
altArgbsCpk - Static variable in class org.jmol.viewer.JmolConstants
 
altElementCounts - Variable in class org.jmol.util.JmolMolecule
 
altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
 
altElementMax - Static variable in class org.jmol.util.Elements
length of the altElementSymbols, altElementNames, altElementNumbers arrays
altElementMax - Variable in class org.jmol.util.JmolMolecule
 
altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
 
altElementNames - Static variable in class org.jmol.util.Elements
 
altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
 
altElementNumbers - Static variable in class org.jmol.util.Elements
 
altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
 
altElementSymbols - Static variable in class org.jmol.util.Elements
 
alternateLocationID - Variable in class org.jmol.adapter.smarter.Atom
 
alternateLocationID - Variable in class org.jmol.modelset.Atom
 
altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
 
altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
 
altloc - Static variable in class org.jmol.script.Token
 
altlocs - Variable in class org.jmol.popup.SimplePopup
 
altNames - Variable in class org.jmol.adapter.readers.more.P2nReader
 
altVertices - Variable in class org.jmol.util.MeshSurface
 
ambientFraction - Static variable in class org.jmol.g3d.Shade3D
 
ambientPercent - Static variable in class org.jmol.g3d.Shade3D
 
ambientpercent - Static variable in class org.jmol.script.Token
 
ambientPercent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ambiguityType - Variable in class org.jmol.symmetry.SpaceGroup
 
ambiguousNames - Static variable in class org.jmol.symmetry.SpaceGroup
 
amino - Static variable in class org.jmol.script.Token
 
AMINO - Static variable in class org.jmol.util.ColorEncoder
 
AminoMonomer - Class in org.jmol.modelsetbio
 
AminoMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.AminoMonomer
 
AminoPolymer - Class in org.jmol.modelsetbio
 
AminoPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.AminoPolymer
 
AminoPolymer.Bridge - Class in org.jmol.modelsetbio
 
AminoPolymer.Bridge(Atom, Atom, Map<int[][], Boolean>) - Constructor for class org.jmol.modelsetbio.AminoPolymer.Bridge
 
ampacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
AmpacReader - Class in org.jmol.adapter.readers.simple
A reader for AMPAC output.
AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
 
AMPLITUDE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for vibration scale.
AMPLITUDE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Precision of the vibration scale slider
AMPLITUDE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Initial value of vibration scale.
amplitudeSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
anaglyphChannelBytes - Variable in class org.jmol.g3d.Graphics3D
 
anaglyphLength - Variable in class org.jmol.g3d.Graphics3D
 
and(FastBitSet) - Method in class org.jmol.util.FastBitSet
 
andBitSet(BitSet) - Method in class org.jmol.shapespecial.Polyhedra
 
andequals - Static variable in class org.jmol.script.Token
 
andNot(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
 
andNot(FastBitSet) - Method in class org.jmol.util.FastBitSet
 
angle - Static variable in class org.jmol.script.Token
 
angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
angles - Variable in class org.jmol.minimize.forcefield.Calculations
 
angles - Variable in class org.jmol.minimize.Minimizer
 
angleUnits - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
angleUnitsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
angleXY - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
angleXY - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
angleXYSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
angleZSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
angMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
angstroms - Static variable in class org.jmol.script.Token
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.Parameters
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JmolConstants
 
angstromsToPixels(float) - Method in class org.jmol.viewer.TransformManager
 
angularPart(double, double, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
animation() - Method in class org.jmol.script.ScriptEvaluator
 
animation - Static variable in class org.jmol.script.Token
 
animationDirection() - Method in class org.jmol.script.ScriptEvaluator
 
animationDirection - Variable in class org.jmol.viewer.AnimationManager
 
animationfps - Static variable in class org.jmol.script.Token
 
animationFps - Variable in class org.jmol.viewer.AnimationManager
 
animationFps - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
AnimationManager - Class in org.jmol.viewer
 
AnimationManager(Viewer) - Constructor for class org.jmol.viewer.AnimationManager
 
animationManager - Variable in class org.jmol.viewer.Viewer
 
AnimationManager.AnimationThread - Class in org.jmol.viewer
 
AnimationManager.AnimationThread(int, int, int) - Constructor for class org.jmol.viewer.AnimationManager.AnimationThread
 
animationMode() - Method in class org.jmol.script.ScriptEvaluator
 
animationOn - Variable in class org.jmol.viewer.AnimationManager
 
animationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
 
animationPaused - Variable in class org.jmol.viewer.AnimationManager
 
animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
 
animationThread - Variable in class org.jmol.viewer.AnimationManager
 
animThread - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
anionLookupTable - Static variable in class org.jmol.util.Elements
 
aniosU - Variable in class org.jmol.jvxl.readers.Parameters
 
ANISO_B11 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B12 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B13 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B22 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B23 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B33 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_11 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_12 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_13 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_22 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_23 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_33 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_LABEL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U11 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U12 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U13 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U22 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U23 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U33 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U11 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U12 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U13 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U22 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U23 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U33 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
anisoB - Variable in class org.jmol.jvxl.readers.Parameters
 
anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
 
anisotropy - Variable in class org.jmol.jvxl.readers.Parameters
 
anisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
anisotropy - Static variable in class org.jmol.script.Token
 
anisou() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
antialias - Variable in class org.jmol.shape.MeshRenderer
 
antialias - Variable in class org.jmol.viewer.TransformManager
 
antialias2 - Variable in class org.jmol.g3d.Graphics3D
 
antiAliasCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
antialiasdisplay - Static variable in class org.jmol.script.Token
 
antialiasDisplay - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
antialiasDisplay - Variable in class org.jmol.viewer.Viewer
 
antialiasEnabled - Variable in class org.jmol.g3d.Graphics3D
 
antialiasimages - Static variable in class org.jmol.script.Token
 
antialiasImages - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
antialiasThisFrame - Variable in class org.jmol.g3d.Graphics3D
 
antialiastranslucent - Static variable in class org.jmol.script.Token
 
antialiasTranslucent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
anum - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
aoMax - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
aoMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
aPar - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
 
ApbsReader - Class in org.jmol.jvxl.readers
 
ApbsReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.ApbsReader
 
aperatureAngle - Variable in class org.jmol.export.___Exporter
 
aperatureAngle - Variable in class org.jmol.viewer.TransformManager
 
ApiPlatform - Interface in org.jmol.api
 
apiPlatform - Variable in class org.jmol.api.JmolSimpleViewer
 
apiPlatform - Variable in class org.jmol.g3d.Font3D
 
apiPlatform - Variable in class org.jmol.g3d.Graphics3D
 
apiPlatform - Variable in class org.jmol.g3d.Platform3D
 
apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
 
appConsole - Variable in class org.jmol.viewer.Viewer
 
AppConsole - Class in org.openscience.jmol.app.jmolpanel
 
AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole
general entry point
AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole
 
AppConsole.ConsoleDocument - Class in org.openscience.jmol.app.jmolpanel
 
AppConsole.ConsoleDocument() - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
AppConsole.ConsoleTextPane - Class in org.openscience.jmol.app.jmolpanel
 
AppConsole.ConsoleTextPane(AppConsole) - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
AppConsole.ExecuteCommandThread - Class in org.openscience.jmol.app.jmolpanel
 
AppConsole.ExecuteCommandThread(String) - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole.ExecuteCommandThread
 
append - Variable in class org.jmol.export.dialog.FilePreview
 
append - Static variable in class org.jmol.script.Token
 
append(String) - Method in class org.jmol.util.OutputStringBuffer
 
append(char) - Method in class org.jmol.util.OutputStringBuffer
 
appendAtomProperties(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
appendAtomSetCollection(List<?>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Appends an AtomSetCollection
appendAtomTokenValue(Viewer, Atom, LabelToken, StringBuffer, int[]) - Static method in class org.jmol.modelset.LabelToken
 
appendAttrib(StringBuffer, Object, Object) - Static method in class org.jmol.util.XmlUtil
 
appendCdata(StringBuffer, String, Object[], String) - Static method in class org.jmol.util.XmlUtil
" will convert ]]> to ]] >
appendCmd(StringBuffer, String) - Static method in class org.jmol.shape.Shape
 
appendCmd(StringBuffer, String) - Static method in class org.jmol.viewer.StateManager
 
appendContourTriangleIntersection(int, float, float, StringBuffer) - Static method in class org.jmol.jvxl.data.JvxlCoder
appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded.
appendEncodedBitSetTag(StringBuffer, String, BitSet, int, Object[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
appendLoadStates(StringBuffer) - Method in class org.jmol.modelset.ModelCollection
 
appendLoadStates(StringBuffer) - Method in class org.jmol.viewer.Viewer
 
appendLogData(String) - Method in class org.jmol.minimize.forcefield.Calculations
 
appendNew - Variable in class org.jmol.modelset.ModelLoader
 
appendnew - Static variable in class org.jmol.script.Token
 
appendNew - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
appendTag(StringBuffer, String, Object[], Object, boolean, boolean) - Static method in class org.jmol.util.XmlUtil
 
appendTag(StringBuffer, String, Object[], Object) - Static method in class org.jmol.util.XmlUtil
standard data"
appendTag(StringBuffer, String, Object) - Static method in class org.jmol.util.XmlUtil
standard data" standard "
appendTickInfo(StringBuffer, int) - Method in class org.jmol.shape.FontLineShape
 
appendXmlColorData(StringBuffer, String, String, boolean, float, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
appendXmlEdgeData(StringBuffer, JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
appendXmlTriangleData(StringBuffer, int[][], int, BitSet, int[], boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
encode triangle data -- [ia ib ic] [ia ib ic] [ia ib ic] ...
appendXmlVertexData(StringBuffer, JvxlData, int[], Point3f[], float[], int, String, int, BitSet, boolean, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
encode the vertex data.
appendXmlVertexOnlyData(StringBuffer, JvxlData, MeshData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
appletCodeBase - Variable in class org.jmol.viewer.FileManager
 
appletCodeBase - Variable in class org.jmol.viewer.Viewer
 
AppletConsole - Class in org.jmol.console
 
AppletConsole(JmolViewer, Container) - Constructor for class org.jmol.console.AppletConsole
general entry point
AppletConsole() - Constructor for class org.jmol.console.AppletConsole
 
AppletConsole.ControlEnterTextArea - Class in org.jmol.console
 
AppletConsole.ControlEnterTextArea() - Constructor for class org.jmol.console.AppletConsole.ControlEnterTextArea
 
appletContext - Variable in class org.jmol.viewer.Viewer
 
appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
appletDocumentBase - Variable in class org.jmol.viewer.FileManager
 
appletDocumentBase - Variable in class org.jmol.viewer.Viewer
 
appletInfoDivs - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
AppletOnly - Variable in class org.jmol.popup.SimplePopup
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
appletPath - Variable in class org.openscience.jmol.app.webexport.Molecules
 
appletPath - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
appletPath - Variable in class org.openscience.jmol.app.webexport.Test
 
appletproxy - Static variable in class org.jmol.script.Token
 
appletProxy - Variable in class org.jmol.viewer.FileManager
 
appletProxy - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
appletSizeSpinnerH - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
appletSizeSpinnerP - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
appletSizeSpinnerW - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
AppletWrapper - Class in org.jmol.applet
 
AppletWrapper(String, String, int, String[]) - Constructor for class org.jmol.applet.AppletWrapper
 
appletWrapper - Variable in class org.jmol.applet.ClassPreloader
 
appletWrapper - Variable in class org.jmol.applet.Jmol
 
appletWrapper - Variable in class org.jmol.applet.TickerThread
 
appletWrapper - Variable in class org.jmol.applet.WrappedAppletLoader
 
apply() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
applyAllSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applyBlueAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
applyColorScale() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
applyColorTranslucencyLevel(short, float) - Static method in class org.jmol.g3d.Graphics3D
 
applyCustomAnaglyph(int[]) - Method in class org.jmol.g3d.Graphics3D
 
applyCyanAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyGreenAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyLeftMouse(int) - Static method in class org.jmol.awt.Mouse
 
applyRotation(Matrix3f, boolean, BitSet, Vector3f) - Method in class org.jmol.viewer.TransformManager
 
applySelectStyle(String, int) - Method in class org.jmol.viewer.ActionManager
 
applyStereochemistry() - Method in class org.jmol.modelset.ModelLoader
 
applySymmetry - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
applySymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetry(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetry(List<Matrix4f>, float[], boolean, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
applysymmetrytobonds - Static variable in class org.jmol.script.Token
 
applySymmetryToBonds - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
approx(Tuple3f) - Static method in class org.jmol.symmetry.SymmetryOperation
 
approx(float) - Static method in class org.jmol.symmetry.SymmetryOperation
 
approx(float, float) - Static method in class org.jmol.symmetry.SymmetryOperation
 
approx0(Tuple3f) - Static method in class org.jmol.symmetry.SymmetryOperation
 
arc - Static variable in class org.jmol.script.Token
 
arcBall0 - Variable in class org.jmol.viewer.TransformManager
 
arcBall0Rotation - Variable in class org.jmol.viewer.TransformManager
 
arcBall1 - Variable in class org.jmol.viewer.TransformManager
 
arcBallAxis - Variable in class org.jmol.viewer.TransformManager
 
area - Static variable in class org.jmol.script.Token
 
areAxesTainted() - Method in class org.jmol.viewer.Viewer
 
areEqual(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
areEqual(ScriptVariable, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
 
areEqual(String, String) - Method in class org.jmol.smiles.SmilesMatcher
 
areEqual(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
for JUnit test, mainly
areEqual(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
 
argbCurrent - Variable in class org.jmol.g3d.Graphics3D
 
argbEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
argbNoisyDn - Variable in class org.jmol.g3d.Graphics3D
 
argbNoisyUp - Variable in class org.jmol.g3d.Graphics3D
 
argbs - Static variable in class org.jmol.g3d.Colix3D
 
argbsAmino - Variable in class org.jmol.util.ColorEncoder
 
argbsAmino - Static variable in class org.jmol.viewer.JmolConstants
 
argbsChainAtom - Static variable in class org.jmol.viewer.JmolConstants
some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
argbsChainHetero - Static variable in class org.jmol.viewer.JmolConstants
 
argbsCpk - Static variable in enum org.jmol.constant.EnumPalette
Default table of CPK atom colors.
argbsCpk - Variable in class org.jmol.util.ColorEncoder
 
argbsCpk - Variable in class org.jmol.viewer.ColorManager
 
argbsCpkRasmol - Static variable in enum org.jmol.constant.EnumPalette
 
argbsFormalCharge - Static variable in class org.jmol.viewer.JmolConstants
 
argbsGreyscale - Static variable in class org.jmol.g3d.Colix3D
 
argbShapelyBackbone - Static variable in class org.jmol.viewer.JmolConstants
 
argbShapelyDefault - Static variable in class org.jmol.viewer.JmolConstants
 
argbShapelySpecial - Static variable in class org.jmol.viewer.JmolConstants
 
argbsHbondType - Static variable in class org.jmol.util.JmolEdge
 
argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JmolConstants
 
argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JmolConstants
 
argbsRoygb - Variable in class org.jmol.util.ColorEncoder
 
argbsRoygbScale - Static variable in class org.jmol.viewer.JmolConstants
 
argbsRwb - Variable in class org.jmol.util.ColorEncoder
 
argbsRwbScale - Static variable in class org.jmol.viewer.JmolConstants
 
argbsShapely - Variable in class org.jmol.util.ColorEncoder
 
argbsShapely - Static variable in class org.jmol.viewer.JmolConstants
 
argusImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
aromatic - Static variable in class org.jmol.script.Token
 
aromaticAmbiguous - Variable in class org.jmol.smiles.SmilesAtom
 
array - Static variable in class org.jmol.script.Token
 
arrayCopy(int[], int, int, boolean) - Static method in class org.jmol.util.ArrayUtil
 
arrayListHandler - Variable in class org.openscience.jmol.app.webexport.Test
 
ArrayListTransferHandler - Class in org.openscience.jmol.app.webexport
 
ArrayListTransferHandler(WebPanel) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
ArrayListTransferHandler.ArrayListTransferable - Class in org.openscience.jmol.app.webexport
 
ArrayListTransferHandler.ArrayListTransferable(List<String>) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
arrayPt - Variable in class org.jmol.script.ScriptVariable.Sort
 
ArrayUtil - Class in org.jmol.util
 
ArrayUtil() - Constructor for class org.jmol.util.ArrayUtil
 
arrow - Static variable in class org.jmol.script.Token
 
arrowHeadBase - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
arrowHeadFaces - Static variable in class org.jmol.shapebio.RocketsRenderer
 
arrowHeadOffset - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
arrowHeadOffset - Static variable in class org.jmol.shapespecial.VectorsRenderer
 
arrowHeadTip - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
arrowHeadWidthFactor - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
as - Static variable in class org.jmol.script.Token
 
asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
 
asBoolean() - Method in class org.jmol.script.ScriptVariable
 
ascent - Variable in class org.jmol.g3d.Text3D
 
ascent - Variable in class org.jmol.shape.LabelsRenderer
 
ascent - Variable in class org.jmol.shape.Text
 
asFloat() - Method in class org.jmol.script.ScriptVariable
 
ashades - Static variable in class org.jmol.g3d.Colix3D
 
ashadesGreyscale - Static variable in class org.jmol.g3d.Colix3D
 
ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
 
ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
asInt() - Method in class org.jmol.script.ScriptVariable
 
aspectRatio - Variable in class org.jmol.shapebio.BioShapeRenderer
 
asPopup - Variable in class org.jmol.popup.SimplePopup
 
assign() - Method in class org.jmol.script.ScriptEvaluator
 
assign - Static variable in class org.jmol.script.Token
 
assignAromaticBonds() - Method in class org.jmol.modelset.BondCollection
 
assignAromaticBonds(boolean, BitSet) - Method in class org.jmol.modelset.BondCollection
algorithm discussed above.
assignAromaticBonds(boolean) - Method in class org.jmol.modelset.ModelSet
 
assignAromaticBonds() - Method in class org.jmol.viewer.Viewer
 
assignAromaticDouble(Bond) - Method in class org.jmol.modelset.BondCollection
try to assign AROMATICDOUBLE to this bond.
assignAromaticDouble(Atom) - Method in class org.jmol.modelset.BondCollection
N atoms with 3 bonds cannot also have a double bond; other atoms need one and only one double bond; the rest must be single bonds.
assignAromaticNandO(BitSet) - Method in class org.jmol.modelset.BondCollection
 
assignAromaticSingle(Bond) - Method in class org.jmol.modelset.BondCollection
try to assign AROMATICSINGLE to this bond.
assignAromaticSingle(Atom, int) - Method in class org.jmol.modelset.BondCollection
N atoms with 3 bonds cannot also have a double bond; other atoms needs all single bonds, because the bond leading up to it is double.
assignAromaticSingleHetero(Atom) - Method in class org.jmol.modelset.BondCollection
 
assignAtom(int, String, boolean) - Method in class org.jmol.modelset.ModelCollection
 
assignAtom(int, Point3f, String) - Method in class org.jmol.viewer.Viewer
 
assignBond(int, char) - Method in class org.jmol.viewer.Viewer
 
assignConnect(int, int) - Method in class org.jmol.viewer.Viewer
 
assignPotentials(Atom[], float[], BitSet, BitSet, BitSet, String) - Method in interface org.jmol.api.MepCalculationInterface
 
assignPotentials(Atom[], float[], BitSet, BitSet, BitSet, String) - Method in class org.jmol.quantum.MepCalculation
 
assignPotentials(Atom[], float[], BitSet, BitSet, BitSet, String) - Method in class org.jmol.quantum.MlpCalculation
 
assignValueFromGapColorForKin(String) - Method in class org.jmol.jvxl.readers.KinemageReader
C++ code gives these as " value > x.x ? "xxxxx", etc.
assocCutoff - Variable in class org.jmol.jvxl.readers.Parameters
 
assocCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
assocGridPointMap - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
assocGridPointNormals - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
associatedAtoms - Variable in class org.jmol.modelset.Bond.BondSet
 
associateNormals - Variable in class org.jmol.shapesurface.Isosurface
 
asString() - Method in class org.jmol.script.ScriptVariable
 
assumeAtomRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
asThread - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
astrType - Static variable in class org.jmol.script.Token
 
asVector - Variable in class org.jmol.script.ScriptMathProcessor
 
asVector - Variable in class org.jmol.smiles.SmilesSearch
 
ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atokenInfix - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
atom(int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atom - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
Atom - Class in org.jmol.adapter.smarter
 
Atom() - Constructor for class org.jmol.adapter.smarter.Atom
 
atom - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
atom - Variable in class org.jmol.minimize.MinAtom
 
Atom - Class in org.jmol.modelset
 
Atom(int, int, float, float, float, float, BitSet, int, short, int, boolean, char) - Constructor for class org.jmol.modelset.Atom
 
atom - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
atom1 - Variable in class org.jmol.modelset.Bond
 
atom1 - Variable in class org.jmol.smiles.SmilesBond
 
atom2 - Variable in class org.jmol.modelset.Bond
 
atom2 - Variable in class org.jmol.smiles.SmilesBond
 
ATOM_COUNT_MAX - Static variable in class org.jmol.symmetry.PointGroup
 
ATOM_IN_FRAME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOM_SLABBED - Static variable in class org.jmol.viewer.JmolConstants
 
ATOM_TYPE_OXIDATION_NUMBER - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ATOM_TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomA - Variable in class org.jmol.shape.FontLineShapeRenderer
 
atomA - Variable in class org.jmol.shape.SticksRenderer
 
atomA0 - Variable in class org.jmol.shape.SticksRenderer
 
atomArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
atomB - Variable in class org.jmol.shape.FontLineShapeRenderer
 
atomB - Variable in class org.jmol.shape.SticksRenderer
 
atomB0 - Variable in class org.jmol.shape.SticksRenderer
 
atomC - Variable in class org.jmol.shape.FontLineShapeRenderer
 
atomCenterOrCoordinateParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
atomCharges - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
AtomCollection - Class in org.jmol.modelset
 
AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
 
AtomCollection.AtomSorter - Class in org.jmol.modelset
 
AtomCollection.AtomSorter() - Constructor for class org.jmol.modelset.AtomCollection.AtomSorter
 
atomCoordAngstroms - Variable in class org.jmol.quantum.MepCalculation
 
atomCount - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomCount - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.MdTopReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
atomCount - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
atomCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
atomCount - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
atomCount - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
 
atomCount - Variable in class org.jmol.adapter.readers.simple.AmpacReader
 
atomCount - Variable in class org.jmol.adapter.readers.simple.CubeReader
 
atomCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
atomCount - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
atomCount - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomCount - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
atomCount - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
atomCount - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
atomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomCount - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
atomCount - Variable in class org.jmol.atomdata.AtomData
 
atomCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
atomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomCount - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
atomCount - Variable in class org.jmol.minimize.forcefield.Calculations
 
atomCount - Variable in class org.jmol.minimize.forcefield.ForceField
 
atomCount - Variable in class org.jmol.minimize.Minimizer
 
atomCount - Variable in class org.jmol.modelset.AtomCollection
 
atomCount - Variable in class org.jmol.modelset.Model
 
atomCount - Variable in class org.jmol.popup.SimplePopup
 
atomCount - Variable in class org.jmol.shape.AtomShape
 
atomCount - Variable in class org.jmol.shapesurface.Contact
 
atomCount - Variable in class org.jmol.smiles.SmilesGenerator
 
atomCount - Variable in class org.jmol.util.JmolMolecule
 
atomD - Variable in class org.jmol.shape.FontLineShapeRenderer
 
AtomData - Class in org.jmol.atomdata
 
AtomData() - Constructor for class org.jmol.atomdata.AtomData
 
atomData - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
atomData - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
AtomDataReader - Class in org.jmol.jvxl.readers
 
AtomDataReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.AtomDataReader
 
AtomDataServer - Interface in org.jmol.atomdata
 
atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
atomDataServer - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
atomExpression(int) - Method in class org.jmol.script.ScriptEvaluator
 
atomExpression(Token[], int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
atomExpression - Static variable in class org.jmol.viewer.PropertyManager
 
atomExpressionCommand - Static variable in class org.jmol.script.Token
 
atomFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
atomFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
atomFormats - Variable in class org.jmol.shape.Hover
 
atomFrag - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
ATOMIC_ORBITAL_ZERO_CUT_OFF - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
atomicAndIsotopeNumber - Variable in class org.jmol.modelset.Atom
 
atomicMass - Variable in class org.jmol.smiles.SmilesAtom
 
atomicMass - Static variable in class org.jmol.util.Elements
 
atomicNumber - Variable in class org.jmol.atomdata.AtomData
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
atomicorbital - Static variable in class org.jmol.script.Token
 
atomID - Variable in class org.jmol.modelset.Atom
 
atomid - Static variable in class org.jmol.script.Token
 
ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_BACKBONE_MIN - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C4 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C5 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C5M - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C6 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C7 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C8 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N1 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N3 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N4 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N6 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N7 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N9 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O1 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O1P - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O2P - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O4 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O6 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_OP1 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_OP2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_S4 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_SG - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JmolConstants
 
atomIdNames - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
atomIndex - Variable in class org.jmol.adapter.readers.simple.HyperChemReader
 
atomIndex - Variable in class org.jmol.adapter.smarter.Atom
 
atomIndex - Variable in class org.jmol.atomdata.AtomData
 
atomIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
atomIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
 
atomindex - Static variable in class org.jmol.script.Token
 
atomIndex - Variable in class org.jmol.shape.Hover
 
atomIndex - Variable in class org.jmol.shape.Mesh
 
atomIndex - Variable in class org.jmol.shapesurface.Isosurface
 
atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
 
atomIndex1 - Variable in class org.jmol.shapespecial.Dipoles
 
atomIndex1 - Variable in class org.jmol.viewer.StateManager.Connection
 
atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
 
atomIndex2 - Variable in class org.jmol.shapespecial.Dipoles
 
atomIndex2 - Variable in class org.jmol.viewer.StateManager.Connection
 
atomIndexes - Variable in class org.jmol.minimize.MinBond
 
AtomIndexIterator - Interface in org.jmol.api
note: YOU MUST RELEASE THE ITERATOR
atomIndexLast - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
AtomIteratorWithinModel - Class in org.jmol.modelset
 
AtomIteratorWithinModel() - Constructor for class org.jmol.modelset.AtomIteratorWithinModel
 
AtomIteratorWithinModelSet - Class in org.jmol.modelset
 
AtomIteratorWithinModelSet(BitSet) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
 
AtomIteratorWithinModelSet() - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
 
atomLabels - Variable in class org.jmol.shape.Labels
 
atomList - Variable in class org.jmol.util.JmolMolecule
 
atomMap - Variable in class org.jmol.minimize.Minimizer
 
atomMolecule - Variable in class org.jmol.atomdata.AtomData
 
atomName - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomName - Variable in class org.jmol.adapter.smarter.Atom
 
atomname - Static variable in class org.jmol.script.Token
 
atomName - Variable in class org.jmol.smiles.SmilesAtom
 
atomName1 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atomName2 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atomNames - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
atomNames - Variable in class org.jmol.adapter.readers.quantum.PsiReader
 
atomNames - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
atomNames - Variable in class org.jmol.modelset.AtomCollection
 
atomNo - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomno - Static variable in class org.jmol.script.Token
 
atomOrPointPicked(int, Point3fi, int) - Method in class org.jmol.viewer.ActionManager
 
atompicking - Static variable in class org.jmol.script.Token
 
atomPicking - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
atomPickingMode - Variable in class org.jmol.viewer.ActionManager
 
atomPositions - Variable in class org.jmol.adapter.readers.simple.AmpacReader
 
atomProp - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomproperty - Static variable in class org.jmol.script.Token
 
atomPropertyFloat(Viewer, Atom, int) - Static method in class org.jmol.modelset.Atom
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
atomPropertyInt(Atom, int) - Static method in class org.jmol.modelset.Atom
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
AtomPropertyMapper - Class in org.jmol.jvxl.readers
 
AtomPropertyMapper(SurfaceGenerator, String) - Constructor for class org.jmol.jvxl.readers.AtomPropertyMapper
 
atomPropertyString(Viewer, Atom, int) - Static method in class org.jmol.modelset.Atom
 
atomPropertyTuple(Atom, int) - Static method in class org.jmol.modelset.Atom
 
atomPts - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
atomRadius - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomRadius - Variable in class org.jmol.atomdata.AtomData
 
atomRadius - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomRadiusData - Variable in class org.jmol.jvxl.readers.Parameters
 
atoms - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atoms - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
atoms - Variable in class org.jmol.minimize.forcefield.Calculations
 
atoms - Variable in class org.jmol.minimize.forcefield.ForceField
 
atoms - Variable in class org.jmol.minimize.Minimizer
 
atoms - Variable in class org.jmol.modelset.AtomCollection
 
atoms - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
atoms - Variable in class org.jmol.modelset.MeasurementData
 
atoms - Static variable in class org.jmol.script.Token
 
atoms - Variable in class org.jmol.shape.AtomShape
 
atoms - Variable in class org.jmol.shape.Measures
 
atoms - Variable in class org.jmol.shapebio.BioShapeCollection
 
atoms - Variable in class org.jmol.shapespecial.Dipole
 
atoms - Variable in class org.jmol.shapesurface.Contact
 
atoms - Variable in class org.jmol.smiles.SmilesGenerator
 
atoms - Variable in class org.jmol.symmetry.PointGroup
 
atomSerial - Variable in class org.jmol.adapter.smarter.Atom
 
atomSerials - Variable in class org.jmol.modelset.AtomCollection
 
atomSetAtomCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetAuxiliaryInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetBondCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetChooser - Class in org.openscience.jmol.app.jmolpanel
A JFrame that allows for choosing an Atomset to view.
AtomSetChooser(JmolViewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
atomSetChooser - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
AtomSetChooser.AtomSet - Class in org.openscience.jmol.app.jmolpanel
Objects in the AtomSetChooser tree
AtomSetChooser.AtomSet(int, String) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
 
atomsetchooserAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
AtomSetCollection - Class in org.jmol.adapter.smarter
 
AtomSetCollection(String, AtomSetCollectionReader) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetCollection(AtomSetCollection[]) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
Creates an AtomSetCollection based on an array of AtomSetCollection
AtomSetCollection(List<?>) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
Creates an AtomSetCollection based on a Vector of AtomSetCollection or Vector (from zipped zip files)
atomSetCollection - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
atomSetCollection - Variable in class org.jmol.viewer.FileManager.DOMReader
 
atomSetCollection - Variable in class org.jmol.viewer.FileManager.FileReader
 
atomSetCollection - Variable in class org.jmol.viewer.FileManager.FilesReader
 
atomSetCollectionAuxiliaryInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetCollectionReader - Class in org.jmol.adapter.smarter
 
AtomSetCollectionReader() - Constructor for class org.jmol.adapter.smarter.AtomSetCollectionReader
 
atomSetCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetIndex - Variable in class org.jmol.adapter.smarter.Atom
 
atomSetIndex - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
The index of that AtomSet
atomSetName - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
The name of the AtomSet
atomSetNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomShape - Class in org.jmol.shape
 
AtomShape() - Constructor for class org.jmol.shape.AtomShape
 
atomSite - Variable in class org.jmol.adapter.smarter.Atom
 
atomSite - Variable in class org.jmol.modelset.Atom
 
atomSite - Variable in class org.jmol.smiles.SmilesAtom
 
atomsOr - Variable in class org.jmol.smiles.SmilesAtom
 
atomSym - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSymmetry - Variable in class org.jmol.modelset.Atom
 
atomSyms - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomTest - Variable in class org.jmol.symmetry.SymmetryOperation
 
atomtype - Static variable in class org.jmol.script.Token
 
atomTypeFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomTypes - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
atomTypes - Variable in class org.jmol.adapter.readers.more.MdTopReader
 
atomTypes - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
atomTypes - Static variable in class org.jmol.minimize.Minimizer
 
atomTypes - Variable in class org.jmol.modelset.AtomCollection
 
atomtypes - Static variable in class org.jmol.script.Token
 
atomTypes - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
atomx - Static variable in class org.jmol.script.Token
 
atomXyz - Variable in class org.jmol.atomdata.AtomData
 
atomXyz - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomy - Static variable in class org.jmol.script.Token
 
atomz - Static variable in class org.jmol.script.Token
 
attEcho - Variable in class org.jmol.console.ScriptEditor
 
attEcho - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
attError - Variable in class org.jmol.console.ScriptEditor
 
attError - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
attHighlight - Variable in class org.jmol.console.ScriptEditor
 
attPrompt - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
attributesCommand - Variable in class org.jmol.console.AppletConsole
 
atts - Variable in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
attStatus - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
attUserInput - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
augmentGroup3List(Object, String, boolean) - Method in class org.jmol.popup.JmolPopup
 
AUTH_ATOM - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
auto - Static variable in class org.jmol.script.Token
 
autoBond(BitSet, BitSet, BitSet, BitSet, short, boolean) - Method in class org.jmol.modelset.ModelCollection
 
autoBond(BitSet, BitSet, BitSet, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
 
autobond - Static variable in class org.jmol.script.Token
 
autoBond - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
autoBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
autoBond_Pre_11_9_24(BitSet, BitSet, BitSet, BitSet, short) - Method in class org.jmol.modelset.ModelCollection
 
autoCalculate(int) - Method in class org.jmol.viewer.Viewer
 
autoExit - Variable in class org.jmol.viewer.Viewer
 
autofps - Static variable in class org.jmol.script.Token
 
autoFps - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
autoHbond(BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.
autoHbond(BitSet, BitSet) - Method in class org.jmol.viewer.Viewer
 
autoScaleOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
auxiliaryInfo - Variable in class org.jmol.modelset.Model
 
average - Static variable in class org.jmol.script.Token
 
averageAtomPoint - Variable in class org.jmol.modelset.ModelCollection
 
averageBufferPixel(int[], int[], int, int) - Static method in class org.jmol.g3d.Graphics3D
 
AviCreator - Class in org.jmol.export.image
 
AviCreator() - Constructor for class org.jmol.export.image.AviCreator
 
ax - Variable in class org.jmol.g3d.Triangle3D
 
axE - Variable in class org.jmol.g3d.Triangle3D
 
axes(int) - Method in class org.jmol.script.ScriptEvaluator
 
axes - Static variable in class org.jmol.script.Token
 
Axes - Class in org.jmol.shape
 
Axes() - Constructor for class org.jmol.shape.Axes
 
axes - Variable in class org.jmol.shapespecial.DrawMesh
 
axes - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
axes - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
axes - Variable in class org.jmol.symmetry.PointGroup
 
AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
axesAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
axesAreTainted - Variable in class org.jmol.viewer.Viewer
 
axescolor - Static variable in class org.jmol.script.Token
 
axesMaxN - Static variable in class org.jmol.symmetry.PointGroup
 
axesmode - Static variable in class org.jmol.script.Token
 
axesMode - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
axesmolecular - Static variable in class org.jmol.script.Token
 
axesorientationrasmol - Static variable in class org.jmol.script.Token
 
axesOrientationRasmol - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
axesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
AxesRenderer - Class in org.jmol.shape
 
AxesRenderer() - Constructor for class org.jmol.shape.AxesRenderer
 
axesscale - Static variable in class org.jmol.script.Token
 
axesScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
axesunitcell - Static variable in class org.jmol.script.Token
 
axeswindow - Static variable in class org.jmol.script.Token
 
axis - Static variable in class org.jmol.script.Token
 
axis - Variable in class org.jmol.shapespecial.DrawMesh
 
axis1color - Static variable in class org.jmol.script.Token
 
axis2color - Static variable in class org.jmol.script.Token
 
axis3color - Static variable in class org.jmol.script.Token
 
axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisangle - Static variable in class org.jmol.script.Token
 
axisangleT - Variable in class org.jmol.viewer.TransformManager
 
axisB - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisChoice - Variable in class org.jmol.symmetry.SpaceGroup
 
axisLabels - Static variable in class org.jmol.shape.AxesRenderer
 
axisNX - Static variable in class org.jmol.viewer.JmolConstants
 
axisNY - Static variable in class org.jmol.viewer.JmolConstants
 
axisNZ - Static variable in class org.jmol.viewer.JmolConstants
 
axisPoints - Variable in class org.jmol.shape.Axes
 
axisPoints - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
axisType - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisX - Static variable in class org.jmol.viewer.JmolConstants
 
axisXY - Variable in class org.jmol.shape.Axes
 
axisY - Static variable in class org.jmol.viewer.JmolConstants
 
axisZ - Static variable in class org.jmol.viewer.JmolConstants
 
axW - Variable in class org.jmol.g3d.Triangle3D
 
ay - Variable in class org.jmol.g3d.Triangle3D
 
az - Variable in class org.jmol.g3d.Triangle3D
 
azE - Variable in class org.jmol.g3d.Triangle3D
 
azW - Variable in class org.jmol.g3d.Triangle3D
 

B

b - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
b - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
b - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
b - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
b - Variable in class org.jmol.jvxl.readers.MapFileReader
 
b - Variable in class org.jmol.minimize.forcefield.Calculation
 
b - Variable in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
b - Variable in class org.jmol.util.SimpleUnitCell
 
b1 - Variable in class org.jmol.g3d.Hermite3D
 
b2 - Variable in class org.jmol.g3d.Hermite3D
 
b8 - Static variable in class org.jmol.jvxl.readers.MrcBinaryReader
 
b_ - Variable in class org.jmol.util.SimpleUnitCell
 
B_ISO - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
babel - Static variable in class org.jmol.script.Token
 
babel21 - Static variable in class org.jmol.script.Token
 
back - Static variable in class org.jmol.script.Token
 
backbone - Static variable in class org.jmol.script.Token
 
Backbone - Class in org.jmol.shapebio
 
Backbone() - Constructor for class org.jmol.shapebio.Backbone
 
BACKBONE_VISIBILITY_FLAG - Static variable in class org.jmol.modelset.Atom
 
BackboneRenderer - Class in org.jmol.shapebio
 
BackboneRenderer() - Constructor for class org.jmol.shapebio.BackboneRenderer
 
background(int) - Method in class org.jmol.script.ScriptEvaluator
 
background - Static variable in class org.jmol.script.Token
 
backgroundColix - Variable in class org.jmol.export.___Exporter
 
backgroundColix - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
backgroundcolor - Static variable in class org.jmol.script.Token
 
backgroundImage - Variable in class org.jmol.g3d.Graphics3D
 
backgroundImageFileName - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
backgroundmodel - Static variable in class org.jmol.script.Token
 
backgroundModelIndex - Variable in class org.jmol.viewer.AnimationManager
 
backgroundTransparent - Static variable in class org.jmol.g3d.Platform3D
 
backlit - Static variable in class org.jmol.script.Token
 
BallandStick - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
Balls - Class in org.jmol.shape
 
Balls() - Constructor for class org.jmol.shape.Balls
 
BallsRenderer - Class in org.jmol.shape
 
BallsRenderer() - Constructor for class org.jmol.shape.BallsRenderer
 
BannerFrame - Class in org.openscience.jmol.app.jmolpanel
A simple class that throws up a white rectangle that has a single centered label.
BannerFrame(int, int) - Constructor for class org.openscience.jmol.app.jmolpanel.BannerFrame
 
bannerFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
bannerFrame - Variable in class org.openscience.molecularplayground.MPJmolApp
 
bannerLabel - Variable in class org.openscience.jmol.app.jmolpanel.BannerFrame
 
barb - Static variable in class org.jmol.script.Token
 
Base64 - Class in org.jmol.util
 
Base64() - Constructor for class org.jmol.util.Base64
 
base64 - Static variable in class org.jmol.util.Base64
 
baseAtomIndex - Variable in class org.jmol.adapter.readers.simple.HyperChemReader
 
baseAtomIndex - Variable in class org.jmol.adapter.readers.simple.MopacReader
 
baseAtomIndex - Variable in class org.jmol.modelset.ModelLoader
 
baseBondIndex - Variable in class org.jmol.modelsetbio.Resolver
 
baseCenter - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
baseFont3d - Variable in class org.jmol.shape.Frank
 
baseGroupIndex - Variable in class org.jmol.modelset.ModelLoader
 
baseModelCount - Variable in class org.jmol.modelset.ModelLoader
 
baseModelIndex - Variable in class org.jmol.modelset.ModelLoader
 
baseOffset - Variable in class org.jmol.shapebio.StrandsRenderer
 
basepair - Static variable in class org.jmol.script.Token
 
baseSymmetryAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
baseTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
 
BASIS_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
basisBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
BasisFunctionReader - Class in org.jmol.adapter.readers.quantum
 
BasisFunctionReader() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
basisFunctions - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
basisType - Variable in class org.jmol.quantum.MOCalculation
 
Bbcage - Class in org.jmol.shape
 
Bbcage() - Constructor for class org.jmol.shape.Bbcage
 
BbcageRenderer - Class in org.jmol.shape
 
BbcageRenderer() - Constructor for class org.jmol.shape.BbcageRenderer
 
bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
 
bbCenter - Variable in class org.jmol.util.BoxInfo
 
bbCorner0 - Variable in class org.jmol.util.BoxInfo
 
bbCorner1 - Variable in class org.jmol.util.BoxInfo
 
bboxAtoms - Variable in class org.jmol.modelset.ModelCollection
 
bboxModels - Variable in class org.jmol.modelset.ModelCollection
 
bButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
bbVector - Variable in class org.jmol.util.BoxInfo
 
bbVertices - Variable in class org.jmol.util.BoxInfo
 
bdSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
beenSliced - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
BEG_ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
BEG_INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
BEG_SEQ_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
beginRendering(Matrix3f) - Method in class org.jmol.g3d.Graphics3D
 
beta - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
beta - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
beta - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
beta - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
beta - Variable in class org.jmol.jvxl.readers.MapFileReader
 
beta - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
beta - Variable in class org.jmol.util.SimpleUnitCell
 
betas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
bfactor - Variable in class org.jmol.adapter.smarter.Atom
 
bfactor100Hi - Variable in class org.jmol.modelset.AtomCollection
 
bfactor100Lo - Variable in class org.jmol.modelset.AtomCollection
 
bfactor100s - Variable in class org.jmol.modelset.AtomCollection
 
bfactorMax - Variable in class org.jmol.shapebio.BioShape
 
bfactorMin - Variable in class org.jmol.shapebio.BioShape
 
bfxn_ang - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
bgcolix - Variable in class org.jmol.shape.Object2d
 
bgcolixes - Variable in class org.jmol.shape.Labels
 
bgcolor - Variable in class org.jmol.applet.AppletWrapper
 
bgcolor - Variable in class org.jmol.g3d.Graphics3D
 
bgColor - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
BGYOR - Static variable in class org.jmol.util.ColorEncoder
 
bin - Static variable in class org.jmol.script.Token
 
binary - Static variable in class org.jmol.script.Token
 
BinaryDcdReader - Class in org.jmol.adapter.readers.more
DCD binary trajectory file reader.
BinaryDcdReader() - Constructor for class org.jmol.adapter.readers.more.BinaryDcdReader
 
binarydoc - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
BinaryDocument - Class in org.jmol.util
 
BinaryDocument() - Constructor for class org.jmol.util.BinaryDocument
 
BinaryDocument(BufferedInputStream) - Constructor for class org.jmol.util.BinaryDocument
 
BinaryReader - Class in org.jmol.adapter.readers.more
 
BinaryReader() - Constructor for class org.jmol.adapter.readers.more.BinaryReader
 
bind() - Method in class org.jmol.script.ScriptEvaluator
 
bind - Static variable in class org.jmol.script.Token
 
bind(int, int) - Method in class org.jmol.viewer.binding.Binding
 
bind(int, String) - Method in class org.jmol.viewer.binding.Binding
 
bindAction(String, String, Point3f, Point3f) - Method in class org.jmol.viewer.ActionManager
 
bindAction(String, String, Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
binding - Variable in class org.jmol.viewer.ActionManager
 
Binding - Class in org.jmol.viewer.binding
 
Binding(String) - Constructor for class org.jmol.viewer.binding.Binding
 
bindings - Variable in class org.jmol.viewer.binding.Binding
 
biomolecules - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
biomts - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
BioPolymer - Class in org.jmol.modelsetbio
 
BioPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.BioPolymer
 
bioPolymer - Variable in class org.jmol.modelsetbio.Monomer
 
bioPolymer - Variable in class org.jmol.shapebio.BioShape
 
bioPolymerCount - Variable in class org.jmol.modelset.Model
 
bioPolymerIndexInModel - Variable in class org.jmol.modelset.Polymer
 
bioPolymers - Variable in class org.jmol.modelset.Model
 
BioShape - Class in org.jmol.shapebio
 
BioShape(BioShapeCollection, int, BioPolymer) - Constructor for class org.jmol.shapebio.BioShape
 
BioShapeCollection - Class in org.jmol.shapebio
Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set.
BioShapeCollection() - Constructor for class org.jmol.shapebio.BioShapeCollection
 
BioShapeRenderer - Class in org.jmol.shapebio
 
BioShapeRenderer() - Constructor for class org.jmol.shapebio.BioShapeRenderer
 
bioShapes - Variable in class org.jmol.shapebio.BioShapeCollection
 
biosymmetryCount - Variable in class org.jmol.modelset.Model
 
bioType - Variable in class org.jmol.smiles.SmilesAtom
 
bioType - Variable in class org.jmol.smiles.SmilesParser
 
BIRTH - Static variable in class org.jmol.multitouch.ActionManagerMT
 
bitmap - Variable in class org.jmol.g3d.Text3D
 
bitmap - Variable in class org.jmol.util.FastBitSet
 
bitmapAnd(int[], int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapAndNot(int[], int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapClear(int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapClearBit(int[], int) - Static method in class org.jmol.util.FastBitSet
 
bitmapClearRange(int[], int, int) - Static method in class org.jmol.util.FastBitSet
 
bitmapGetBit(int[], int) - Static method in class org.jmol.util.FastBitSet
 
bitmapGetCardinality(int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapGetMinimumWordCount(int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapGetSizeInBits(int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapIsEmpty(int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapIsEqual(int[], int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapNextSetBit(int[], int) - Static method in class org.jmol.util.FastBitSet
 
bitmapOr(int[], int[]) - Static method in class org.jmol.util.FastBitSet
 
bitmapSetBit(int[], int) - Static method in class org.jmol.util.FastBitSet
 
bitmapSetRange(int[], int, int) - Static method in class org.jmol.util.FastBitSet
 
bitmapXor(int[], int[]) - Static method in class org.jmol.util.FastBitSet
 
BITS - Static variable in class org.jmol.export.image.GifEncoder
 
bitsACchrominance - Static variable in class org.jmol.util.Huffman
 
bitsACluminance - Static variable in class org.jmol.util.Huffman
 
bitsDCchrominance - Static variable in class org.jmol.util.Huffman
 
bitsDCluminance - Static variable in class org.jmol.util.Huffman
 
bitset - Static variable in class org.jmol.script.Token
 
bitSetForModelFileNumber(int) - Method in class org.jmol.script.ScriptEvaluator
 
BitSetUtil - Class in org.jmol.util
 
BitSetUtil() - Constructor for class org.jmol.util.BitSetUtil
 
bitsetVariableVector(Object) - Method in class org.jmol.script.ScriptEvaluator
 
BLACK - Static variable in class org.jmol.g3d.Graphics3D
 
blockCubeData - Variable in class org.jmol.jvxl.readers.Parameters
 
blockdata - Static variable in class org.jmol.script.Token
 
BlockHeight - Variable in class org.jmol.util.JpegInfo
 
BlockWidth - Variable in class org.jmol.util.JpegInfo
 
blue - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
BLUE - Static variable in class org.jmol.g3d.Graphics3D
 
bohr_per_angstrom - Static variable in class org.jmol.quantum.QuantumCalculation
 
BOND - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
Bond - Class in org.jmol.adapter.smarter
 
Bond() - Constructor for class org.jmol.adapter.smarter.Bond
 
Bond(int, int, int) - Constructor for class org.jmol.adapter.smarter.Bond
 
bond - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
Bond - Class in org.jmol.modelset
 
Bond(Atom, Atom, int, short, short) - Constructor for class org.jmol.modelset.Bond
 
bond - Variable in class org.jmol.shape.SticksRenderer
 
bond - Variable in class org.jmol.shapespecial.Dipole
 
Bond.BondSet - Class in org.jmol.modelset
 
Bond.BondSet() - Constructor for class org.jmol.modelset.Bond.BondSet
 
Bond.BondSet(BitSet) - Constructor for class org.jmol.modelset.Bond.BondSet
 
Bond.BondSet(BitSet, int[]) - Constructor for class org.jmol.modelset.Bond.BondSet
 
BOND_AROMATIC - Static variable in class org.jmol.util.JmolEdge
 
BOND_AROMATIC_DOUBLE - Static variable in class org.jmol.util.JmolEdge
 
BOND_AROMATIC_MASK - Static variable in class org.jmol.util.JmolEdge
 
BOND_AROMATIC_SINGLE - Static variable in class org.jmol.util.JmolEdge
 
BOND_COVALENT_DOUBLE - Static variable in class org.jmol.util.JmolEdge
 
BOND_COVALENT_MASK - Static variable in class org.jmol.util.JmolEdge
 
BOND_COVALENT_QUADRUPLE - Static variable in class org.jmol.util.JmolEdge
 
BOND_COVALENT_SINGLE - Static variable in class org.jmol.util.JmolEdge
 
BOND_COVALENT_TRIPLE - Static variable in class org.jmol.util.JmolEdge
 
BOND_GROWTH_INCREMENT - Static variable in class org.jmol.modelset.BondCollection
 
BOND_H_CALC - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_CALC_MASK - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_MINUS_3 - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_MINUS_4 - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_NUCLEOTIDE - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_PLUS_2 - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_PLUS_3 - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_PLUS_4 - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_PLUS_5 - Static variable in class org.jmol.util.JmolEdge
 
BOND_H_REGULAR - Static variable in class org.jmol.util.JmolEdge
 
BOND_HBOND_SHIFT - Static variable in class org.jmol.util.JmolEdge
 
BOND_HYDROGEN_MASK - Static variable in class org.jmol.util.JmolEdge
 
BOND_NEW - Static variable in class org.jmol.util.JmolEdge
 
BOND_ORDER_ANY - Static variable in class org.jmol.util.JmolEdge
 
BOND_ORDER_NULL - Static variable in class org.jmol.util.JmolEdge
 
BOND_ORDER_UNSPECIFIED - Static variable in class org.jmol.util.JmolEdge
 
BOND_PARTIAL01 - Static variable in class org.jmol.util.JmolEdge
 
BOND_PARTIAL12 - Static variable in class org.jmol.util.JmolEdge
 
BOND_PARTIAL23 - Static variable in class org.jmol.util.JmolEdge
 
BOND_PARTIAL32 - Static variable in class org.jmol.util.JmolEdge
 
BOND_PARTIAL_MASK - Static variable in class org.jmol.util.JmolEdge
 
BOND_STEREO_FAR - Static variable in class org.jmol.util.JmolEdge
 
BOND_STEREO_MASK - Static variable in class org.jmol.util.JmolEdge
Extended Bond Definition Types
BOND_STEREO_NEAR - Static variable in class org.jmol.util.JmolEdge
 
BOND_STRUT - Static variable in class org.jmol.util.JmolEdge
 
BOND_SULFUR_MASK - Static variable in class org.jmol.util.JmolEdge
 
bondArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
bondAtoms(Atom, Atom, int, short, BitSet, float, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
 
bondAtoms(Object, Object, short) - Method in class org.jmol.modelset.ModelLoader
 
bondCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
BondCollection - Class in org.jmol.modelset
 
BondCollection() - Constructor for class org.jmol.modelset.BondCollection
 
bondCount - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
 
bondCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
bondCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bondCount - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
bondCount - Variable in class org.jmol.minimize.forcefield.Calculations
 
bondCount - Variable in class org.jmol.minimize.forcefield.ForceField
 
bondCount - Variable in class org.jmol.minimize.Minimizer
 
bondCount - Variable in class org.jmol.modelset.BondCollection
 
bondCount - Variable in class org.jmol.modelset.BondIteratorSelected
 
bondCount - Variable in class org.jmol.modelset.Model
 
bondcount - Static variable in class org.jmol.script.Token
 
bondCount - Variable in class org.jmol.smiles.SmilesAtom
 
bondCount - Variable in class org.jmol.viewer.StateManager.Connections
 
bondCount0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bondData - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
bondData - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
bondedAtoms - Variable in class org.jmol.minimize.MinAtom
 
bondedOnly - Variable in class org.jmol.shapespecial.Polyhedra
 
bondFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
bondFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
bondIndex0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
BondIterator - Interface in org.jmol.modelset
 
BondIteratorSelected - Class in org.jmol.modelset
 
BondIteratorSelected(Bond[], int, int, BitSet, boolean) - Constructor for class org.jmol.modelset.BondIteratorSelected
 
BondIteratorSelected(Bond[], int, BitSet) - Constructor for class org.jmol.modelset.BondIteratorSelected
 
bondmode - Static variable in class org.jmol.script.Token
 
bondmodeor - Static variable in class org.jmol.script.Token
 
bondModeOr - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
bondMutually(Atom, Atom, int, short, float) - Method in class org.jmol.modelset.BondCollection
 
bondOrder - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
bondorder() - Method in class org.jmol.script.ScriptEvaluator
 
bondorder - Static variable in class org.jmol.script.Token
 
bondOrder - Variable in class org.jmol.shape.SticksRenderer
 
bondpicking - Static variable in class org.jmol.script.Token
 
bondPicking - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
bondPickingMode - Variable in class org.jmol.viewer.ActionManager
 
bondradiusmilliangstroms - Static variable in class org.jmol.script.Token
 
bondRadiusMilliAngstroms - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
bonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bonds - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
bonds - Variable in class org.jmol.minimize.forcefield.Calculations
 
bonds - Variable in class org.jmol.minimize.forcefield.ForceField
 
bonds - Variable in class org.jmol.minimize.MinAtom
 
bonds - Variable in class org.jmol.modelset.Atom
 
bonds - Variable in class org.jmol.modelset.BondCollection
 
bonds - Variable in class org.jmol.modelset.BondIteratorSelected
 
bonds - Static variable in class org.jmol.script.Token
 
bonds - Variable in class org.jmol.smiles.SmilesAtom
 
bondsBackbone - Variable in class org.jmol.shape.SticksRenderer
 
bondSelectionModeOr - Variable in class org.jmol.modelset.BondIteratorSelected
 
bondset - Static variable in class org.jmol.script.Token
 
bondsOr - Variable in class org.jmol.smiles.SmilesBond
 
bondtolerance - Static variable in class org.jmol.script.Token
 
bondTolerance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
bondTolerance - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
bondType - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
bondType - Variable in class org.jmol.modelset.BondIteratorSelected
 
bondTypes - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
booleanparam - Static variable in class org.jmol.script.Token
 
booleanParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
border - Variable in class org.openscience.jmol.app.JmolApp
 
border - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
BORDERCOLOR - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
 
BORDERSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
 
bottom - Static variable in class org.jmol.script.Token
 
bottomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
boundaryPlaneCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
boundbox(int) - Method in class org.jmol.script.ScriptEvaluator
 
boundbox - Static variable in class org.jmol.script.Token
 
boundBox - Variable in class org.jmol.shapespecial.Draw
 
boundboxAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
boundBoxCenter - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
boundboxcolor - Static variable in class org.jmol.script.Token
 
boundBoxNegCorner - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
boundBoxPosCorner - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
boundingBox - Variable in class org.jmol.jvxl.data.JvxlData
 
boundingBox - Variable in class org.jmol.jvxl.readers.Parameters
 
boundingBox - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
Box(String) - Static method in class org.jmol.popup.MainPopupResourceBundle
 
boxFaces - Static variable in class org.jmol.shapebio.RocketsRenderer
 
boxHeight - Variable in class org.jmol.shape.Object2d
 
boxInfo - Variable in class org.jmol.modelset.ModelCollection
 
BoxInfo - Class in org.jmol.util
 
BoxInfo() - Constructor for class org.jmol.util.BoxInfo
 
boxVec - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
boxWidth - Variable in class org.jmol.shape.Object2d
 
boxX - Variable in class org.jmol.shape.Object2d
 
boxXY - Variable in class org.jmol.shape.Object2d
 
boxY - Variable in class org.jmol.shape.Object2d
 
br - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
br - Variable in class org.jmol.util.CifDataReader
 
br - Variable in class org.jmol.util.XmlReader
 
braceCount - Variable in class org.jmol.script.ScriptCompiler
 
braceCount - Variable in class org.jmol.script.ScriptMathProcessor
 
braceCount - Variable in class org.jmol.smiles.SmilesParser
 
bracketCount - Variable in class org.jmol.script.ScriptCompiler
 
branch - Static variable in class org.jmol.script.Token
 
branchLevel - Variable in class org.jmol.smiles.SmilesParser
 
breakCmd(int) - Method in class org.jmol.script.ScriptEvaluator
 
breakcmd - Static variable in class org.jmol.script.Token
 
breakOutAtomTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
breakOutBondTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
breakOutTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
brickLayer - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
brickLayerByteCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
brickLayerVoxelCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
brickRowByteCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
browseButton - Variable in class org.openscience.chimetojmol.ChimePanel
 
bs - Variable in class org.jmol.jvxl.data.MeshData.SSet
 
bsAdded - Variable in class org.jmol.modelset.Group
 
bsAddedHydrogens - Variable in class org.jmol.modelsetbio.Resolver
 
bsAll - Variable in class org.jmol.modelset.ModelCollection
 
bsAllModels - Variable in class org.jmol.shapespecial.Draw
 
bsAnions - Static variable in class org.jmol.util.Elements
 
bsAromatic - Variable in class org.jmol.minimize.Minimizer
 
bsAromatic - Variable in class org.jmol.modelset.BondCollection
 
bsAromatic - Variable in class org.jmol.smiles.SmilesGenerator
 
bsAromatic - Variable in class org.jmol.smiles.SmilesSearch
 
bsAromaticDouble - Variable in class org.jmol.modelset.BondCollection
 
bsAromaticSingle - Variable in class org.jmol.modelset.BondCollection
 
bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
bsAtomOK - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
bsAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bsAtoms - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
bsAtoms - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
bsAtoms - Variable in class org.jmol.minimize.Minimizer
 
bsAtoms - Variable in class org.jmol.modelset.Model
 
bsAtoms - Variable in class org.jmol.symmetry.PointGroup
 
bsAtoms - Variable in class org.jmol.viewer.RepaintManager
 
bsAtoms - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
bsAtoms1 - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
bsAtoms2 - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
bsAtomsDeleted - Variable in class org.jmol.modelset.Model
 
bsAtomsForHs - Variable in class org.jmol.modelsetbio.Resolver
 
bsBackbone - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
bsBadIndex - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
bsBgColixSet - Variable in class org.jmol.shape.Labels
 
bsBonds - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
bsBondsDn - Variable in class org.jmol.smiles.SmilesGenerator
 
bsBondsUp - Variable in class org.jmol.smiles.SmilesGenerator
 
bScaled - Variable in class org.jmol.g3d.Rgb16
 
bsCations - Static variable in class org.jmol.util.Elements
 
bsColixSet - Variable in class org.jmol.shape.AtomShape
 
bsColixSet - Variable in class org.jmol.shape.Measures
 
bsColixSet - Variable in class org.jmol.shape.Sticks
 
bsColixSet - Variable in class org.jmol.shapebio.BioShape
 
bsConnected - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
bsDeleted - Variable in class org.jmol.viewer.SelectionManager
 
bsDisplay - Variable in class org.jmol.shape.MeshCollection
 
bsDisplay - Variable in class org.jmol.util.MeshSurface
 
bsEmpty - Variable in class org.jmol.modelset.AtomCollection
 
bsExclude - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
bsExcluded - Variable in class org.jmol.jvxl.readers.Parameters
 
bsExcluded - Variable in class org.jmol.quantum.QuantumCalculation
 
bsExcludedPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsExcludedTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsExcludedVertices - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
bsFixed - Variable in class org.jmol.minimize.forcefield.ForceField
 
bsFixed - Variable in class org.jmol.minimize.Minimizer
 
bsFixed - Variable in class org.jmol.viewer.SelectionManager
 
bsFixedDefault - Variable in class org.jmol.minimize.Minimizer
 
bsFontSet - Variable in class org.jmol.shape.Labels
 
bsFound - Variable in class org.jmol.smiles.SmilesSearch
 
bsFoundRectangle - Variable in class org.jmol.modelset.AtomCollection
 
bsFrameOffsets - Variable in class org.jmol.viewer.Viewer
 
bsFree - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
bsHandles - Variable in class org.jmol.shapespecial.DrawRenderer
 
bsHBondsRasmol - Variable in class org.jmol.modelset.BondCollection
 
bsHidden - Variable in class org.jmol.modelset.AtomCollection
 
bsHidden - Variable in class org.jmol.viewer.SelectionManager
 
bsHighlight - Variable in class org.jmol.shape.Halos
 
bsIgnore - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsIgnore - Variable in class org.jmol.jvxl.readers.Parameters
 
bsIgnore - Variable in class org.jmol.shapespecial.Dots
 
bsIgnored - Variable in class org.jmol.atomdata.AtomData
 
bsIncludingH - Variable in class org.jmol.smiles.SmilesGenerator
 
bsLocale - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
bsMeshesVisible - Variable in class org.jmol.shapespecial.DrawMesh
 
bsMinFixed - Variable in class org.jmol.minimize.Minimizer
 
bsModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
bsModels - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
 
bsMolecule - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
bsMolecules - Variable in class org.jmol.atomdata.AtomData
 
bsMyIgnored - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsMySelected - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsMySelected - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsNearby - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsNull - Static variable in class org.jmol.util.BitSetUtil
 
bsOK - Variable in class org.jmol.quantum.NciCalculation
 
bsOn - Variable in class org.jmol.shapespecial.Dots
 
bsOrderSet - Variable in class org.jmol.shape.Sticks
 
Bspf - Class in org.jmol.bspt
A Binary Space Partitioning Forest
Bspf(int) - Constructor for class org.jmol.bspt.Bspf
 
bspf - Variable in class org.jmol.modelset.AtomCollection
 
bspf - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
bsPolygons - Variable in class org.jmol.shape.MeshRenderer
 
bsPolygons - Variable in class org.jmol.util.MeshSurface
 
Bspt - Class in org.jmol.bspt
a Binary Space Partitioning Tree
Bspt(int, int) - Constructor for class org.jmol.bspt.Bspt
Create a bspt with the specified number of dimensions.
bspt - Variable in class org.jmol.bspt.CubeIterator
 
bspt - Variable in class org.jmol.bspt.Element
 
bspts - Variable in class org.jmol.bspt.Bspf
 
bsptsValid - Variable in class org.jmol.bspt.Bspf
 
bsRenderable - Variable in class org.jmol.viewer.ShapeManager
 
bsRequired - Variable in class org.jmol.smiles.SmilesSearch
 
bsReturn - Variable in class org.jmol.smiles.SmilesSearch
 
bsRotateBranch - Variable in class org.jmol.viewer.Viewer
 
bsSelect(Token) - Static method in class org.jmol.script.ScriptVariable
 
bsSelect(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
 
bsSelected - Variable in class org.jmol.atomdata.AtomData
 
bsSelected - Variable in class org.jmol.jvxl.readers.Parameters
 
bsSelected - Variable in class org.jmol.minimize.Minimizer
 
bsSelected - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
bsSelected - Variable in class org.jmol.modelset.BondIteratorSelected
 
bsSelected - Variable in class org.jmol.quantum.MepCalculation
 
bsSelected - Variable in class org.jmol.shape.Measures
 
bsSelected - Variable in class org.jmol.shapebio.Backbone
 
bsSelected - Variable in class org.jmol.shapespecial.Dots
 
bsSelected - Variable in class org.jmol.smiles.SmilesGenerator
 
bsSelected - Variable in class org.jmol.smiles.SmilesSearch
 
bsSelectedGroups - Variable in class org.jmol.modelset.Chain
 
bsSelectedMonomers - Variable in class org.jmol.modelsetbio.BioPolymer
 
bsSelection - Variable in class org.jmol.viewer.SelectionManager
 
bsSelectRange(Token, int) - Static method in class org.jmol.script.ScriptVariable
 
bsSets - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
bsSizeDefault - Variable in class org.jmol.shapebio.BioShape
 
bsSizeSet - Variable in class org.jmol.shape.AtomShape
 
bsSizeSet - Variable in class org.jmol.shape.Sticks
 
bsSizeSet - Variable in class org.jmol.shapebio.BioShape
 
bsSlab - Variable in class org.jmol.shape.MeshRenderer
 
bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
 
bsSlabGhost - Variable in class org.jmol.util.MeshSurface
 
bsSolvent - Variable in class org.jmol.jvxl.readers.Parameters
 
bsSubset - Variable in class org.jmol.viewer.SelectionManager
 
bsSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsSurface - Variable in class org.jmol.modelset.AtomCollection
 
bsSurfaceDone - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
bsSurfacePoints - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
bsSurfaceVoxels - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsSymmetry - Variable in class org.jmol.adapter.smarter.Atom
 
bsSymmetry - Variable in class org.jmol.modelset.ModelCollection
 
bsTaint - Variable in class org.jmol.minimize.Minimizer
 
bsTemp - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
bsTemp - Variable in class org.jmol.viewer.SelectionManager
 
bsToDo - Variable in class org.jmol.smiles.SmilesGenerator
 
bsUserVdws - Variable in class org.jmol.viewer.DataManager
 
bsValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsValues - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
bsVdw - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
bsVdw - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
bsVertexCount - Variable in class org.jmol.shapespecial.Polyhedra
 
bsVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
bsVisible - Variable in class org.jmol.shapebio.BioShapeRenderer
 
bsVisibleFrames - Variable in class org.jmol.viewer.AnimationManager
 
bsVoxelBitSet - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
bsVoxels - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsVoxels - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
bTest - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
btSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buf - Variable in class org.jmol.adapter.smarter.LimitedLineReader
 
buf - Variable in class org.jmol.util.LimitedLineReader
 
buf - Variable in class org.jmol.util.ZipUtil.GZipData
 
bufferHasBeenCleared - Variable in class org.jmol.g3d.Platform3D.ClearingThread
 
bufferHeight - Variable in class org.jmol.g3d.Platform3D
 
bufferIt(BufferedOutputStream, int, int) - Method in class org.jmol.util.Huffman
 
bufferPutBits - Variable in class org.jmol.util.Huffman
 
bufferPutBuffer - Variable in class org.jmol.util.Huffman
 
bufferSize - Variable in class org.jmol.g3d.Graphics3D
 
bufferSize - Variable in class org.jmol.g3d.Platform3D
 
bufferSizeT - Variable in class org.jmol.g3d.Platform3D
 
bufferWidth - Variable in class org.jmol.g3d.Platform3D
 
build(String, Object, PopupResource) - Method in class org.jmol.popup.SimplePopup
 
buildAdvancedPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
buildArrowHeadBox(Point3f, Vector3f, Vector3f, Point3f) - Method in class org.jmol.shapebio.RocketsRenderer
 
buildAtomsPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildBasicPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
buildBioPolymer(Group, Group[], int, boolean) - Method in interface org.jmol.api.JmolBioResolver
 
buildBioPolymer(Group, Group[], int, boolean) - Method in class org.jmol.modelsetbio.Resolver
 
buildBondPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildBox(Point3f, Vector3f, Vector3f, Vector3f) - Method in class org.jmol.shapebio.RocketsRenderer
 
buildButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
buildDispPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildFilePanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
buildPolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
 
buildSpaceGroup(String) - Method in class org.jmol.symmetry.SpaceGroup
 
buildStructure(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
buildStructure(String) - Method in class org.jmol.popup.MainPopupResourceBundle
 
buildStructure(String) - Method in class org.jmol.popup.PopupResource
 
BumpPixel() - Method in class org.jmol.export.image.GifEncoder
 
button - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
 
BUTTON_MODIFIER_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
buttonModelkit - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
buttonPanel - Variable in class org.jmol.console.ScriptEditor
 
buttonPanel - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
buttonRotate - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
buttons - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
bValue(Token) - Static method in class org.jmol.script.ScriptVariable
 
bw - Variable in class org.jmol.export.___Exporter
 
BW - Static variable in class org.jmol.util.ColorEncoder
 
bw - Variable in class org.jmol.util.OutputStringBuffer
 
BWR - Static variable in class org.jmol.util.ColorEncoder
 
bwSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
BYELEMENT_JMOL - Static variable in class org.jmol.util.ColorEncoder
 
BYELEMENT_PREFIX - Static variable in class org.jmol.util.ColorEncoder
 
BYELEMENT_RASMOL - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_AMINO - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_PREFIX - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_SHAPELY - Static variable in class org.jmol.util.ColorEncoder
 
byteArrayOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
byteFactor - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
bytePos - Variable in class org.jmol.export.image.PngEncoder
 
bytesPerPixel - Variable in class org.jmol.export.image.PngEncoder
 
bytesToDoubleToFloat(byte[], int) - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 

C

c - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
c - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
c - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
c - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
c - Variable in class org.jmol.jvxl.readers.MapFileReader
 
c - Variable in class org.jmol.minimize.forcefield.Calculation
 
C - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
c - Variable in class org.jmol.quantum.MOCalculation
 
c - Static variable in class org.jmol.quantum.NciCalculation
 
c - Variable in class org.jmol.util.SimpleUnitCell
 
c1 - Variable in class org.jmol.g3d.Hermite3D
 
C1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c2 - Variable in class org.jmol.g3d.Hermite3D
 
C2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c2 - Static variable in class org.jmol.symmetry.PointGroup
 
c3 - Static variable in class org.jmol.symmetry.PointGroup
 
C3Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
C4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c4 - Static variable in class org.jmol.symmetry.PointGroup
 
C4P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
C5 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c5 - Static variable in class org.jmol.symmetry.PointGroup
 
C6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c6 - Static variable in class org.jmol.symmetry.PointGroup
 
C8 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c8 - Static variable in class org.jmol.symmetry.PointGroup
 
c_ - Variable in class org.jmol.util.SimpleUnitCell
 
CA - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
cA_ - Variable in class org.jmol.util.SimpleUnitCell
 
CageRenderer - Class in org.jmol.shape
 
CageRenderer() - Constructor for class org.jmol.shape.CageRenderer
 
calc(int, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
calc - Variable in class org.jmol.minimize.forcefield.ForceField
 
calc(double[][]) - Method in class org.jmol.util.Eigen
 
calc1Screen(Point3f, Vector3f, short, float, Point3i) - Method in class org.jmol.shapebio.BioShapeRenderer
 
CALC_ANGLE - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_DISTANCE - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_ES - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_MAX - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_OOP - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_TORSION - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_VDW - Static variable in class org.jmol.minimize.forcefield.Calculations
 
calcArgbEndcap(boolean, boolean) - Method in class org.jmol.g3d.Cylinder3D
 
calcArgbsGreyscale() - Static method in class org.jmol.g3d.Colix3D
 
calcAtomsMinMax(BitSet, BoxInfo) - Method in class org.jmol.api.JmolViewer
 
calcAtomsMinMax(BitSet, BoxInfo) - Method in class org.jmol.modelset.ModelCollection
 
calcAtomsMinMax(BitSet, BoxInfo) - Method in class org.jmol.viewer.Viewer
 
calcAveragePoint(Point3f, Point3f, Point3f) - Static method in class org.jmol.util.Measure
 
calcAveragePointN(Point3f[], int, Point3f) - Static method in class org.jmol.util.Measure
 
calcAxis() - Method in class org.jmol.modelsetbio.Helix
 
calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
 
calcAxis() - Method in class org.jmol.modelsetbio.Sheet
 
calcBestAxisThroughPoints(Point3f[], Point3f, Vector3f, Vector3f, int) - Static method in class org.jmol.util.Measure
 
calcBfactorRange(BitSet) - Method in class org.jmol.modelset.AtomCollection
 
calcBfactorRange() - Method in class org.jmol.shapebio.BioShape
 
calcBioParameters() - Method in class org.jmol.modelset.Group
 
calcBioParameters() - Method in class org.jmol.modelsetbio.Monomer
 
calcBoundBoxDimensions(BitSet, float) - Method in class org.jmol.modelset.ModelCollection
 
calcBoundBoxDimensions(BitSet, float) - Method in class org.jmol.viewer.Viewer
 
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
sets all camera and scale factors needed by the specific perspective model instantiated
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager10
 
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager11
 
calcContourPoint(float, float, float, Point3f) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
calcConvexBits() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calcConvexMap(boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.NucleicPolymer
 
calcFactors(int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
calcGreyscaleRgbFromRgb(int) - Static method in class org.jmol.g3d.Graphics3D
Return a greyscale rgb value 0-FF using NTSC color luminance algorithm
calcHbondEnergy(Point3f, Point3f, AminoMonomer, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
based on RasMol 2.7.2.1.1 model checkDistances: When we are seriously looking for H bonds, we want to also check that distCN > distCH and that the OH distance is less than 3 Angstroms.
calcLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcMeanPositionalDisplacement(int) - Method in class org.jmol.shapebio.BioShape
Calculates the mean positional displacement in milliAngstroms.
calcMetrics() - Method in class org.jmol.shape.Frank
 
calcNavigationDepthPercent() - Method in class org.jmol.viewer.TransformManager11
 
calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager
all navigation effects go through this method
calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager11
All the magic happens here.
calcNavSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager11
 
calcNormalizedNormal(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
 
calcOptions - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
calcParameters() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcPhiPsiAngles(AminoMonomer, AminoMonomer) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcPlane(int, float[]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
Fill this plane with data based on the current set of raw data planes.
calcPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
For reduced density only; coloring is done point by point.
calcRasmolHydrogenBonds(BitSet, BitSet, List<Bond>, boolean, int, boolean) - Method in class org.jmol.modelset.ModelCollection
These are not actual hydrogen bonds.
calcRasmolHydrogenBonds(Polymer, BitSet, BitSet, List<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelset.Polymer
 
calcRasmolHydrogenBonds(Polymer, BitSet, BitSet, List<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcRasmolHydrogenBonds(Polymer, BitSet, BitSet, List<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
calcRectRubberBand() - Method in class org.jmol.viewer.ActionManager
 
calcRopeMidPoints(boolean) - Method in class org.jmol.shapebio.RocketsRenderer
 
calcRotatedPoint(float, int, boolean) - Method in class org.jmol.g3d.Cylinder3D
 
calcRotationRadius(int, Point3f) - Method in class org.jmol.modelset.ModelCollection
 
calcRotationRadius(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcRotationRadius(Point3f) - Method in class org.jmol.viewer.Viewer
 
calcRotationRadius(BitSet) - Method in class org.jmol.viewer.Viewer
 
calcScreenControlPoints() - Method in class org.jmol.shapebio.BioShapeRenderer
 
calcScreenControlPoints(Point3f[]) - Method in class org.jmol.shapebio.BioShapeRenderer
 
calcScreenPoints(FastBitSet, float, int, int, int) - Method in class org.jmol.shapespecial.DotsRenderer
calculates the screen xy coordinates for the dots or faces
calcScreens(float) - Method in class org.jmol.shapebio.BioShapeRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
 
calcSelectedGroupsCount(BitSet) - Method in class org.jmol.modelset.Chain
prior to coloring by group, we need the chain count per chain that is selected
calcSelectedGroupsCount(BitSet) - Method in class org.jmol.modelset.Model
 
calcSelectedGroupsCount(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcSelectedGroupsCount() - Method in class org.jmol.viewer.Viewer
 
calcSelectedMoleculesCount(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcSelectedMoleculesCount() - Method in class org.jmol.viewer.Viewer
 
calcSelectedMonomersCount(BitSet) - Method in class org.jmol.modelset.Model
 
calcSelectedMonomersCount(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcSelectedMonomersCount(BitSet) - Method in class org.jmol.modelset.Polymer
 
calcSelectedMonomersCount(BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
calcSelectedMonomersCount() - Method in class org.jmol.viewer.Viewer
 
calcSheetUnitVectors() - Method in class org.jmol.modelsetbio.Sheet
 
calcSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager
sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.
calcSP(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
 
calcSphereShading() - Static method in class org.jmol.g3d.Shade3D
 
calcSurfaceDistances() - Method in class org.jmol.modelset.AtomCollection
 
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
 
calcType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
calculate(VolumeDataInterface, BitSet, Point3f[], float[], int) - Method in interface org.jmol.api.MepCalculationInterface
 
calculate(RadiusData, float, BitSet, BitSet, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calculate(VolumeDataInterface, BitSet, Point3f[], float[], int) - Method in class org.jmol.quantum.MepCalculation
 
calculate() - Method in class org.jmol.script.ScriptEvaluator
 
calculate - Static variable in class org.jmol.script.Token
 
calculateAnglesInDegrees() - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateCodes(float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculatedArea - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
calculatedArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
calculatedDipole - Variable in class org.jmol.shapespecial.Dipoles
 
calculatedVolume - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
calculatedVolume - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
calculateElectronDensity() - Method in class org.jmol.quantum.MOCalculation
 
calculateFractionalPoint(float, Point3f, Point3f, float, float, Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
calculateGeodesicSurface(BitSet, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
calculateGeodesicSurface(BitSet, float) - Method in class org.jmol.shapesurface.Isosurface
 
calculateHydrogens(BitSet, int[], boolean, boolean, List<Atom>) - Method in class org.jmol.modelset.AtomCollection
get a list of potential H atom positions based on elemental valence and formal charge
calculateMad(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
 
calculateMolecularDipole(int) - Method in class org.jmol.modelset.ModelCollection
 
calculateMolecularDipole() - Method in class org.jmol.viewer.Viewer
 
calculatePointGroup(BitSet) - Method in class org.jmol.modelset.ModelSet
 
calculatePointGroup() - Method in class org.jmol.viewer.Viewer
 
calculatePointGroupForFirstModel(BitSet, boolean, boolean, boolean, String, int, float) - Method in class org.jmol.modelset.ModelSet
 
calculatePolymers(Group[], int, int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calculateQuaternionRotation(Point3f[][], float[], boolean) - Static method in class org.jmol.util.Measure
 
calculateR0(double, double, double, double, double) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
 
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.BioPolymer
 
calculateRunsFourOrMore(AlphaPolymer.Code[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateStraightness() - Method in class org.jmol.modelset.ModelCollection
 
calculateStraightness() - Method in class org.jmol.viewer.Viewer
 
calculateStructures(boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.Model
 
calculateStructures(BitSet, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
calculateStructures(Polymer[], int, List<Bond>, boolean, boolean, boolean) - Method in class org.jmol.modelset.Polymer
 
calculateStructures(boolean) - Method in class org.jmol.modelset.Polymer
 
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calculateStructures(Polymer[], int, List<Bond>, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
calculateStructures(BitSet, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
calculateStructuresAllExcept(BitSet, boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
allows rebuilding of PDB structures; also accessed by ModelManager from Eval
calculateStructuresDssp(Polymer[], int, List<Bond>, boolean, boolean, boolean) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
calculateStruts(BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.
calculateStruts(BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.
calculateStruts(ModelSet, BitSet, BitSet, List<Atom>, float, int, boolean) - Method in class org.jmol.modelset.Polymer
 
calculateStruts(ModelSet, BitSet, BitSet, List<Atom>, float, int, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous).
calculateStruts(BitSet, BitSet) - Method in class org.jmol.viewer.Viewer
 
calculateStrutsStatic(ModelSet, BitSet, BitSet, List<Atom>, float, int, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateSurface(BitSet, float) - Method in class org.jmol.modelset.AtomCollection
 
calculateSurface(BitSet, float) - Method in class org.jmol.viewer.Viewer
 
calculateVolume(BitSet, EnumVdw) - Method in class org.jmol.modelset.AtomCollection
 
calculateVolumeOrArea(int, boolean, boolean) - Method in class org.jmol.jvxl.data.MeshData
 
calculateVolumeOrArea(boolean) - Method in class org.jmol.shapesurface.Isosurface
 
calculateVolumes() - Method in class org.jmol.jvxl.data.MeshData
 
Calculation - Class in org.jmol.minimize.forcefield
 
Calculation() - Constructor for class org.jmol.minimize.forcefield.Calculation
 
calculationNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
The number of the calculation being interpreted.
calculationNumber - Variable in class org.jmol.adapter.readers.quantum.QchemReader
The number of the calculation being interpreted.
Calculations - Class in org.jmol.minimize.forcefield
 
Calculations(ForceField, MinAtom[], MinBond[], int[][], int[][], double[], List<Object[]>) - Constructor for class org.jmol.minimize.forcefield.Calculations
 
calculations - Variable in class org.jmol.minimize.forcefield.Calculations
 
CalculationsUFF - Class in org.jmol.minimize.forcefield
 
CalculationsUFF(ForceField, MinAtom[], MinBond[], int[][], int[][], double[], List<Object[]>) - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF
 
CalculationsUFF.AngleCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.AngleCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.AngleCalc
 
CalculationsUFF.DistanceCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.DistanceCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
CalculationsUFF.ESCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.ESCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.ESCalc
 
CalculationsUFF.OOPCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.OOPCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.OOPCalc
 
CalculationsUFF.PairCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.PairCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.PairCalc
 
CalculationsUFF.TorsionCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.TorsionCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.TorsionCalc
 
CalculationsUFF.VDWCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.VDWCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.VDWCalc
 
calculationType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
calculationType - Variable in class org.jmol.jvxl.readers.Parameters
 
calculationType - Variable in class org.jmol.quantum.MOCalculation
 
calcUnitCellMinMax() - Method in class org.jmol.modelset.ModelCollection
 
calcUnitcellVertices() - Method in class org.jmol.symmetry.UnitCell
 
calcVertexPoint(int, int, int, int, Point3f) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
calcVoxelPlaneDistance(int, int, int) - Method in interface org.jmol.api.VolumeDataInterface
 
calcVoxelPlaneDistance(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
calcVoxelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
callbacks - Variable in class org.jmol.applet.Jmol
 
cameradepth - Static variable in class org.jmol.script.Token
 
cameraDepth - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
cameraDepth - Variable in class org.jmol.viewer.TransformManager
 
cameraDepthSetting - Variable in class org.jmol.viewer.TransformManager
 
cameraDistance - Variable in class org.jmol.export.___Exporter
 
cameraDistance - Variable in class org.jmol.viewer.TransformManager
 
cameraDistanceFromCenter - Variable in class org.jmol.viewer.TransformManager
 
cameraPosition - Variable in class org.jmol.export.___Exporter
 
cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
 
canAdd(AminoPolymer.Bridge) - Method in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
canBeNormalized(Vector3d) - Static method in class org.jmol.minimize.Util
 
canBeSquared(double) - Static method in class org.jmol.minimize.Util
 
cancel - Static variable in class org.jmol.script.Token
 
cancel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
cancel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cancel() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
cancelPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Responds to cancel being press- or equivalent eg window closed.
canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
 
canDownsample - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
canImport(JComponent, DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
canIncrement() - Method in class org.jmol.script.ScriptVariable
 
canNavigate() - Method in class org.jmol.viewer.TransformManager
 
canNavigate() - Method in class org.jmol.viewer.TransformManager11
 
CANONICAL_DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
CANONICAL_DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
CANONICAL_FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
CANONICAL_FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
canonicalSeitzList - Static variable in class org.jmol.symmetry.SpaceGroup
 
canonizeAlphaDigit(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeChainID(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter
 
cap - Static variable in class org.jmol.script.Token
 
capCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
capData(Point4f, float) - Method in interface org.jmol.api.VolumeDataInterface
 
capData(Point4f, float) - Method in class org.jmol.jvxl.data.VolumeData
 
capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
cappingObject - Variable in class org.jmol.shape.Mesh
 
cappingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
 
capPlanesPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
carbohydrate - Static variable in class org.jmol.script.Token
 
CarbohydrateMonomer - Class in org.jmol.modelsetbio
 
CarbohydrateMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.CarbohydrateMonomer
 
CarbohydratePolymer - Class in org.jmol.modelsetbio
 
CarbohydratePolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.CarbohydratePolymer
 
cardinality() - Method in class org.jmol.util.FastBitSet
 
cardinality(int) - Method in class org.jmol.util.FastBitSet
 
cardinalityOf(BitSet) - Static method in class org.jmol.util.BitSetUtil
cardinality = "total number of set bits"
cartesianOffset - Variable in class org.jmol.symmetry.UnitCell
 
cartesians - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
CARTN_X - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CARTN_Y - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CARTN_Z - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
cartoon - Static variable in class org.jmol.script.Token
 
Cartoon - Class in org.jmol.shapebio
 
Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
 
CARTOON_VISIBILITY_FLAG - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
cartoonbaseedges - Static variable in class org.jmol.script.Token
 
cartoonBaseEdges - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
CartoonRenderer - Class in org.jmol.shapebio
 
CartoonRenderer() - Constructor for class org.jmol.shapebio.CartoonRenderer
 
cartoonrockets - Static variable in class org.jmol.script.Token
 
cartoonRockets - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
casecmd - Static variable in class org.jmol.script.Token
 
CastepDensityReader - Class in org.jmol.jvxl.readers
 
CastepDensityReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.CastepDensityReader
 
CastepReader - Class in org.jmol.adapter.readers.xtal
CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer or "q={1/4 1/4 0}" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where -- the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example -- following this with ".1" ".2" etc.
CastepReader() - Constructor for class org.jmol.adapter.readers.xtal.CastepReader
 
catchcmd - Static variable in class org.jmol.script.Token
 
cationLookupTable - Static variable in class org.jmol.util.Elements
 
cavity - Static variable in class org.jmol.script.Token
 
cavityRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
cavityRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
cb - Variable in class org.jmol.export.dialog.Dialog
 
cB_ - Variable in class org.jmol.util.SimpleUnitCell
 
cbAxesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbClearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbOpenFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbPerspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbShowAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbShowBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cc1 - Variable in class org.jmol.g3d.Line3D
 
cc2 - Variable in class org.jmol.g3d.Line3D
 
cch - Variable in class org.jmol.util.CifDataReader
 
cchBuf - Variable in class org.jmol.adapter.smarter.LimitedLineReader
 
cchBuf - Variable in class org.jmol.util.LimitedLineReader
 
cchScript - Variable in class org.jmol.script.ScriptCompiler
 
cchToken - Variable in class org.jmol.script.ScriptCompiler
 
cd() - Method in class org.jmol.script.ScriptEvaluator
 
cd - Static variable in class org.jmol.script.Token
 
cd(String) - Method in class org.jmol.viewer.Viewer
 
cell() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
cell - Static variable in class org.jmol.script.Token
 
cell0 - Variable in class org.jmol.shape.UccageRenderer
 
cell1 - Variable in class org.jmol.shape.UccageRenderer
 
cellParameterType - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
cellParamNames - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
cellParams - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
 
cellRange - Variable in class org.jmol.symmetry.SymmetryInfo
 
center - Variable in class org.jmol.export.___Exporter
 
center - Variable in class org.jmol.jvxl.readers.Parameters
 
center - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
center - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
 
center(int) - Method in class org.jmol.script.ScriptEvaluator
 
center - Static variable in class org.jmol.script.Token
 
center - Variable in class org.jmol.shapespecial.Dipole
 
center - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
center - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
center - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
center - Variable in class org.jmol.shapesurface.Isosurface
 
center - Variable in class org.jmol.symmetry.PointGroup
 
center - Static variable in class org.jmol.viewer.JmolConstants
 
center - Variable in class org.jmol.viewer.StateManager.Orientation
 
center - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
center - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
centerAt() - Method in class org.jmol.script.ScriptEvaluator
 
centerAt - Static variable in class org.jmol.script.Token
 
centerAt(int, int, Point3f) - Method in class org.jmol.viewer.TransformManager
 
centerAt(int, int, Point3f) - Method in class org.jmol.viewer.Viewer
 
centerAtomIndex - Variable in class org.jmol.symmetry.PointGroup
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Centers the dialog on the screen.
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
 
centerDipole() - Method in class org.jmol.shapespecial.Dipole
 
centerI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
centerParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
centerParameter(int, int) - Method in class org.jmol.script.ScriptEvaluator
 
centers - Variable in class org.jmol.shapespecial.Polyhedra
 
centers - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
centerT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
centerValues - Variable in class org.jmol.bspt.CubeIterator
 
centralAtom - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
cH - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
ch1 - Variable in class org.jmol.modelset.LabelToken
 
Chain - Class in org.jmol.modelset
 
Chain(ModelSet, Model, char) - Constructor for class org.jmol.modelset.Chain
 
chain - Variable in class org.jmol.modelset.Group
 
chain - Static variable in class org.jmol.script.Token
 
chainAtomCounts - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
chaincasesensitive - Static variable in class org.jmol.script.Token
 
chainCaseSensitive - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
chainCount - Variable in class org.jmol.modelset.Model
 
chainID - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
chainID - Variable in class org.jmol.adapter.smarter.Atom
 
chainID - Variable in class org.jmol.modelset.Chain
 
chainOf - Variable in class org.jmol.modelset.ModelLoader
 
chains - Variable in class org.jmol.modelset.Model
 
CHANGEABLE_MASK - Static variable in class org.jmol.g3d.Graphics3D
 
changeableColixMap - Variable in class org.jmol.g3d.Graphics3D
changeable colixes give me a short ID and a color, and I will give you a colix later, you can reassign the color if you want Used only for colorManager coloring of elements
changeColixArgb(short, int) - Method in class org.jmol.g3d.Graphics3D
 
changeElementColor(String, int) - Method in class org.jmol.script.ScriptEvaluator
 
char_init() - Method in class org.jmol.export.image.GifEncoder
 
char_out(byte, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
characters(char[], int, int) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
charge - Variable in class org.jmol.smiles.SmilesAtom
 
charge - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
chargesFound - Variable in class org.jmol.adapter.readers.simple.MopacReader
 
ChargesOnly - Variable in class org.jmol.popup.SimplePopup
 
chargeSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
charToken() - Method in class org.jmol.script.ScriptCompiler
 
check - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
check - Static variable in class org.jmol.script.Token
 
check() - Method in class org.jmol.smiles.SmilesMeasure
 
check(int, int, int, long, long) - Method in class org.jmol.viewer.ActionManager.Mouse
 
check - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
checkAction(ActionEvent) - Method in class org.jmol.console.ScriptEditor
 
checkAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
 
checkAims(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkAlchemy(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkAtomArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkAtomLine(boolean, boolean, String, String, StringBuffer) - Static method in class org.jmol.jvxl.readers.VolumeFileReader
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAutoBondLegacy() - Method in class org.jmol.viewer.Viewer
 
checkAxisOrder(int, Vector3f, Point3f) - Method in class org.jmol.symmetry.PointGroup
 
checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[], float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
checkBinary(String) - Method in class org.jmol.jvxl.readers.PmeshReader
 
checkBioType(String, int) - Method in class org.jmol.smiles.SmilesParser
 
checkBondArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkBoolean(Map<String, Object>, String) - Method in class org.jmol.popup.SimplePopup
 
checkBoundsMinMax(Point3f, Point3f) - Method in class org.jmol.shape.Shape
 
checkBoxListener - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
checkBrace(SmilesSearch, char, char) - Method in class org.jmol.smiles.SmilesParser
 
checkBridge(AminoPolymer.Bridge, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, boolean, int, int) - Static method in class org.jmol.modelsetbio.AminoPolymer
check to see if another bridge exists offset by n1 and n2 from the two ends of a bridge
checkBulge(AminoPolymer.Bridge, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, boolean, int) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
checkButton - Variable in class org.jmol.console.ScriptEditor
 
checkButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
checkByteCount - Variable in class org.jmol.shape.Mesh
 
checkCalculationType() - Method in class org.jmol.quantum.MOCalculation
 
checkCarbohydrate(String) - Static method in class org.jmol.viewer.JmolConstants
 
checkCastep(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkCharge(String, int, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
 
checkChirality(String, int, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
 
checkClick(TouchPoint, List<Event>, boolean) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
 
checkCommand() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
checkContinue() - Method in class org.jmol.script.ScriptEvaluator
checks to see if there is a pause condition, during which commands can still be issued, but with the ! first.
checkContour(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
checkCoordinatesChanged() - Method in class org.jmol.viewer.Viewer
 
checkCount - Variable in class org.jmol.util.MeshSurface
 
checkCp(ContactPair, ContactPair, int, int) - Static method in class org.jmol.shapesurface.Contact
 
checkCrystal(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkCube(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkCutoff(int, int, int, float[]) - Static method in class org.jmol.jvxl.data.MeshData
 
checkDiameter(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
checkDistance(Point3f, Point3f, float, float, int, int, int, Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
checkDistance(Point3f, Point3f, float, float, int, int, int, Point3f) - Method in class org.jmol.symmetry.Symmetry
 
checkDistance(Point3f, Point3f, float, float, int, int, int, Point3f) - Method in class org.jmol.symmetry.UnitCell
 
checkedSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkExplicit(String) - Method in class org.jmol.shape.MeshCollection
 
checkField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
checkFilenames - Variable in class org.openscience.chimetojmol.ChimePanel
 
checkFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkFilter(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkFloatRange(float, float, float) - Static method in class org.jmol.viewer.Viewer
 
checkFlowCommand(String) - Method in class org.jmol.script.ScriptCompiler
 
checkFlowEnd(int, String, int) - Method in class org.jmol.script.ScriptCompiler
 
checkFlowEndBrace() - Method in class org.jmol.script.ScriptCompiler
 
checkFlowStartBrace(boolean) - Method in class org.jmol.script.ScriptCompiler
 
checkFoldingXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkForceEndIf() - Method in class org.jmol.script.ScriptFlowContext
 
checkForCoordinate(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
checkForItemSelector(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
checkformat(int) - Method in class org.openscience.jmol.app.webexport.Molecules
 
checkformat(int) - Method in class org.openscience.jmol.app.webexport.Orbitals
 
checkGenNBO(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkGreater - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
checkGromacs(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkHalt(String, boolean) - Method in class org.jmol.api.JmolViewer
 
checkHalt(String, boolean) - Method in class org.jmol.viewer.Viewer
 
checkHeaderContains(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkImpliedScriptCmd - Variable in class org.jmol.script.ScriptCompiler
 
checkIn(String, Applet) - Static method in class org.jmol.applet.JmolAppletRegistry
 
checking - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
 
checking - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
checkInternalSlab(Point3f) - Method in class org.jmol.viewer.TransformManager
 
checkIntRange(int, int, int) - Static method in class org.jmol.viewer.Viewer
 
checkLast(int) - Method in class org.jmol.script.ScriptEvaluator
 
checkLastModel() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
sets continuing and doProcessLines
checkLength(int) - Method in class org.jmol.script.ScriptEvaluator
 
checkLength(int, int) - Method in class org.jmol.script.ScriptEvaluator
 
checkLength23() - Method in class org.jmol.script.ScriptEvaluator
 
checkLength34() - Method in class org.jmol.script.ScriptEvaluator
 
checkLine() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
checkLine() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
checkLine() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Reads a Collection of AtomSets from a BufferedReader.
checkLine() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.AmpacReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
checkLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkLineContinuation() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkLineStarts(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkLogic(SmilesSearch, String, SmilesAtom, SmilesBond, SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
 
checkMatch(SmilesAtom, int, int, boolean) - Method in class org.jmol.smiles.SmilesSearch
Check for a specific match of a model set atom with a pattern position
checkMatchBond(SmilesAtom, SmilesAtom, SmilesBond, int, int, JmolEdge) - Method in class org.jmol.smiles.SmilesSearch
 
checkMemory() - Static method in class org.jmol.util.Logger
 
checkMenuClick(Object, String) - Method in class org.jmol.modelkit.ModelKitPopup
 
checkMenuClick(Object, String) - Method in class org.jmol.popup.SimplePopup
 
checkMesh(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
checkMeshBB(Shape[], int, BoxInfo) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
checkMinAttachedAngle(Atom, float, Vector3f, Vector3f, boolean) - Static method in class org.jmol.modelset.ModelCollection
 
checkMinimization() - Method in class org.jmol.viewer.Viewer
 
checkMinZ(Atom, int[]) - Method in class org.jmol.modelset.Group
 
checkMol(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkMopacGraphf(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkMotion(int) - Method in class org.jmol.viewer.ActionManager
 
checkMotionRotateZoom(int, int, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
 
checkNboLine() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
checkNested(SmilesSearch, SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
 
checkNewGroup(JmolAdapter, char, String, int, char, boolean) - Method in class org.jmol.modelset.ModelLoader
 
checkNewSetCommand() - Method in class org.jmol.script.ScriptCompiler
 
checkNormals(short, short, short) - Method in class org.jmol.shape.MeshRenderer
 
checkNotPDB() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
checkObjectClicked(int, int, BitSet) - Method in class org.jmol.shape.Object2d
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shape.Object2dShape
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shape.Shape
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shape.Sticks
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shapespecial.Draw
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shapesurface.Isosurface
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.viewer.ShapeManager
 
checkObjectClicked(int, int, int) - Method in class org.jmol.viewer.Viewer
 
checkObjectDragged(int, int, int, int, int, BitSet) - Method in class org.jmol.shape.Labels
 
checkObjectDragged(int, int, int, int, int, BitSet) - Method in class org.jmol.shape.Shape
 
checkObjectDragged(int, int, int, int, int, BitSet) - Method in class org.jmol.shapespecial.Draw
 
checkObjectDragged(int, int, int, int, int, BitSet, int) - Method in class org.jmol.viewer.ShapeManager
 
checkObjectDragged(int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shape.Frank
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shape.Object2dShape
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shape.Shape
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shape.Sticks
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shapespecial.Draw
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shapesurface.Isosurface
 
checkObjectHovered(int, int, BitSet, boolean) - Method in class org.jmol.viewer.ShapeManager
 
checkObjectHovered(int, int) - Method in class org.jmol.viewer.Viewer
 
checkOdyssey(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkOffscreenSize(int, int) - Method in class org.jmol.g3d.Platform3D
 
checkOperation(Quaternion, Point3f, int) - Method in class org.jmol.symmetry.PointGroup
 
checkOption(JmolViewer, String) - Static method in class org.jmol.api.JmolViewer
 
checkOptional(byte[], byte, int, int) - Static method in class org.jmol.modelsetbio.Monomer
 
checkOptions(CommandLine, Options) - Method in class org.openscience.jmol.app.JmolApp
 
checkOrbitalType(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
checkOut(String) - Static method in class org.jmol.applet.JmolAppletRegistry
 
checkPhiPsi(float[], float, float) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
checkPoint(Tuple3f) - Method in class org.jmol.export._IdtfExporter
 
checkPoint(Point3fi) - Method in class org.jmol.modelset.MeasurementPending
 
checkPointOrAtomClicked(int, int, int, int, long, boolean, int) - Method in class org.jmol.viewer.ActionManager
 
checkPrimitiveAtom(SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
 
checkPrimitiveBond(SmilesBond, int, int, JmolEdge) - Method in class org.jmol.smiles.SmilesSearch
 
checkPrivateKey(double) - Method in class org.jmol.api.JmolViewer
 
checkPrivateKey(double) - Method in class org.jmol.viewer.Viewer
Simple method to ensure that the image creator (which writes files) was in fact opened by this viewer and not by some manipulation of the applet.
checkPt(float[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
two values -- v1, and v2, which need not be ordered v1 < v2.
checkRasmolHydrogenBond(AminoMonomer, Polymer, int, Point3f, BitSet, List<Bond>, int[][], boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
 
checkResume(String) - Method in class org.jmol.viewer.Viewer
 
checkScript() - Method in class org.jmol.console.ScriptEditor
 
checkScriptAndOpenFiles - Variable in class org.openscience.jmol.app.JmolApp
 
checkScriptExecution(String, boolean) - Method in class org.jmol.viewer.Viewer
 
checkScriptNoFiles - Variable in class org.openscience.jmol.app.JmolApp
 
checkScriptSilent(String) - Method in class org.jmol.script.ScriptEvaluator
a method for just checking a script
checkSigned - Variable in class org.openscience.chimetojmol.ChimePanel
 
checkSlab(int, Point3f, float, float, Point4f, Point3f[]) - Static method in class org.jmol.util.MeshSurface
 
checkSlideZoom(int) - Method in class org.jmol.viewer.ActionManager
 
checkSpecial - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
checkSpecial(int, String[], boolean) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkSpecialData(InputStream, String[]) - Static method in class org.jmol.adapter.smarter.Resolver
called by SmarterJmolAdapter to see if we have a Spartan directory and, if so, open it and get all the data into the correct order.
checkSpecialInZip(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
called by SmarterJmolAdapter to see if we can automatically assign a file from the zip file.
checkSpecialMenu(String, Object, String) - Method in class org.jmol.popup.JmolPopup
 
checkSpecialMenu(String, Object, String) - Method in class org.jmol.popup.SimplePopup
 
checkSpecialParameterSyntax() - Method in class org.jmol.script.ScriptCompiler
 
checkSpecialVoxel(Point3f, float, Point3f, float, float, Point3f) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
checkStandardDeviation(Vector3f[], Vector3f, int, float) - Static method in class org.jmol.smiles.SmilesAromatic
 
checkStepping(String) - Method in class org.jmol.viewer.Viewer
 
checkStereochemistry() - Method in class org.jmol.smiles.SmilesSearch
 
checkStereochemistry(boolean, JmolNode, int, int, JmolNode, JmolNode, JmolNode, JmolNode, JmolNode, JmolNode, SmilesSearch.VTemp) - Static method in class org.jmol.smiles.SmilesSearch
 
checkStereoPairs(JmolNode, int, JmolNode[], int) - Method in class org.jmol.smiles.SmilesGenerator
 
checkSubs - Variable in class org.openscience.chimetojmol.ChimePanel
 
checkTicks(int, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
checkTimer(String) - Static method in class org.jmol.util.Logger
 
checkToken(int) - Method in class org.jmol.script.ScriptEvaluator
 
checkTrailingText(String, int, int) - Static method in class org.jmol.util.Parser
 
checkTranslucent(boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
checkTranslucent(boolean) - Method in class org.jmol.export.Export3D
 
checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
 
checkTwoAtomAction(int, Point3fi, int) - Method in class org.jmol.viewer.ActionManager
 
checkType(String[][], String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
checkUnitCell(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkUnitCellItem(String[], String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkUnitCellOffset() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkUnquotedFileName() - Method in class org.jmol.script.ScriptCompiler
 
checkUserAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
 
checkValencesAndBond(Atom, Atom, int, short, BitSet) - Method in class org.jmol.modelset.BondCollection
 
checkWien2k(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkWithin(Point3f, List<Point3f>, float, boolean) - Static method in class org.jmol.shape.Mesh
 
checkXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
chem3dImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
CHEM_COMP_AC_CHARGE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_NAME - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_SYM - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_X - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_X_IDEAL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_Y - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_Y_IDEAL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_Z - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_AC_Z_IDEAL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_BOND_AROMATIC_FLAG - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_BOND_ATOM_ID_1 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_BOND_ATOM_ID_2 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_BOND_VALUE_ORDER - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_NAME - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
chemCompBondFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
chemCompFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
chemFileProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
chemical - Static variable in class org.jmol.script.Token
 
chemicalName - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
chFirst - Variable in class org.jmol.script.ScriptCompiler
 
ChimePanel - Class in org.openscience.chimetojmol
 
ChimePanel() - Constructor for class org.openscience.chimetojmol.ChimePanel
 
chimePath - Variable in class org.openscience.chimetojmol.ChimePanel
 
ChimeToJmol - Class in org.openscience.chimetojmol
 
ChimeToJmol() - Constructor for class org.openscience.chimetojmol.ChimeToJmol
 
ChimeToJmol.ApplicationCloser - Class in org.openscience.chimetojmol
 
ChimeToJmol.ApplicationCloser() - Constructor for class org.openscience.chimetojmol.ChimeToJmol.ApplicationCloser
 
chiralClass - Variable in class org.jmol.smiles.SmilesAtom
 
chiralOrder - Variable in class org.jmol.smiles.SmilesAtom
 
choice - Variable in class org.jmol.export.dialog.Dialog
 
chooseBestBoundBox() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
chooser - Variable in class org.jmol.export.dialog.FilePreview
 
chooser - Variable in class org.openscience.chimetojmol.ChimePanel
 
chop(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
chord - Variable in class org.jmol.util.ContactPair
 
chpt0 - Variable in class org.jmol.script.ScriptFunction
 
chrg - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
CifDataReader - Class in org.jmol.util
 
CifDataReader(JmolLineReader) - Constructor for class org.jmol.util.CifDataReader
 
CifDataReader(BufferedReader) - Constructor for class org.jmol.util.CifDataReader
 
cifLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CifReader - Class in org.jmol.adapter.readers.cifpdb
A true line-free CIF file reader for CIF and mmCIF files.
CifReader() - Constructor for class org.jmol.adapter.readers.cifpdb.CifReader
 
circle - Static variable in class org.jmol.script.Token
 
Circle3D - Class in org.jmol.g3d
Implements flat circle drawing/filling routines.
Circle3D(Graphics3D) - Constructor for class org.jmol.g3d.Circle3D
 
circle3d - Variable in class org.jmol.g3d.Graphics3D
 
CIRCLE_FRACTION - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
circleNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
cl_block(OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
cl_hash(int) - Method in class org.jmol.export.image.GifEncoder
 
clash - Static variable in class org.jmol.script.Token
 
classBase - Static variable in class org.jmol.adapter.smarter.Resolver
 
CLASSBASE_OPTIONS - Static variable in class org.jmol.viewer.JmolConstants
 
classifyName(String, boolean) - Method in class org.jmol.viewer.FileManager
 
ClassPreloader - Class in org.jmol.applet
 
ClassPreloader(AppletWrapper) - Constructor for class org.jmol.applet.ClassPreloader
 
clauseAlternateSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseAnd() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseAtomSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseCell() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseChainSpec(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseComparator(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseConnected() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseDefine(boolean, boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseItemSelector() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseModelSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseNot() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseOr(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clausePrimitive() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseResidueSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseResNameSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseSequenceSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseSubstructure() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clauseWithin(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
clean() - Method in class org.jmol.shape.MeshCollection
 
clean() - Method in class org.jmol.shapespecial.Draw
 
cleanPattern(String, boolean) - Static method in class org.jmol.smiles.SmilesParser
 
cleanRegistry() - Static method in class org.jmol.applet.JmolAppletRegistry
 
cleanScriptComments(String) - Method in class org.jmol.script.ScriptCompiler
allows for three kinds of comments.
cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
clear() - Method in class org.jmol.awt.Mouse
 
clear() - Method in class org.jmol.export.history.HistoryFile
 
clear() - Method in class org.jmol.jvxl.data.JvxlData
 
clear() - Method in class org.jmol.minimize.Minimizer
 
clear() - Method in class org.jmol.multitouch.ActionManagerMT
 
clear - Static variable in class org.jmol.script.Token
 
clear() - Method in class org.jmol.shape.Measures
 
clear(String) - Method in class org.jmol.shape.Mesh
 
clear(boolean) - Method in class org.jmol.shapespecial.Dipoles
 
clear(String, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
clear() - Method in class org.jmol.util.CommandHistory
clears the history.
clear() - Method in class org.jmol.util.FastBitSet
 
clear(int) - Method in class org.jmol.util.FastBitSet
 
clear(int, int) - Method in class org.jmol.util.FastBitSet
 
clear() - Method in class org.jmol.util.TempArray
 
clear() - Method in class org.jmol.viewer.ActionManager
 
clear() - Method in class org.jmol.viewer.AnimationManager
 
clear() - Method in class org.jmol.viewer.ColorManager
 
clear() - Method in class org.jmol.viewer.DataManager
 
clear() - Method in class org.jmol.viewer.FileManager
 
clear() - Method in class org.jmol.viewer.RepaintManager
 
clear(int) - Method in class org.jmol.viewer.RepaintManager
 
clear() - Method in class org.jmol.viewer.ScriptManager
 
clear() - Method in class org.jmol.viewer.SelectionManager
 
clear(StateManager.GlobalSettings) - Method in class org.jmol.viewer.StateManager
 
clear() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
clear() - Method in class org.jmol.viewer.TransformManager
 
clear() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
clear_flg - Variable in class org.jmol.export.image.GifEncoder
 
clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
 
clearAtomSets() - Method in class org.jmol.viewer.Viewer
 
clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
 
clearBfactorRange() - Method in class org.jmol.viewer.Viewer
 
clearBindings() - Method in class org.jmol.viewer.ActionManager
 
clearBioPolymers(Group[], int, BitSet) - Method in interface org.jmol.api.JmolBioResolver
 
clearBioPolymers(Group[], int, BitSet) - Method in class org.jmol.modelsetbio.Resolver
 
clearBonds() - Method in class org.jmol.modelset.Atom
 
clearButton - Variable in class org.jmol.console.ScriptEditor
 
clearButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
clearClickCount() - Method in class org.jmol.viewer.Viewer
 
ClearCode - Variable in class org.jmol.export.image.GifEncoder
 
clearConsole() - Method in class org.jmol.viewer.StatusManager
 
clearConsole() - Method in class org.jmol.viewer.Viewer
 
clearContent(String) - Method in class org.jmol.console.AppletConsole
 
clearContent(String) - Method in class org.jmol.console.JmolConsole
 
clearContent() - Method in class org.jmol.console.ScriptEditor.EditorDocument
Removes all content of the script window, and add a new prompt.
clearContent() - Method in class org.jmol.console.ScriptEditor.EditorTextPane
 
clearContent(String) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
 
clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
clearContent() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
Removes all content of the script window, and add a new prompt.
clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelCollection
 
clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptEvaluator
 
clearFontCache() - Static method in class org.jmol.g3d.Text3D
 
clearForces() - Method in class org.jmol.minimize.forcefield.ForceField
 
clearFunctions() - Method in class org.jmol.viewer.StateManager
 
clearFunctions() - Method in class org.jmol.viewer.Viewer
 
clearGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
clearHighlight() - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
clearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
clearInButton - Variable in class org.jmol.console.AppletConsole
 
clearingThread - Variable in class org.jmol.g3d.Platform3D
 
clearKeyBuffer() - Method in class org.jmol.awt.Mouse
 
clearMeasurements() - Method in class org.jmol.api.JmolViewer
 
clearMeasurements() - Method in class org.jmol.viewer.Viewer
 
clearMinimization() - Method in class org.jmol.viewer.Viewer
 
clearModelDependentObjects() - Method in class org.jmol.viewer.Viewer
 
clearMouse() - Method in interface org.jmol.api.ApiPlatform
 
clearMouse() - Method in class org.jmol.awt.Platform
 
clearMouseInfo() - Method in class org.jmol.viewer.ActionManager
 
clearOutButton - Variable in class org.jmol.console.AppletConsole
 
clearQueue() - Method in class org.jmol.viewer.ScriptManager
 
clearRasmolHydrogenBonds(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
clearScreenBuffer() - Method in class org.jmol.g3d.Platform3D
 
clearScreenBufferThreaded() - Method in class org.jmol.g3d.Platform3D
 
clearScriptQueue() - Method in class org.jmol.viewer.Viewer
 
clearSelection() - Method in class org.jmol.api.JmolViewer
 
clearSelection(boolean) - Method in class org.jmol.viewer.SelectionManager
 
clearSelection() - Method in class org.jmol.viewer.Viewer
 
clearSg() - Method in class org.jmol.shapesurface.Isosurface
 
clearSg() - Method in class org.jmol.shapesurface.MolecularOrbital
 
clearShapeManager(Error) - Method in class org.jmol.script.ParallelProcessor
 
clearShapeRenderers() - Method in class org.jmol.viewer.Viewer
 
clearSpin() - Method in class org.jmol.viewer.TransformManager
 
clearState(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
clearStructures() - Method in class org.jmol.modelset.Polymer
 
clearStructures() - Method in class org.jmol.modelsetbio.BioPolymer
 
clearSymbolicMap() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
clearTBuffer() - Method in class org.jmol.g3d.Platform3D
 
clearTempPoints() - Method in class org.jmol.util.TempArray
 
clearTempScreens() - Method in class org.jmol.util.TempArray
 
clearTimeout(String) - Method in class org.jmol.viewer.Viewer
 
clearTimeouts() - Method in class org.jmol.viewer.ActionManager
 
clearUnitCell() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
clearVibration() - Method in class org.jmol.viewer.TransformManager
 
CLICK - Static variable in class org.jmol.multitouch.ActionManagerMT
 
CLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
clickabilityFlags - Variable in class org.jmol.modelset.Atom
 
clickable - Static variable in class org.jmol.script.Token
 
clickableMax - Static variable in class org.jmol.viewer.ShapeManager
 
clicked - Variable in class org.jmol.viewer.ActionManager
 
CLICKED - Static variable in class org.jmol.viewer.binding.Binding
 
clickedCount - Variable in class org.jmol.viewer.ActionManager
 
client - Variable in class org.jmol.modelset.MeasurementData
 
client - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
clientHasBuffer - Variable in class org.jmol.g3d.Platform3D.ClearingThread
 
clipboard - Static variable in class org.jmol.script.Token
 
clipCode(int, int, int) - Method in class org.jmol.export.Export3D
 
clipCode(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
clipCode(int) - Method in class org.jmol.g3d.Graphics3D
 
clipImage(String) - Method in interface org.jmol.api.JmolImageCreatorInterface
 
clipImage(String) - Method in class org.jmol.api.JmolViewer
 
clipImage(String) - Method in class org.jmol.export.image.ImageCreator
 
clipImage(String) - Method in class org.jmol.viewer.Viewer
 
clipped - Variable in class org.jmol.g3d.Cylinder3D
 
clockBaseline - Variable in class org.jmol.applet.AppletWrapper
 
clockWidth - Variable in class org.jmol.applet.AppletWrapper
 
clockX - Variable in class org.jmol.applet.AppletWrapper
 
clone() - Method in class org.jmol.util.FastBitSet
 
cloneAtom() - Method in class org.jmol.adapter.smarter.Atom
 
cloneAtomSetProperties(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Clones the properties of an atom set and associated it with the current atom set.
cloneFirstAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneFirstAtomSetWithBonds(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSet(int, Point3f[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSet(int, Point3f[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
cloneLastAtomSetProperties() - Method in class org.jmol.adapter.smarter.AtomSetCollection
Clones the properties of the last atom set and associates it with the current atom set.
cloneMenu(Object) - Method in class org.jmol.popup.SimplePopup
 
close() - Method in class org.jmol.util.BinaryDocument
 
close() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
close() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
close() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
closeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
closeButton - Variable in class org.jmol.console.ScriptEditor
 
closeButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
closePreview() - Method in class org.jmol.export.dialog.Dialog
 
closeReader() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
closeReader() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
closeReader() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
closeReader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
closest - Variable in class org.jmol.modelset.ModelSet
 
closeTag(StringBuffer, String) - Static method in class org.jmol.util.XmlUtil
 
cM - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cmdpt0 - Variable in class org.jmol.script.ScriptFunction
 
cmil - Variable in class org.jmol.popup.SimplePopup
 
CML - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CML_NAMESPACE_URI - Static variable in class org.jmol.adapter.smarter.Resolver
 
cmlImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
code - Variable in enum org.jmol.constant.EnumAxesMode
Code of axes mode.
code - Variable in class org.jmol.i18n.GT.Language
 
code - Variable in enum org.jmol.util.JmolEdge.EnumBondOrder
 
code - Variable in enum org.jmol.viewer.FileManager.EnumFileStatus
 
codetab - Variable in class org.jmol.export.image.GifEncoder
 
coef - Variable in class org.jmol.g3d.Sphere3D
 
coef - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
coef - Variable in class org.jmol.quantum.SlaterData
 
coef - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
coef - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
coef1 - Static variable in class org.jmol.quantum.NciCalculation
 
coef2 - Static variable in class org.jmol.quantum.NciCalculation
 
coef3 - Static variable in class org.jmol.quantum.NciCalculation
 
coef_indices - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
coefCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
coeffs - Variable in class org.jmol.quantum.MOCalculation
 
coefs - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
coefs - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
coefs - Variable in class org.jmol.quantum.MOCalculation
 
col - Static variable in class org.jmol.script.Token
 
colix - Variable in class org.jmol.export.Export3D
 
colix - Variable in class org.jmol.modelset.Bond
 
colix - Variable in class org.jmol.modelset.Measurement
 
colix - Variable in class org.jmol.shape.Measures
 
colix - Variable in class org.jmol.shape.MeshCollection
 
colix - Variable in class org.jmol.shape.Object2d
 
colix - Variable in class org.jmol.shape.ShapeRenderer
 
colix - Variable in class org.jmol.shapespecial.Dipole
 
colix - Variable in class org.jmol.shapespecial.Dipoles
 
colix - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
colix - Variable in class org.jmol.util.MeshSurface
 
colix - Variable in class org.jmol.viewer.StateManager.Connection
 
Colix3D - Class in org.jmol.g3d
Implements a color index model using a colix as a COLor IndeX.
Colix3D() - Constructor for class org.jmol.g3d.Colix3D
 
colixA - Variable in class org.jmol.g3d.Cylinder3D
 
colixA - Variable in class org.jmol.shape.SticksRenderer
 
colixAtom - Variable in class org.jmol.modelset.Atom
 
colixB - Variable in class org.jmol.g3d.Cylinder3D
 
colixB - Variable in class org.jmol.shape.SticksRenderer
 
colixBackgroundContrast - Variable in class org.jmol.viewer.ColorManager
 
colixCurrent - Variable in class org.jmol.g3d.Graphics3D
 
colixEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
colixes - Variable in class org.jmol.shape.AtomShape
 
colixes - Variable in class org.jmol.shape.AxesRenderer
 
colixes - Variable in class org.jmol.shapebio.BioShape
 
colixes - Variable in class org.jmol.shapebio.BioShapeRenderer
 
colixHash - Static variable in class org.jmol.g3d.Colix3D
 
colixHighlight - Variable in class org.jmol.shape.Halos
 
colixHoogsteenEdge - Variable in class org.jmol.shapebio.CartoonRenderer
 
colixMax - Static variable in class org.jmol.g3d.Colix3D
 
colixRubberband - Variable in class org.jmol.viewer.ColorManager
 
colixSelection - Variable in class org.jmol.shape.Halos
 
colixSugarEdge - Variable in class org.jmol.shapebio.CartoonRenderer
 
colixWatsonCrickEdge - Variable in class org.jmol.shapebio.CartoonRenderer
 
collapsed - Static variable in class org.jmol.script.Token
 
collapsed - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
COLLECTION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
String for prefix/resource identifier for the collection area.
collectionName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
colon - Static variable in class org.jmol.script.Token
 
color - Variable in enum org.jmol.constant.EnumStructure
 
color - Variable in class org.jmol.jvxl.data.JvxlData
 
color() - Method in class org.jmol.script.ScriptEvaluator
 
color - Static variable in class org.jmol.script.Token
 
COLOR - Static variable in class org.jmol.shape.Echo
 
color - Variable in class org.jmol.shape.Mesh
 
color - Variable in class org.jmol.shape.MeshCollection
 
color - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
color4(short) - Method in class org.jmol.export._PovrayExporter
 
colorArgbs - Static variable in class org.jmol.g3d.Graphics3D
 
colorAtoms(short, BitSet) - Method in class org.jmol.shapesurface.IsosurfaceMesh
color a specific set of vertices based on a set of atoms
colorByPhase - Variable in class org.jmol.jvxl.readers.Parameters
 
colorBySets - Variable in class org.jmol.jvxl.readers.Parameters
 
colorBySign - Variable in class org.jmol.jvxl.readers.Parameters
 
colorCommand - Variable in class org.jmol.shape.Mesh
 
colorCommand(SimpleAttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
colorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
colorData - Variable in class org.jmol.viewer.ColorManager
 
colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
colorDensity - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
colorDensity - Variable in class org.jmol.jvxl.data.JvxlData
 
colorDensity - Variable in class org.jmol.jvxl.readers.Parameters
 
colorDensity - Variable in class org.jmol.shape.Mesh
 
colorEncoder - Variable in class org.jmol.jvxl.readers.Parameters
 
colorEncoder - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
ColorEncoder - Class in org.jmol.util
 
ColorEncoder(ColorEncoder) - Constructor for class org.jmol.util.ColorEncoder
 
colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
 
colorFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
 
colorFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
colorHash - Variable in class org.jmol.export.image.GifEncoder
 
colorIndex(int, int) - Static method in class org.jmol.util.ColorEncoder
 
colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
ColorManager - Class in org.jmol.viewer
 
ColorManager(Viewer, Graphics3D) - Constructor for class org.jmol.viewer.ColorManager
 
colorManager - Variable in class org.jmol.viewer.Viewer
 
colorNames - Static variable in class org.jmol.applet.AppletWrapper
 
colorNames - Static variable in class org.jmol.g3d.Graphics3D
 
colorNeg - Variable in class org.jmol.jvxl.readers.Parameters
 
colorNegLCAO - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPhase - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPhases - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
colorPointFromInt(int, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
colorPointFromInt2(int) - Static method in class org.jmol.g3d.Graphics3D
 
colorPointFromString(String, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
colorPos - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPosLCAO - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
colorPtr - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
colorPtToInt(Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
colorrasmol - Static variable in class org.jmol.script.Token
 
colorRgb - Variable in class org.jmol.jvxl.readers.Parameters
 
colors - Static variable in class org.jmol.applet.AppletWrapper
 
colorScheme - Variable in class org.jmol.jvxl.data.JvxlData
 
colorscheme - Static variable in class org.jmol.script.Token
 
colorSchemes - Static variable in class org.jmol.util.ColorEncoder
 
colorSchemeTranslucent - Variable in class org.jmol.jvxl.readers.Parameters
 
colorShape(int, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
colorShape(int, int, int, String, float, BitSet) - Method in class org.jmol.script.ScriptEvaluator
 
colorTriadToInt(float, float, float) - Static method in class org.jmol.g3d.Graphics3D
 
colorVertices(short, BitSet) - Method in class org.jmol.shapesurface.IsosurfaceMesh
color a specific set of vertices
colorVertices(short, BitSet, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
color a specific set of vertices a specific color
combineSurfaces(List<ContactPair>, int, int, float[], Object, boolean, boolean) - Method in class org.jmol.shapesurface.Contact
 
comma - Static variable in class org.jmol.script.Token
 
command - Static variable in class org.jmol.script.Token
 
commandExpected() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
CommandHistory - Class in org.jmol.util
Implements a queue for a bash-like command history.
CommandHistory() - Constructor for class org.jmol.util.CommandHistory
Creates a new instance using the default size (100)
CommandHistory(int) - Constructor for class org.jmol.util.CommandHistory
Creates a new instance.
commandHistory - Variable in class org.jmol.viewer.Viewer
 
commandHistoryLevelMax - Variable in class org.jmol.script.ScriptEvaluator
 
commandLineOptions - Variable in class org.jmol.export.___Exporter
 
commandList - Variable in class org.jmol.util.CommandHistory
Array of commands.
commandOptions - Variable in class org.openscience.jmol.app.JmolApp
 
commands - Static variable in class org.jmol.script.Token
 
commands - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
commands - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
commandStart - Variable in class org.jmol.script.ScriptFlowContext
 
commandWatcherThread - Variable in class org.jmol.viewer.ScriptManager
 
comment - Variable in class org.jmol.script.ScriptCompiler
 
Comment - Variable in class org.jmol.util.JpegInfo
 
commentChar - Variable in class org.jmol.export.___Exporter
 
COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
comparator - Static variable in class org.jmol.script.Token
 
compare(Map<String, Object>, Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
 
compare(SlaterData, SlaterData) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
 
compare(GifEncoder.ColorItem, GifEncoder.ColorItem) - Method in class org.jmol.export.image.GifEncoder.ColorVector.CountComparator
 
compare(MeshData.SSet, MeshData.SSet) - Method in class org.jmol.jvxl.data.MeshData.SortSet
 
compare(Atom, Atom) - Method in class org.jmol.modelset.AtomCollection.AtomSorter
 
compare(String[], String[]) - Method in class org.jmol.modelsetbio.Resolver.BondSorter
 
compare() - Method in class org.jmol.script.ScriptEvaluator
 
compare(ScriptVariable, ScriptVariable) - Method in class org.jmol.script.ScriptVariable.Sort
 
compare - Static variable in class org.jmol.script.Token
 
compare(Object[], Object[]) - Method in class org.jmol.symmetry.UnitCell.Esort
 
compareFloat(int, float[], int, float) - Method in class org.jmol.script.ScriptEvaluator
 
compareFloat(int, float, float) - Static method in class org.jmol.script.ScriptEvaluator
 
compareInt(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
 
compareString(int, int, String) - Method in class org.jmol.script.ScriptEvaluator
 
compareString(int, String, String) - Method in class org.jmol.script.ScriptEvaluator
 
compHeight - Variable in class org.jmol.util.JpegInfo
 
CompID - Variable in class org.jmol.util.JpegInfo
 
compile(Viewer, String, char, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
Compiles a set of tokens for each primitive element of a label.
compile(String, String, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
 
compile0(boolean) - Method in class org.jmol.script.ScriptCompiler
 
compileCommand() - Method in class org.jmol.script.ScriptCompiler
 
compileExpression() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
compileExpressions() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
compiler - Variable in class org.jmol.script.ScriptEvaluator
 
compiler - Variable in class org.jmol.script.ScriptFlowContext
 
compiler - Variable in class org.jmol.viewer.Viewer
 
compileScript(String, String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
compileScriptFile(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
compileScriptFileInternal(String, String, String, String) - Method in class org.jmol.script.ScriptEvaluator
 
compileScriptString(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
completeCommand(String) - Method in class org.jmol.console.AppletConsole
 
completeCommand(String) - Method in class org.jmol.console.JmolConsole
 
completeCommand(Map<String, Token>, boolean, boolean, String, int) - Static method in class org.jmol.script.Token
 
completeCommand(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
completeInitialization(Graphics, Dimension) - Method in class org.jmol.applet.AppletWrapper
 
compnd - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
compndOld() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
compndSource(boolean) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
component - Variable in class org.jmol.smiles.SmilesAtom
 
componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
Components - Variable in class org.jmol.util.JpegInfo
 
componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
CompoundDocument - Class in org.jmol.util
 
CompoundDocument(BufferedInputStream) - Constructor for class org.jmol.util.CompoundDocument
 
CompoundDocument.CmpDocDirectoryEntry - Class in org.jmol.util
 
CompoundDocument.CmpDocDirectoryEntry() - Constructor for class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
CompoundDocument.CmpDocHeader - Class in org.jmol.util
 
CompoundDocument.CmpDocHeader() - Constructor for class org.jmol.util.CompoundDocument.CmpDocHeader
 
compress(int, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
Compress() - Method in class org.jmol.util.JpegEncoder
 
compressionLevel - Variable in class org.jmol.export.image.PngEncoder
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
 
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.Calculations
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.AngleCalc
 
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.ESCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.OOPCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.TorsionCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.VDWCalc
 
computeAngle(Tuple3f, Tuple3f, Tuple3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
 
computeAngle(Tuple3f, Tuple3f, Tuple3f, boolean) - Static method in class org.jmol.util.Measure
 
computeHelicalAxis(String, int, Point3f, Point3f, Quaternion) - Static method in class org.jmol.util.Measure
 
computeTorsion(Tuple3f, Tuple3f, Tuple3f, Tuple3f, boolean) - Static method in class org.jmol.util.Measure
 
compWidth - Variable in class org.jmol.util.JpegInfo
 
concatList(ScriptVariable, ScriptVariable, boolean) - Static method in class org.jmol.script.ScriptVariable
 
concatTokens(String[], int, int) - Static method in class org.jmol.util.Parser
 
conect() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
coneNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
CONF_TYPE_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
configuration() - Method in class org.jmol.script.ScriptEvaluator
 
configuration - Static variable in class org.jmol.script.Token
 
configurationPtr - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
configurationPtr - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
configurationSelected - Variable in class org.jmol.popup.JmolPopup
 
conformationIndex - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
conformationIndex - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
connect(float[][]) - Method in class org.jmol.modelset.ModelSet
 
connect(int) - Method in class org.jmol.script.ScriptEvaluator
 
connect - Static variable in class org.jmol.script.Token
 
connect(float[][]) - Method in class org.jmol.viewer.Viewer
 
connectAll(int, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
connectAllBad(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
connected - Static variable in class org.jmol.script.Token
 
connections - Variable in class org.jmol.shape.Mesh
 
connections - Variable in class org.jmol.shape.MeshCollection
 
connections - Variable in class org.jmol.viewer.StateManager.Connections
 
connectivity - Variable in class org.jmol.smiles.SmilesAtom
 
connectLast - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
connectNextAtomIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
connectNextAtomSet - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
connectorFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
connectorFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
connectors - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
console() - Method in class org.jmol.script.ScriptEvaluator
 
console - Static variable in class org.jmol.script.Token
 
console - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
consoleAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
consoleButton - Variable in class org.jmol.console.ScriptEditor
 
consoleDoc - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
consoleframe - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
consoleMessage(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
ConsoleTextArea - Class in org.openscience.jmol.app.jmolpanel
 
ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.jmolpanel.ConsoleTextArea
 
ConsoleTextArea(boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.ConsoleTextArea
 
consoleTextPane - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
constrainQuadratic(double, double, double, int) - Method in class org.jmol.minimize.forcefield.Calculations
 
constraint - Static variable in class org.jmol.script.Token
 
constraintEnergy(int) - Method in class org.jmol.minimize.forcefield.Calculations
 
constraintMap - Variable in class org.jmol.minimize.Minimizer
 
constraints - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
constraints - Variable in class org.jmol.minimize.forcefield.Calculations
 
constraints - Variable in class org.jmol.minimize.Minimizer
 
constructBitSetPolyhedron(int) - Method in class org.jmol.shapespecial.Polyhedra
 
constructBondsPolyhedron(int) - Method in class org.jmol.shapespecial.Polyhedra
 
constructDismissButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
constructMeasurementButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
constructMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
constructRadiusPolyhedron(int, AtomIndexIterator) - Method in class org.jmol.shapespecial.Polyhedra
 
contact() - Method in class org.jmol.script.ScriptEvaluator
 
contact - Static variable in class org.jmol.script.Token
 
Contact - Class in org.jmol.shapesurface
 
Contact() - Constructor for class org.jmol.shapesurface.Contact
 
contactPair - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
contactPair - Variable in class org.jmol.jvxl.readers.Parameters
 
ContactPair - Class in org.jmol.util
 
ContactPair(Atom[], int, int, float, float, float, float) - Constructor for class org.jmol.util.ContactPair
 
ContactRenderer - Class in org.jmol.shapesurface
 
ContactRenderer() - Constructor for class org.jmol.shapesurface.ContactRenderer
 
contactType - Variable in class org.jmol.util.ContactPair
 
container - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
contains(int, int) - Method in class org.jmol.util.Rectangle
 
contentPath - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
context - Variable in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
context - Variable in class org.jmol.script.ParallelProcessor.Process
 
contextPath - Variable in class org.jmol.script.ScriptContext
 
contextPath - Variable in class org.jmol.script.ScriptEvaluator
 
ContextToken - Class in org.jmol.script
 
ContextToken(int, int, Object) - Constructor for class org.jmol.script.ContextToken
 
ContextToken(int, Object) - Constructor for class org.jmol.script.ContextToken
 
contextVariables - Variable in class org.jmol.script.ContextToken
 
contextVariables - Variable in class org.jmol.script.ScriptCompiler
 
contextVariables - Variable in class org.jmol.script.ScriptContext
 
contextVariables - Variable in class org.jmol.script.ScriptEvaluator
 
CONTINUE - Static variable in class org.jmol.script.ScriptCompiler
 
CONTINUE_MAX - Static variable in class org.jmol.util.JpegEncoder
 
CONTINUE_MAX_BUFFER - Static variable in class org.jmol.util.JpegEncoder
 
CONTINUE_STRING - Static variable in class org.jmol.util.JpegEncoder
 
continuecmd - Static variable in class org.jmol.script.Token
 
continueMatch(int, int, boolean) - Method in class org.jmol.smiles.SmilesSearch
 
continuing - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
contour - Static variable in class org.jmol.script.Token
 
CONTOUR_BITSET - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_COLIX - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_COLOR - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_FDATA - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_NPOLYGONS - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
CONTOUR_POINTS - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_VALUE - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
contourColixes - Variable in class org.jmol.jvxl.data.JvxlData
 
contourColixes - Variable in class org.jmol.jvxl.readers.Parameters
 
contourColixes - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
contourColors - Variable in class org.jmol.jvxl.data.JvxlData
 
contourFromZero - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourFromZero - Variable in class org.jmol.jvxl.readers.Parameters
 
contourIncrements - Variable in class org.jmol.jvxl.readers.Parameters
 
contourIndex - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
contourlines - Static variable in class org.jmol.script.Token
 
contourPlaneMaximumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourPlaneMinimumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contours - Static variable in class org.jmol.script.Token
 
contoursDiscrete - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contoursDiscrete - Variable in class org.jmol.jvxl.readers.Parameters
 
contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourType - Variable in class org.jmol.jvxl.readers.Parameters
 
contourValues - Variable in class org.jmol.jvxl.data.JvxlData
 
contourValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
contourValuesUsed - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourValuesUsed - Variable in class org.jmol.jvxl.data.JvxlData
 
contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourVertexCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
contourVertexes - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contractions - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
controlHermites - Variable in class org.jmol.shapebio.BioShapeRenderer
 
controlHermites - Variable in class org.jmol.shapespecial.DrawRenderer
 
controlPoints - Variable in class org.jmol.modelset.Polymer
 
controlPoints - Variable in class org.jmol.shapebio.BioShapeRenderer
 
controlPointScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
 
converged - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
convertToMegabytes(long) - Method in class org.jmol.popup.JmolPopup
 
coord - Variable in class org.jmol.minimize.MinAtom
 
coord - Static variable in class org.jmol.script.Token
 
coordinateInRange(int, int, Point3f, int, Point3i) - Method in class org.jmol.shape.Shape
 
coordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
coordinatesAreFractional(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
coordinatesAreFractional(Object) - Method in class org.jmol.api.JmolAdapter
Get the boolean whether coordinates are fractional.
coordinatesAreFractional - Variable in class org.jmol.script.ScriptEvaluator
 
coordinatesAreFractional - Variable in class org.jmol.symmetry.SymmetryInfo
 
coordinatesArePrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
coords - Variable in class org.jmol.shapespecial.Dipole
 
coords - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
coordSaved - Variable in class org.jmol.minimize.forcefield.ForceField
 
coordSaved - Variable in class org.jmol.minimize.Minimizer
 
Coorfile - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
CooropenButton - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
copy(BitSet) - Static method in class org.jmol.util.BitSetUtil
 
copy(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
 
copyBinaryFile(String, String) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
copyColixTranslucency(short, short) - Static method in class org.jmol.g3d.Graphics3D
 
copyDirectory(String, File, File, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
copyFile(String, File, File, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
copyImageAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
copyImageActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
copyInvert(BitSet, int) - Static method in class org.jmol.util.BitSetUtil
 
copyright - Static variable in class org.jmol.viewer.JmolConstants
 
copyScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
copyScriptActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
cordMidPoints - Variable in class org.jmol.shapebio.RocketsRenderer
 
corner - Variable in class org.jmol.shape.Axes
 
corners - Static variable in class org.jmol.script.Token
 
corners - Variable in class org.jmol.shapebio.RocketsRenderer
 
cos - Static variable in class org.jmol.script.Token
 
cosAlpha - Variable in class org.jmol.util.SimpleUnitCell
 
cosBeta - Variable in class org.jmol.util.SimpleUnitCell
 
cosGamma - Variable in class org.jmol.util.SimpleUnitCell
 
cosPhi - Variable in class org.jmol.g3d.Cylinder3D
 
cossin - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
cosTheta - Variable in class org.jmol.g3d.Cylinder3D
 
cosTolerance - Variable in class org.jmol.symmetry.PointGroup
 
count - Variable in class org.jmol.bspt.Element
 
count - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
count - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
count - Variable in class org.jmol.modelset.Measurement
 
count - Static variable in class org.jmol.script.Token
 
countBitsInWord(int) - Static method in class org.jmol.util.FastBitSet
 
countData(String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
countData(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
CountDown - Variable in class org.jmol.export.image.GifEncoder
 
counter - Variable in class org.jmol.script.ParallelProcessor
 
countGroup(int, String, String) - Method in class org.jmol.modelset.ModelLoader
 
countPlusIndices - Variable in class org.jmol.modelset.Measurement
 
countStereo(String) - Method in class org.jmol.smiles.SmilesMatcher
 
countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
 
countTokens(String, int) - Static method in class org.jmol.util.Parser
 
covalent - Static variable in class org.jmol.script.Token
 
covalentHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
 
covalentMars - Static variable in class org.jmol.util.Elements
Default table of covalent Radii stored as a short mar ...
crc - Variable in class org.jmol.export.image.PngEncoder
 
crcValue - Variable in class org.jmol.export.image.PngEncoder
 
create - Static variable in class org.jmol.script.Token
 
createAndShowGUI(JmolViewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
createArrayOfArrayList(int) - Static method in class org.jmol.util.ArrayUtil
Helper method for creating a List[] without warnings.
createArrayOfHashtable(int) - Static method in class org.jmol.util.ArrayUtil
Helper method for creating a Map[] without warnings.
createAtomDataSet(int, Object, BitSet) - Method in class org.jmol.modelset.ModelSet
 
createAtomSeCollectionFromArrayData(List<Object>, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomSeCollectionFromStrings(String[], StringBuffer, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomSerialMap() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
createAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
 
createAtomSetCollectionFromFile(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomSetCollectionFromFiles(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomSetCollectionFromReader(String, String, Reader, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
not used in Jmol project -- will close reader
createAtomSetCollectionFromString(String, StringBuffer, Map<String, Object>, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
createBonds(boolean) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
Use the site bitset to check for atoms that are within +/-dx Angstroms of the specified distances in GEOM_BOND where dx is determined by the uncertainty (dx) in the record.
createContours(float, float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
createCube() - Method in interface org.jmol.api.QuantumCalculationInterface
 
createCube() - Method in class org.jmol.quantum.MOCalculation
 
createCube() - Method in class org.jmol.quantum.NciCalculation
 
createDialog(Component) - Method in class org.jmol.export.dialog.FileChooser
 
createEllipsoidShades() - Static method in class org.jmol.g3d.Sphere3D
 
createExportPanel(String[], String[], String) - Method in class org.jmol.export.dialog.Dialog
 
createFrankPopup() - Method in class org.jmol.popup.JmolPopup
 
createFunction(String, String, String) - Method in class org.jmol.script.ScriptEvaluator
for the ISOSURFACE command
createGeodesic() - Static method in class org.jmol.geodesic.Geodesic
 
createImage(Object) - Method in interface org.jmol.api.ApiPlatform
can be ignored (return null) if platform cannot save images
createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolImageCreatorInterface
 
createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
Starting with Jmol 11.8.RC5, for a context where the Jmol application is embedded in another application simply to send the returned message to the application.
createImage(String, String, Object, int, int, int) - Method in class org.jmol.api.JmolViewer
 
createImage(String, String, Object, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
createImage(Object) - Static method in class org.jmol.awt.Image
 
createImage(Object) - Method in class org.jmol.awt.Platform
 
createImage(String, String, Object, int, int) - Method in class org.jmol.export._ObjExporter
 
createImage(String, String, Object, int) - Method in class org.jmol.export.image.ImageCreator
 
createImage(String, String, Object, int) - Method in class org.jmol.viewer.StatusManager
offer to let application do the image creation.
createImage(String, String, Object, int, int, int, BitSet, String[]) - Method in class org.jmol.viewer.Viewer
from eval write command only includes option to write set of files
createImage(String, String, Object, int, int, int) - Method in class org.jmol.viewer.Viewer
 
createImage(String, String, Object, int, int, int, String[]) - Method in class org.jmol.viewer.Viewer
general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
createImage(String, String, Object, int, int, int, String[], boolean) - Method in class org.jmol.viewer.Viewer
 
createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
createImageStatus(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Starting with Jmol 11.8.RC5, this is just informational if type == null and null is returned, then it means "Jmol, you handle it"
createInstance(ApiPlatform) - Static method in class org.jmol.g3d.Platform3D
 
createIsosurface(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
createLadders(List<AminoPolymer.Bridge>, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, boolean) - Static method in class org.jmol.modelsetbio.AminoPolymer
"ladder =: one or more consecutive bridges of identical type" (p.
createLanguageList() - Method in class org.jmol.i18n.GT
This is the place to put the list of supported languages.
createLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
 
createLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
createLcaoLobe(Vector3f, float, int) - Method in class org.jmol.shapesurface.Isosurface
 
createMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create a menu for the app.
createMenubar() - Method in class org.jmol.console.AppletConsole
 
createMenubar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create the menubar for the app.
createMenuItem(String) - Method in class org.jmol.console.AppletConsole
 
createMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
This is the hook through which all menu items are created.
createMeshCylinder(int, int, int, int, int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
createModelSet(JmolAdapter, Object, BitSet) - Method in class org.jmol.modelset.ModelLoader
 
createModelSet(String, String, StringBuffer, Object, BitSet, boolean) - Method in class org.jmol.viewer.ModelManager
 
createModelSetAndReturnError(Object, boolean, StringBuffer) - Method in class org.jmol.viewer.Viewer
finally(!) we are ready to create the "model set" from the "atom set collection"
createMonteCarloOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
createMovie(Viewer, String[], int, int, int, String) - Method in interface org.jmol.api.JmolMovieCreatorInterface
create a movie from a set of image files
createMovie(Viewer, String[], int, int, int, String) - Method in class org.jmol.export.image.AviCreator
 
createNewAtomSet(Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
createOrbital() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
createPdfDocument(String, Object) - Method in interface org.jmol.api.JmolPdfCreatorInterface
 
createPdfDocument(String, Object) - Method in class org.openscience.jmol.app.jmolpanel.PdfCreator
 
createSet(int, int, int) - Method in class org.jmol.jvxl.data.MeshData
 
createSlaterData(int, String, String) - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
createSpaceGroup(int, String, float[]) - Method in interface org.jmol.api.SymmetryInterface
 
createSpaceGroup(int, String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
 
createSpaceGroup(String) - Static method in class org.jmol.symmetry.SpaceGroup
 
createSpaceGroup(int, String, float[]) - Method in class org.jmol.symmetry.Symmetry
 
createSphereShape(int) - Static method in class org.jmol.g3d.Sphere3D
 
createSphericalSlaterByType(int, int, String, float, float) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSurfaceTool() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
createTextureFile(String, MeshSurface, Point) - Method in class org.jmol.export._ObjExporter
Writes a texture file with the colors in the colixes array in a way that it can be mapped by the texture coordinates vt.
createTool(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Hook through which every toolbar item is created.
createToolbar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create the toolbar.
createToolbarButton(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create a button to go inside of the toolbar.
createTopoMap(BitSet) - Method in class org.jmol.smiles.SmilesSearch
 
createTransferable(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
createTreeModel() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Creates the treeModel of the AtomSets available in the JmolViewer
createVCRController(String) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Creates a VCR type set of controller inside a JPanel.
createVoxelData() - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
Developer must customize this method
createWebExport() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
createZipSet(String, String, boolean) - Method in class org.jmol.viewer.FileManager
 
creatingImage - Variable in class org.jmol.viewer.Viewer
 
crit - Variable in class org.jmol.minimize.Minimizer
 
criterion - Variable in class org.jmol.minimize.forcefield.ForceField
 
criterion - Static variable in class org.jmol.script.Token
 
cross - Static variable in class org.jmol.script.Token
 
cross - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
cross0 - Variable in class org.jmol.shapespecial.DipolesRenderer
 
cross1 - Variable in class org.jmol.shapespecial.DipolesRenderer
 
crossed - Static variable in class org.jmol.script.Token
 
crossEnd - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
crossOffset - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
crossWidth - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
crossWidthPixels - Variable in class org.jmol.shapespecial.DipolesRenderer
 
crtval - Static variable in class org.jmol.shapespecial.Ellipsoids
 
cryst1() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
CRYSTAL - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SCALAR - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SYMMETRY - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SYMMETRY_TRANSFORM3 - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
crystalContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CrystalReader - Class in org.jmol.adapter.readers.xtal
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
CrystalReader() - Constructor for class org.jmol.adapter.readers.xtal.CrystalReader
 
csfLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CsfReader - Class in org.jmol.adapter.readers.quantum
CSF file reader based on CIF idea -- fluid property fields.
CsfReader() - Constructor for class org.jmol.adapter.readers.quantum.CsfReader
 
CTRL - Static variable in class org.jmol.viewer.binding.Binding
 
CTRL_ALT - Static variable in class org.jmol.viewer.binding.Binding
 
CTRL_MASK - Static variable in class org.jmol.api.Event
 
CTRL_SHIFT - Static variable in class org.jmol.viewer.binding.Binding
 
cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountX - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountY - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountZ - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
cubeFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CubeIterator - Class in org.jmol.bspt
Iterator used for finding all points within a box or a hemi-box
CubeIterator(Bspt) - Constructor for class org.jmol.bspt.CubeIterator
 
cubeIterator - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
cubeIterators - Variable in class org.jmol.bspt.Bspf
 
CubeReader - Class in org.jmol.adapter.readers.simple
Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.
CubeReader() - Constructor for class org.jmol.adapter.readers.simple.CubeReader
 
CubeReader - Class in org.jmol.jvxl.readers
 
CubeReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.CubeReader
 
cubeVertexOffsets - Static variable in class org.jmol.util.BoxInfo
 
cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
 
cubeVertexOffsets - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
cubeVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
cur_accum - Variable in class org.jmol.export.image.GifEncoder
 
cur_bits - Variable in class org.jmol.export.image.GifEncoder
 
current - Variable in class org.jmol.viewer.ActionManager
 
currentAtomSetIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
currentBgColor - Variable in class org.jmol.shape.Object2dShape
 
currentBgTranslucentLevel - Variable in class org.jmol.shape.Object2dShape
 
currentChain - Variable in class org.jmol.modelset.ModelLoader
 
currentChainID - Variable in class org.jmol.modelset.ModelLoader
 
currentColor - Variable in class org.jmol.shape.Object2dShape
 
currentCompnd - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
currentCursor - Variable in class org.jmol.viewer.Viewer
 
currentDipole - Variable in class org.jmol.shapespecial.Dipoles
 
currentDirection - Variable in class org.jmol.viewer.AnimationManager
 
currentFont - Variable in class org.jmol.shape.Object2dShape
 
currentFrankId - Variable in class org.jmol.popup.JmolPopup
 
currentGroup3 - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
currentGroup3 - Variable in class org.jmol.modelset.ModelLoader
 
currentGroupInsertionCode - Variable in class org.jmol.modelset.ModelLoader
 
currentGroupSequenceNumber - Variable in class org.jmol.modelset.ModelLoader
 
currentIndex - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
currentKey - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
currentlocalpath - Static variable in class org.jmol.script.Token
 
currentlyRendering - Variable in class org.jmol.g3d.Graphics3D
 
currentlyRendering() - Method in class org.jmol.g3d.Graphics3D
 
currentMenuItemId - Variable in class org.jmol.popup.SimplePopup
 
currentMesh - Variable in class org.jmol.shape.MeshCollection
 
currentMetricsFont3d - Variable in class org.jmol.shape.Frank
 
currentModel - Variable in class org.jmol.modelset.ModelLoader
 
currentModelIndex - Variable in class org.jmol.modelset.ModelLoader
 
currentModelIndex - Variable in class org.jmol.viewer.AnimationManager
 
currentNormalOrigin - Variable in class org.jmol.export._ObjExporter
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
currentObject - Variable in class org.jmol.shape.Object2dShape
 
currentPalette - Variable in class org.jmol.util.ColorEncoder
 
currentPoints - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
currentProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
currentResno - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
currentSegmentCount - Variable in class org.jmol.util.ColorEncoder
 
currentShadeIndex - Variable in class org.jmol.g3d.Graphics3D
 
currentShapeID - Variable in class org.jmol.viewer.Viewer
 
currentShapeState - Variable in class org.jmol.viewer.Viewer
 
currentSize - Variable in class org.jmol.export.dialog.FilePreview.FPPanel
 
currentSize - Variable in class org.openscience.molecularplayground.MPJmolApp.KioskPanel
 
currentStep - Variable in class org.jmol.minimize.forcefield.ForceField
 
currentTextureOrigin - Variable in class org.jmol.export._ObjExporter
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
currentThread - Variable in class org.jmol.script.ScriptEvaluator
 
currentTranslucentLevel - Variable in class org.jmol.shape.Object2dShape
 
currentVertexOrigin - Variable in class org.jmol.export._ObjExporter
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
cursor - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog.PageLoader
 
cursor - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
 
cursor - Variable in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog.PageLoader
 
CURSOR_CROSSHAIR - Static variable in class org.jmol.viewer.JmolConstants
 
CURSOR_DEFAULT - Static variable in class org.jmol.viewer.JmolConstants
 
CURSOR_HAND - Static variable in class org.jmol.viewer.JmolConstants
 
CURSOR_MOVE - Static variable in class org.jmol.viewer.JmolConstants
 
CURSOR_WAIT - Static variable in class org.jmol.viewer.JmolConstants
 
CURSOR_ZOOM - Static variable in class org.jmol.viewer.JmolConstants
 
cursorPos - Variable in class org.jmol.util.CommandHistory
Current position of the cursor;
curve - Static variable in class org.jmol.script.Token
 
curx - Variable in class org.jmol.export.image.GifEncoder
 
cury - Variable in class org.jmol.export.image.GifEncoder
 
CUSTOM - Static variable in class org.jmol.util.ColorEncoder
 
CUT - Static variable in class org.jmol.quantum.MOCalculation
 
cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cutoff - Variable in class org.jmol.jvxl.data.JvxlData
 
cutoff - Variable in class org.jmol.jvxl.readers.Parameters
 
cutoff - Static variable in class org.jmol.script.Token
 
cutoff - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
cutoffAutomatic - Variable in class org.jmol.jvxl.readers.Parameters
 
cutoffRange - Variable in class org.jmol.shapesurface.Isosurface
 
cx - Variable in class org.jmol.bspt.CubeIterator
 
CX - Variable in class org.jmol.quantum.MOCalculation
 
cxyz - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
 
cy - Variable in class org.jmol.bspt.CubeIterator
 
CY - Variable in class org.jmol.quantum.MOCalculation
 
CYAN - Static variable in class org.jmol.g3d.Graphics3D
 
cylinder - Static variable in class org.jmol.script.Token
 
Cylinder3D - Class in org.jmol.g3d
Draws shaded cylinders in 3D.
Cylinder3D(Graphics3D) - Constructor for class org.jmol.g3d.Cylinder3D
 
cylinder3d - Variable in class org.jmol.g3d.Graphics3D
 
cylinderBase - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
cylinderMatrix - Variable in class org.jmol.export._IdtfExporter
 
cylinderNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
cz - Variable in class org.jmol.bspt.CubeIterator
 
CZ - Variable in class org.jmol.quantum.MOCalculation
 

D

d - Variable in class org.jmol.minimize.forcefield.Calculation
 
d - Variable in class org.jmol.util.ContactPair
 
d - Variable in class org.jmol.util.Eigen
Arrays for internal storage of eigenvalues.
d1 - Variable in class org.jmol.g3d.Hermite3D
 
d2 - Variable in class org.jmol.g3d.Hermite3D
 
da - Variable in class org.jmol.minimize.forcefield.Calculations
 
dashDots - Variable in class org.jmol.shape.SticksRenderer
 
dashes - Static variable in class org.jmol.shape.SticksRenderer
 
data - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
data - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
data - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
data - Variable in class org.jmol.jvxl.readers.IsoFxyzReader
 
data - Variable in class org.jmol.modelset.LabelToken
 
data - Variable in class org.jmol.script.ScriptEvaluator
 
data() - Method in class org.jmol.script.ScriptEvaluator
 
data - Static variable in class org.jmol.script.Token
 
data - Variable in class org.jmol.util.CifDataReader
 
data - Variable in class org.jmol.util.CompoundDocument
 
data - Variable in class org.jmol.viewer.FileManager.ArrayDataReader
 
data - Variable in class org.jmol.viewer.FileManager.VectorDataReader
 
data - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
dataFrames - Variable in class org.jmol.modelset.Model
 
dataIsReducedDensity - Variable in class org.jmol.quantum.NciCalculation
 
DataManager - Class in org.jmol.viewer
 
DataManager(Viewer) - Constructor for class org.jmol.viewer.DataManager
 
dataManager - Variable in class org.jmol.viewer.Viewer
 
dataMax - Variable in class org.jmol.jvxl.data.JvxlData
 
dataMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataMean - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataMin - Variable in class org.jmol.jvxl.data.JvxlData
 
dataMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataPos - Variable in class org.jmol.export.image.PngEncoder
 
dataScaling - Variable in class org.jmol.quantum.NciCalculation
 
dataseparator - Static variable in class org.jmol.script.Token
 
dataSeparator - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dataSourceFrame - Variable in class org.jmol.modelset.Model
 
dataType - Variable in class org.jmol.jvxl.readers.Parameters
 
dataType - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
dataType - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
dataValues - Variable in class org.jmol.viewer.DataManager
 
dataXYReversed - Variable in class org.jmol.jvxl.data.JvxlData
 
dataXYReversed - Variable in class org.jmol.jvxl.readers.Parameters
 
date - Static variable in class org.jmol.viewer.JmolConstants
 
db - Variable in class org.jmol.minimize.forcefield.Calculations
 
DBLCLK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
DBLCLK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
dc - Variable in class org.jmol.minimize.forcefield.Calculations
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
DC_matrix - Variable in class org.jmol.util.Huffman
 
DC_matrix0 - Variable in class org.jmol.util.Huffman
 
DC_matrix1 - Variable in class org.jmol.util.Huffman
 
dcdFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
DCT - Class in org.jmol.util
 
DCT(int) - Constructor for class org.jmol.util.DCT
Constructs a new DCT object.
dct - Variable in class org.jmol.util.JpegEncoder
 
DCtableNumber - Variable in class org.jmol.util.JpegInfo
 
dd - Variable in class org.jmol.minimize.forcefield.Calculations
 
dData - Variable in class org.jmol.minimize.forcefield.Calculation
 
dE - Variable in class org.jmol.minimize.forcefield.Calculation
 
dE - Variable in class org.jmol.minimize.forcefield.ForceField
 
DEATH - Static variable in class org.jmol.multitouch.ActionManagerMT
 
debug - Static variable in class org.jmol.export._ObjExporter
Flag to cause debugging output to stdout.
debug - Static variable in class org.jmol.script.Token
 
debug(String) - Method in class org.jmol.util.DefaultLogger
 
debug(String) - Static method in class org.jmol.util.Logger
Writes a log at DEBUG level.
debug(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at DEBUG level.
debugging - Static variable in class org.jmol.util.Logger
 
debuggingHigh - Static variable in class org.jmol.util.Logger
 
debugPrint(String) - Method in class org.jmol.export._ObjExporter
Debug print utility.
debugScript - Variable in class org.jmol.script.ScriptEvaluator
 
debugscript - Static variable in class org.jmol.script.Token
 
debugScript - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
decimal - Static variable in class org.jmol.script.Token
 
decimalScale - Static variable in class org.jmol.util.Parser
 
decode64 - Static variable in class org.jmol.util.Base64
 
decodeBase64(String) - Static method in class org.jmol.util.Base64
 
deduceElementSymbol(boolean) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed.
deduceElementSymbol(String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
 
deducePdbElementSymbol(boolean, String, String) - Static method in class org.jmol.adapter.readers.more.ForceFieldReader
 
DEFAULT - Static variable in class org.jmol.g3d.Triangle3D
 
DEFAULT_BASIS - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_CHARGE - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
DEFAULT_DISTANCE_FACTOR - Static variable in class org.jmol.shapespecial.Polyhedra
 
DEFAULT_FACECENTEROFFSET - Static variable in class org.jmol.shapespecial.Polyhedra
 
DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_GESTURE_SWIPE_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_MAD - Static variable in class org.jmol.shapespecial.Dipoles
 
DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_MAX_SIZE - Static variable in class org.jmol.util.CommandHistory
 
DEFAULT_METHOD - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_MOUSE_DRAG_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_MOUSE_WHEEL_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_MULT - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
DEFAULT_NAV_FPS - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_OFFSETSIDE - Static variable in class org.jmol.shapespecial.Dipoles
 
DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_PERSPECTIVE_MODEL - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_RHOPARAM - Variable in class org.jmol.quantum.NciCalculation
 
DEFAULT_RHOPLOT_PRO - Variable in class org.jmol.quantum.NciCalculation
 
DEFAULT_RHOPLOT_SCF - Variable in class org.jmol.quantum.NciCalculation
 
DEFAULT_SPIN_FPS - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_SPIN_Y - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_STEREO_DEGREES - Static variable in enum org.jmol.constant.EnumStereoMode
 
DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
 
defaultActions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
Actions defined by the Jmol class
defaultAlignment - Variable in class org.jmol.shape.Labels
 
defaultanglelabel - Static variable in class org.jmol.script.Token
 
defaultAngleLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultBgcolix - Variable in class org.jmol.shape.Labels
 
defaultChoice - Static variable in class org.jmol.export.dialog.Dialog
 
defaultcmd - Static variable in class org.jmol.script.Token
 
defaultColix - Variable in class org.jmol.shape.Labels
 
defaultColix - Variable in class org.jmol.shapesurface.Isosurface
 
defaultColorFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultColorFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultColorFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorNegative - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorNegativeLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorPositive - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorPositiveLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultcolorscheme - Static variable in class org.jmol.script.Token
 
defaultContourCount - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
defaultContourCount - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultCovalentMad - Variable in class org.jmol.modelset.BondCollection
 
defaultCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultCutoff - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
defaultdirectory - Static variable in class org.jmol.script.Token
 
defaultDirectory - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultdistancelabel - Static variable in class org.jmol.script.Token
 
defaultDistanceLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultdrawarrowscale - Static variable in class org.jmol.script.Token
 
defaultDrawArrowScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultFontId - Variable in class org.jmol.shape.Labels
 
defaultFontName - Static variable in class org.jmol.shape.Frank
 
defaultFontSize - Static variable in class org.jmol.shape.Frank
 
defaultFontStyle - Static variable in class org.jmol.shape.Frank
 
defaultGroupCount - Static variable in class org.jmol.modelset.ModelLoader
 
defaultlabelpdb - Static variable in class org.jmol.script.Token
 
defaultLabelPDB - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultlabelxyz - Static variable in class org.jmol.script.Token
 
defaultLabelXYZ - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultlattice - Static variable in class org.jmol.script.Token
 
defaultloadfilter - Static variable in class org.jmol.script.Token
 
defaultLoadFilter - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultloadscript - Static variable in class org.jmol.script.Token
 
defaultLoadScript - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultLobeCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
DefaultLogger - Class in org.jmol.util
Default implementation of the logger.
DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
 
defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
defaultMepCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMepMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMepMin - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMessage - Variable in class org.jmol.console.JmolConsole
 
defaultMode - Variable in class org.jmol.viewer.TransformManager
 
defaultOffset - Variable in class org.jmol.shape.Labels
 
defaultON - Static variable in class org.jmol.script.Token
 
defaultOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultOrbitalCutoffOld - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultPaletteID - Variable in class org.jmol.shape.Labels
 
defaultPointer - Variable in class org.jmol.shape.Labels
 
defaultQMElectronDensityCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultQMOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultRotationRadius - Variable in class org.jmol.modelset.Model
 
defaults - Static variable in class org.jmol.script.Token
 
defaultScaleToScreen(float) - Method in class org.jmol.viewer.TransformManager
 
defaultSolventRadius - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultsOnlyForNone - Variable in class org.jmol.shape.Labels
 
defaultStructure - Variable in class org.jmol.modelset.Model
 
defaultstructuredssp - Static variable in class org.jmol.script.Token
 
defaultStructureDSSP - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultTickInfo - Variable in class org.jmol.shape.Measures
 
defaulttorsionlabel - Static variable in class org.jmol.script.Token
 
defaultTorsionLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaulttranslucent - Static variable in class org.jmol.script.Token
 
defaultTranslucent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultvdw - Static variable in class org.jmol.script.Token
 
defaultVdw - Variable in class org.jmol.viewer.DataManager
 
defaultZPos - Variable in class org.jmol.shape.Labels
 
define(JmolMeasurementClient, ModelSet) - Method in class org.jmol.modelset.MeasurementData
called by the client to generate a set of measurements
define() - Method in class org.jmol.script.ScriptEvaluator
 
define - Static variable in class org.jmol.script.Token
 
define(int, Measurement, boolean, boolean, boolean) - Method in class org.jmol.shape.Measures
 
define(MeasurementData, int) - Method in class org.jmol.shape.Measures
 
defineAtomSet(String) - Method in class org.jmol.script.ScriptEvaluator
 
defineCenterAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
definedAtomSets - Variable in class org.jmol.script.ScriptEvaluator
 
definedAtomSets - Variable in class org.jmol.viewer.Viewer
 
defineMeasurement(int, Measurement, boolean) - Method in class org.jmol.shape.Measures
 
defineSets() - Method in class org.jmol.script.ScriptEvaluator
support for @xxx or define xxx commands
defineStructure(int, EnumStructure, String, int, int, char, int, char, char, int, char) - Method in class org.jmol.modelset.ModelLoader
 
DEG_TO_RAD - Static variable in class org.jmol.minimize.forcefield.Calculations
 
DEG_TO_RAD - Static variable in class org.jmol.minimize.Util
 
degree - Variable in class org.jmol.smiles.SmilesAtom
 
DEGREES - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
degreesPerRadian - Static variable in class org.jmol.export.___Exporter
 
degreesPerRadian - Static variable in class org.jmol.viewer.TransformManager
 
delay() - Method in class org.jmol.script.ScriptEvaluator
 
delay(long) - Method in class org.jmol.script.ScriptEvaluator
 
delay - Static variable in class org.jmol.script.Token
 
delaymaximumms - Static variable in class org.jmol.script.Token
 
delayMaximumMs - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
delete(BitSet) - Method in class org.jmol.modelset.Atom
 
delete() - Method in class org.jmol.script.ScriptEvaluator
 
delete - Static variable in class org.jmol.script.Token
 
delete(Measurement) - Method in class org.jmol.shape.Measures
 
delete(Object) - Method in class org.jmol.shape.Measures
 
delete() - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
deleteAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
deleteAllBonds() - Method in class org.jmol.modelset.BondCollection
 
deleteAllBonds() - Method in class org.jmol.modelset.ModelSet
 
deleteAllButton - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
deleteAtomReferences() - Method in class org.jmol.modelset.Bond
 
deleteAtoms(int, int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
deleteAtoms(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
deleteAtoms(int, BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection.StateScript
 
deleteAtoms(BitSet) - Method in class org.jmol.modelset.ModelLoader
called from org.jmol.modelsetbio.resolver when adding hydrogens.
deleteAtoms(int) - Method in class org.jmol.shapespecial.DrawMesh
 
deleteAtoms(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
deleteAtoms(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
deleteAtomsInVariables(BitSet) - Method in class org.jmol.script.ScriptEvaluator
 
deleteBits(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
this one slides deleted bits out of a pattern.
deleteBond(Bond) - Method in class org.jmol.modelset.Atom
 
deleteBond(int) - Method in class org.jmol.modelset.Atom
 
deleteBonds(BitSet, boolean) - Method in class org.jmol.modelset.BondCollection
 
deleteBonds(BitSet, boolean) - Method in class org.jmol.modelset.ModelCollection
 
deleteBonds(BitSet) - Method in class org.jmol.viewer.Viewer
 
deleteButton - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
deleteConnections(float, float, int, BitSet, BitSet, boolean, boolean, float, float) - Method in class org.jmol.modelset.BondCollection
 
deleteContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
deleteDipole(Dipole) - Method in class org.jmol.shapespecial.Dipoles
 
deleteDirectory(File) - Static method in class org.openscience.chimetojmol.ChimePanel
 
deleteElements(Object, int, int) - Static method in class org.jmol.util.ArrayUtil
 
deleteInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
deleteLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
 
deleteLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
deleteMeasurement(int) - Method in class org.jmol.api.JmolViewer
 
deleteMeasurement(int) - Method in class org.jmol.shape.Measures
 
deleteMeasurement(int) - Method in class org.jmol.viewer.Viewer
 
deleteMesh() - Method in class org.jmol.shape.MeshCollection
 
deleteMesh(String) - Method in class org.jmol.shape.MeshCollection
 
deleteMesh(int) - Method in class org.jmol.shape.MeshCollection
 
deleteModel(int, int, int, BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
deleteModelAtoms(int, int, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
deleteModelAtoms(int, int, BitSet) - Method in class org.jmol.viewer.DataManager
 
deleteModelAtoms(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
deleteModelAtoms(int, int, BitSet) - Method in class org.jmol.viewer.Viewer
 
deleteModels(BitSet) - Method in class org.jmol.modelset.ModelSet
 
deletePolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
 
deleteSaved(String) - Method in class org.jmol.viewer.StateManager
 
deleteSavedState(String) - Method in class org.jmol.viewer.Viewer
 
deleteSavedType(String) - Method in class org.jmol.viewer.StateManager
 
deleteShapeAtoms(Object[], BitSet) - Method in class org.jmol.viewer.ShapeManager
 
deleteShapeAtoms(Object[], BitSet) - Method in class org.jmol.viewer.Viewer
 
deleteUnneededAtoms() - Method in class org.jmol.modelsetbio.Resolver
Delete hydrogen atoms that are still in bsAddedHydrogens, because they were not actually added.
deleteVdwDependentShapes(BitSet) - Method in class org.jmol.viewer.ShapeManager
 
deleteWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
delta - Variable in class org.jmol.minimize.forcefield.Calculation
 
density - Static variable in class org.jmol.script.Token
 
deprecatedparam - Static variable in class org.jmol.script.Token
 
depth - Variable in class org.jmol.g3d.Graphics3D
 
depth - Variable in class org.jmol.g3d.Sphere3D
 
depth - Static variable in class org.jmol.script.Token
 
depth1 - Variable in class org.jmol.g3d.Hermite3D
 
depthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
depthByPixels(int) - Method in class org.jmol.viewer.Viewer
 
depthPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
depthPlane - Variable in class org.jmol.viewer.TransformManager
 
depthToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
depthToPercent(int) - Method in class org.jmol.viewer.Viewer
 
depthValue - Variable in class org.jmol.viewer.TransformManager
 
depthZ - Variable in class org.jmol.export.___Exporter
 
descent - Variable in class org.jmol.shape.LabelsRenderer
 
descent - Variable in class org.jmol.shape.Text
 
desireClearingThread - Static variable in class org.jmol.g3d.Platform3D
 
desiredModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
desiredQ - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
desiredQpt - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
desiredSpaceGroupIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
desiredVibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
destroy() - Method in class org.jmol.applet.AppletWrapper
 
destroy() - Method in class org.jmol.applet.Jmol
 
destroy() - Method in interface org.jmol.applet.WrappedApplet
 
destroy() - Method in class org.jmol.g3d.Graphics3D
 
destroyConsole() - Method in class org.jmol.console.JmolConsole
 
detectExplosion() - Method in class org.jmol.minimize.forcefield.ForceField
 
determineAtomSetCollectionReader(BufferedReader, boolean) - Static method in class org.jmol.adapter.smarter.Resolver
the main resolver method.
determineSpaceGroup(String) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroup(String, SpaceGroup) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroup(String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroup(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroupIndex(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSurfaceFileType(InputStream) - Static method in class org.jmol.util.SurfaceFileTyper
 
determineSurfaceFileType(BufferedReader) - Static method in class org.jmol.util.SurfaceFileTyper
 
determineUniqueAxis(float, float, float, float, float, float) - Static method in class org.jmol.symmetry.SpaceGroup
 
DF_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
dfact2 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
dfBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
dfCoefMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
dfCoefMaps - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
dfCoefMaps - Variable in class org.jmol.quantum.MOCalculation
 
dFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
DFT_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
dgridContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
DgridReader - Class in org.jmol.adapter.readers.quantum
A reader for Dgrid BASISFILE data.
DgridReader() - Constructor for class org.jmol.adapter.readers.quantum.DgridReader
 
diagonal - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
diagonalReferenceAxis - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
Dialog - Class in org.jmol.export.dialog
 
Dialog() - Constructor for class org.jmol.export.dialog.Dialog
 
dialog - Variable in class org.jmol.export.dialog.FileChooser
 
Dialog.ExportChoiceListener - Class in org.jmol.export.dialog
 
Dialog.ExportChoiceListener() - Constructor for class org.jmol.export.dialog.Dialog.ExportChoiceListener
 
Dialog.QualityListener - Class in org.jmol.export.dialog
 
Dialog.QualityListener(boolean, JSlider) - Constructor for class org.jmol.export.dialog.Dialog.QualityListener
 
Dialog.TypeFilter - Class in org.jmol.export.dialog
 
Dialog.TypeFilter(String) - Constructor for class org.jmol.export.dialog.Dialog.TypeFilter
 
dialogAsk(String, String) - Method in class org.jmol.viewer.StatusManager
 
dialogAsk(String, String) - Method in class org.jmol.viewer.Viewer
 
dialogLocation - Variable in class org.jmol.export.dialog.FileChooser
 
dialogSize - Variable in class org.jmol.export.dialog.FileChooser
 
dialogType - Variable in class org.jmol.export.dialog.Dialog
 
diameter - Variable in class org.jmol.g3d.Cylinder3D
 
diameter - Variable in class org.jmol.g3d.Sphere3D
 
diameter - Variable in class org.jmol.jvxl.data.JvxlData
 
diameter - Static variable in class org.jmol.script.Token
 
diameter - Variable in class org.jmol.shape.Mesh
 
diameter - Variable in class org.jmol.shape.MeshRenderer
 
diameter - Variable in class org.jmol.shapespecial.DipolesRenderer
 
diameter - Variable in class org.jmol.shapespecial.Draw
 
diameter - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
diameter - Variable in class org.jmol.shapespecial.VectorsRenderer
 
diameter0 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
diameterBeg - Variable in class org.jmol.shapebio.BioShapeRenderer
 
diameterEnd - Variable in class org.jmol.shapebio.BioShapeRenderer
 
diameterMid - Variable in class org.jmol.shapebio.BioShapeRenderer
 
diameterP - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.g3d.Rgb16
 
diffuseFactor - Static variable in class org.jmol.g3d.Shade3D
 
diffusePercent - Static variable in class org.jmol.g3d.Shade3D
 
diffusepercent - Static variable in class org.jmol.script.Token
 
diffusePercent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dim - Variable in class org.jmol.bspt.Node
 
dimension - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
Dimension - Class in org.jmol.util
 
Dimension() - Constructor for class org.jmol.util.Dimension
 
dimension - Variable in class org.jmol.util.SimpleUnitCell
 
dimMax - Variable in class org.jmol.bspt.Bspf
 
dimMax - Variable in class org.jmol.bspt.Bspt
 
dimScreen - Variable in class org.jmol.viewer.Viewer
 
dimSize - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
dipole() - Method in class org.jmol.script.ScriptEvaluator
 
dipole - Static variable in class org.jmol.script.Token
 
Dipole - Class in org.jmol.shapespecial
 
Dipole() - Constructor for class org.jmol.shapespecial.Dipole
 
Dipole(int, String, String, short, short, boolean) - Constructor for class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_ATOMS - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_BOND - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_MOLECULAR - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_POINTS - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_POINTVECTOR - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_UNKNOWN - Static variable in class org.jmol.shapespecial.Dipole
 
dipoleCount - Variable in class org.jmol.shapespecial.Dipoles
 
dipoleInfo - Variable in class org.jmol.shapespecial.Dipole
 
Dipoles - Class in org.jmol.shapespecial
 
Dipoles() - Constructor for class org.jmol.shapespecial.Dipoles
 
dipoles - Variable in class org.jmol.shapespecial.Dipoles
 
dipolescale - Static variable in class org.jmol.script.Token
 
dipoleScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
DipolesRenderer - Class in org.jmol.shapespecial
 
DipolesRenderer() - Constructor for class org.jmol.shapespecial.DipolesRenderer
 
dipoleValue - Variable in class org.jmol.shapespecial.Dipole
 
dipoleValue - Variable in class org.jmol.shapespecial.Dipoles
 
dipoleVectorScale - Variable in class org.jmol.shapespecial.DipolesRenderer
 
direction - Static variable in class org.jmol.script.Token
 
directLatticeVectors - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
directory - Variable in class org.jmol.util.CompoundDocument
 
disableField(int) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
used for turning off fractional or nonfractional coord.
disablepopupmenu - Static variable in class org.jmol.script.Token
 
disablePopupMenu - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
discardLinesUntilBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilNonBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilStartsWith(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
discardTempData(boolean) - Method in class org.jmol.shapesurface.Isosurface
 
discrete - Static variable in class org.jmol.script.Token
 
DISORDER_ASSEMBLY - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
DISORDER_GROUP - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
disorderAssembly - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
displacement - Static variable in class org.jmol.script.Token
 
Display - Class in org.jmol.awt
methods required by Jmol that access java.awt.Component private to org.jmol.awt
Display() - Constructor for class org.jmol.awt.Display
 
display - Variable in class org.jmol.export.dialog.FilePreview
 
display - Variable in class org.jmol.i18n.GT.Language
 
display - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
display - Variable in class org.jmol.popup.SimplePopup
 
display(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
display - Static variable in class org.jmol.script.Token
 
display(ModelSet, BitSet, Boolean, boolean) - Method in class org.jmol.viewer.SelectionManager
 
display - Variable in class org.jmol.viewer.Viewer
 
display(BitSet, boolean, boolean, Boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
display - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
display - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
displayBonds(Bond.BondSet, boolean) - Method in class org.jmol.modelset.BondCollection
 
displayBonds(Bond.BondSet, boolean) - Method in class org.jmol.viewer.Viewer
 
displaycellparameters - Static variable in class org.jmol.script.Token
 
displayCellParameters - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
displayed - Static variable in class org.jmol.script.Token
 
displayLoadErrors - Variable in class org.jmol.viewer.Viewer
 
displayMaxX - Variable in class org.jmol.g3d.Graphics3D
 
displayMaxY - Variable in class org.jmol.g3d.Graphics3D
 
displayMinX - Variable in class org.jmol.g3d.Graphics3D
 
displayMinY - Variable in class org.jmol.g3d.Graphics3D
 
DisplayPanel - Class in org.openscience.jmol.app.jmolpanel
 
DisplayPanel(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
DisplayPanel.CheckBoxMenuItemAction - Class in org.openscience.jmol.app.jmolpanel
Action calling evalStringQuiet(<action> + CheckBoxState)
DisplayPanel.CheckBoxMenuItemAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
DisplayPanel.DefineCenterAction - Class in org.openscience.jmol.app.jmolpanel
 
DisplayPanel.DefineCenterAction() - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
 
DisplayPanel.HomeAction - Class in org.openscience.jmol.app.jmolpanel
 
DisplayPanel.HomeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
 
DisplayPanel.MoveToAction - Class in org.openscience.jmol.app.jmolpanel
Action calling moveTo()
DisplayPanel.MoveToAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
DisplayPanel.SetStatusAction - Class in org.openscience.jmol.app.jmolpanel
Action calling setStatus()
DisplayPanel.SetStatusAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
displaySpeed - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
displayWhileRenderingCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
displayWithinDistance2 - Variable in class org.jmol.shape.MeshCollection
 
displayWithinPoints - Variable in class org.jmol.shape.MeshCollection
 
dispose() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
dispose() - Method in interface org.jmol.api.JmolGestureServerInterface
 
dispose() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
dispose() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
dispose() - Method in class org.jmol.awt.Mouse
 
dispose() - Method in class org.jmol.console.JmolConsole
 
dispose() - Method in class org.jmol.console.ScriptEditor
 
dispose() - Method in class org.jmol.export.JmolFileDropper
 
dispose() - Method in class org.jmol.multitouch.ActionManagerMT
 
dispose() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
dispose() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
dispose() - Method in class org.jmol.multitouch.jni.JmolJniClientAdapter
 
dispose() - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
dispose() - Method in class org.jmol.viewer.ActionManager
 
dispose(JFrame) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
dispose() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
disposeGraphics(Object) - Method in interface org.jmol.api.ApiPlatform
 
disposeGraphics(Object) - Static method in class org.jmol.awt.Image
 
disposeGraphics(Object) - Method in class org.jmol.awt.Platform
 
disposeMouse() - Method in interface org.jmol.api.ApiPlatform
 
disposeMouse() - Method in class org.jmol.awt.Platform
 
disregardNeighbors - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
distance - Variable in class org.jmol.jvxl.readers.Parameters
 
distance - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
 
distance - Static variable in class org.jmol.script.Token
 
distance2(double[], double[]) - Static method in class org.jmol.minimize.Util
 
distance2(Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
distancefactor - Static variable in class org.jmol.script.Token
 
distanceFactor - Variable in class org.jmol.shapespecial.Polyhedra
 
distanceMode - Variable in class org.jmol.quantum.MepCalculation
 
distancePointToPlane(Point3f) - Method in interface org.jmol.api.VolumeDataInterface
 
distancePointToPlane(Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
distanceSquared - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
distanceTolerance - Variable in class org.jmol.symmetry.PointGroup
 
distanceToMappingPlane(Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
distanceToPlane(Vector3f, float, Point3f) - Static method in class org.jmol.smiles.SmilesSearch
 
distanceToPlane(Point4f, Point3f) - Static method in class org.jmol.util.Measure
 
distanceToPlane(Point4f, float, Point3f) - Static method in class org.jmol.util.Measure
 
distanceToPlane(Vector3f, float, Point3f) - Static method in class org.jmol.util.Measure
 
distanceVerticalToPlane(float, float, Point3f, Point3f, Point3f) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
distinguishAndPropagateGroup(Chain, String, int, int, int, int, int[], Atom[]) - Method in interface org.jmol.api.JmolBioResolver
 
distinguishAndPropagateGroup(int, Chain, String, int, int, int) - Method in class org.jmol.modelset.ModelLoader
 
distinguishAndPropagateGroup(Chain, String, int, int, int, int, int[], Atom[]) - Method in class org.jmol.modelsetbio.Resolver
 
div - Static variable in class org.jmol.script.Token
 
div(Quaternion) - Method in class org.jmol.util.Quaternion
 
div(Quaternion[], Quaternion[], int, boolean) - Static method in class org.jmol.util.Quaternion
 
divide - Static variable in class org.jmol.script.Token
 
divisors - Variable in class org.jmol.util.DCT
 
DivisorsChrominance - Variable in class org.jmol.util.DCT
 
DivisorsLuminance - Variable in class org.jmol.util.DCT
 
divLeft(Quaternion) - Method in class org.jmol.util.Quaternion
 
dList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
dmax - Variable in class org.jmol.jvxl.readers.MapFileReader
 
dMax - Static variable in class org.jmol.quantum.NciCalculation
 
dmean - Variable in class org.jmol.jvxl.readers.MapFileReader
 
dmesh - Variable in class org.jmol.shapespecial.DrawRenderer
 
dmeshes - Variable in class org.jmol.shapespecial.Draw
 
dmin - Variable in class org.jmol.jvxl.readers.MapFileReader
 
dmolContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
DmolReader - Class in org.jmol.adapter.readers.xtal
 
DmolReader() - Constructor for class org.jmol.adapter.readers.xtal.DmolReader
 
dna - Static variable in class org.jmol.script.Token
 
doAddHydrogens - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
doAddHydrogens - Variable in class org.jmol.modelset.ModelLoader
 
doApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doBitsetSelect() - Method in class org.jmol.script.ScriptMathProcessor
 
doBrowse() - Method in class org.openscience.chimetojmol.ChimePanel
 
doc - Variable in class org.jmol.adapter.readers.more.BinaryReader
 
doc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doCalcArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
doCalculateTroughs - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
doCap - Variable in class org.jmol.util.MeshSurface
 
doCap0 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
doCap1 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
doCheckUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doClear - Variable in class org.jmol.util.MeshSurface
 
doClose() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
doConvertToFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doDebug - Variable in class org.jmol.quantum.QuantumCalculation
 
doDrop(PropertyChangeEvent) - Method in class org.jmol.export.JmolFileDropper
 
doFinalize() - Method in class org.jmol.symmetry.SymmetryOperation
 
doFixFilenames - Variable in class org.openscience.chimetojmol.ChimePanel
 
doFixPeriodic - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
doFormatText - Variable in class org.jmol.shape.Text
 
doFullMolecular - Variable in class org.jmol.jvxl.readers.Parameters
 
doGetModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doGetVibration(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doGhost - Variable in class org.jmol.util.MeshSurface
 
doGo() - Method in class org.openscience.chimetojmol.ChimePanel
 
doHighlight(int, int, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
doIterate - Variable in class org.jmol.jvxl.data.VolumeData
 
doJustify - Variable in class org.jmol.shape.MeasuresRenderer
 
dollarsign - Static variable in class org.jmol.script.Token
 
doLocalize - Variable in class org.jmol.shape.UccageRenderer
 
doMinimize - Variable in class org.jmol.modelset.ModelLoader
 
DOMResolve(Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.
doneHere - Variable in class org.jmol.multitouch.ActionManagerMT
 
doneHere - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
doNormalize - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
doNormalize - Variable in class org.jmol.quantum.MOCalculation
 
doNormalize - Variable in class org.jmol.symmetry.SpaceGroup
 
doNormalize - Variable in class org.jmol.symmetry.SymmetryOperation
 
dontsave - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
doOpen() - Method in class org.jmol.console.ScriptEditor
 
doOverWrite(JFileChooser, File) - Static method in class org.jmol.export.dialog.Dialog
 
doPackUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
doPackUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doProcessLines - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doRemoveAddedHydrogens - Variable in class org.jmol.modelset.ModelLoader
 
doRender - Variable in class org.jmol.shape.MeshRenderer
 
doReportProperty(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
doResume() - Method in class org.jmol.console.ScriptEditor
 
doSaveSurfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
doSetOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doShaft - Variable in class org.jmol.shapespecial.VectorsRenderer
 
doShowShellType - Variable in class org.jmol.quantum.MOCalculation
 
doSmoothProperty - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
doStep() - Method in class org.jmol.console.ScriptEditor
 
doSubdirectories - Variable in class org.openscience.chimetojmol.ChimePanel
 
doSymmetry - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
 
doSync() - Method in class org.jmol.viewer.StatusManager
 
dot - Static variable in class org.jmol.script.Token
 
dot(Quaternion) - Method in class org.jmol.util.Quaternion
 
dotCount - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
dotdensity - Static variable in class org.jmol.script.Token
 
dotDensity - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
doTranslate - Variable in class org.jmol.applet.Jmol
 
doTranslate - Variable in class org.jmol.i18n.GT
 
dots - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
dots(int) - Method in class org.jmol.script.ScriptEvaluator
 
dots - Static variable in class org.jmol.script.Token
 
Dots - Class in org.jmol.shapespecial
 
Dots() - Constructor for class org.jmol.shapespecial.Dots
 
dotscale - Static variable in class org.jmol.script.Token
 
dotScale - Variable in class org.jmol.shapespecial.DotsRenderer
 
dotScale - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
dotScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dotsConvexMaps - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
dotsConvexMax - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
DotsRenderer - Class in org.jmol.shapespecial
 
DotsRenderer() - Constructor for class org.jmol.shapespecial.DotsRenderer
 
dotsselectedonly - Static variable in class org.jmol.script.Token
 
dotsSelectedOnly - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dotsurface - Static variable in class org.jmol.script.Token
 
dotSurface - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dotted - Static variable in class org.jmol.script.Token
 
DOUBLE_CLICK - Static variable in class org.jmol.viewer.binding.Binding
 
doubleLength(Object) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(String[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(float[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(int[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(short[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(byte[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(boolean[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
doUseIterator - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
doUseSigned - Variable in class org.openscience.chimetojmol.ChimePanel
 
DOWN - Static variable in class org.jmol.viewer.binding.Binding
 
downsample - Static variable in class org.jmol.script.Token
 
downsampleFactor - Variable in class org.jmol.jvxl.readers.Parameters
 
downsampleFactor - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
downsampleFullSceneAntialiasing(boolean) - Method in class org.jmol.g3d.Graphics3D
 
downsampleRemainders - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
dPX - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
dragAtomIndex - Variable in class org.jmol.viewer.ActionManager
 
dragBinding - Variable in class org.jmol.viewer.ActionManager
 
DragBinding - Class in org.jmol.viewer.binding
 
DragBinding() - Constructor for class org.jmol.viewer.binding.DragBinding
 
dragEnter(DropTargetDragEvent) - Method in class org.jmol.export.JmolFileDropper
 
dragExit(DropTargetEvent) - Method in class org.jmol.export.JmolFileDropper
 
dragged - Variable in class org.jmol.viewer.ActionManager
 
DRAGGED - Static variable in class org.jmol.viewer.binding.Binding
 
dragGesture - Variable in class org.jmol.viewer.ActionManager
 
dragOver(DropTargetDragEvent) - Method in class org.jmol.export.JmolFileDropper
 
dragselected - Static variable in class org.jmol.script.Token
 
dragSelected - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dragSelectedMode - Variable in class org.jmol.viewer.ActionManager
 
drange - Variable in class org.jmol.jvxl.readers.MapFileReader
 
draw() - Method in class org.jmol.script.ScriptEvaluator
 
draw - Static variable in class org.jmol.script.Token
 
Draw - Class in org.jmol.shapespecial
 
Draw() - Constructor for class org.jmol.shapespecial.Draw
 
draw(String, String, Point3f, float) - Method in class org.jmol.util.Quaternion
 
Draw.EnumDrawType - Enum in org.jmol.shapespecial
 
Draw.EnumDrawType(int, String) - Constructor for enum org.jmol.shapespecial.Draw.EnumDrawType
 
draw000 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
drawArcs - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawArrowHeadBox(Point3f, Point3f) - Method in class org.jmol.shapebio.RocketsRenderer
 
drawArrowScale - Variable in class org.jmol.shapespecial.DrawMesh
 
drawAtom(Atom) - Method in interface org.jmol.api.JmolRendererInterface
 
drawAtom(Atom) - Method in class org.jmol.export.___Exporter
 
drawAtom(Atom) - Method in class org.jmol.export.__CartesianExporter
 
drawAtom(Atom) - Method in class org.jmol.export.__RayTracerExporter
 
drawAtom(Atom) - Method in class org.jmol.export.Export3D
 
drawAtom(Atom) - Method in class org.jmol.g3d.Graphics3D
 
drawAxes - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawBackside - Variable in class org.jmol.g3d.Cylinder3D
 
drawBall - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawBond(Atom, Atom, short, short, byte, short) - Method in interface org.jmol.api.JmolRendererInterface
 
drawBond(Atom, Atom, short, short, byte, short) - Method in class org.jmol.export.Export3D
 
drawBond(Atom, Atom, short, short, byte, short) - Method in class org.jmol.g3d.Graphics3D
 
drawBond(int) - Method in class org.jmol.shape.SticksRenderer
 
drawBox(Point3f, Point3f) - Method in class org.jmol.shapebio.RocketsRenderer
 
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.___Exporter
 
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
drawCircle(short, int, int, int, int, boolean) - Method in class org.jmol.export.Export3D
draws a simple circle (draw circle)
drawCylinder(Point3f, Point3f, short, short, byte, int, int) - Method in class org.jmol.export.___Exporter
 
drawCylinder(Point3f, Point3f, short, short, byte, int, int) - Method in class org.jmol.export.__CartesianExporter
 
drawCylinder(Point3f, Point3f, short, short, byte, int, int) - Method in class org.jmol.export.__RayTracerExporter
 
drawCylinderTriangle(int, int, int, int, int, int, int, int, int) - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
drawDashed(int, int, int, int, int, int, int[]) - Method in class org.jmol.shape.SticksRenderer
 
drawDashedLine(int, int, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawDashedLine(int, int, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawDashedLine(int, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawDots - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawDottedLine(Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawDottedLine(Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawDottedLine(Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawEdges - Variable in class org.jmol.shapespecial.Polyhedra
 
drawEdges - Variable in class org.jmol.shapespecial.PolyhedraRenderer
 
drawEllipse(Point3f, Point3f, Point3f, boolean, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
drawEllipse(Point3f, Point3f, Point3f, short, boolean) - Method in class org.jmol.export.___Exporter
 
drawEllipse(Point3f, Point3f, Point3f, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
drawEllipse(Point3f, Point3f, Point3f, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
drawEllipse(Point3f, Point3f, Point3f, boolean, boolean) - Method in class org.jmol.export.Export3D
 
drawEllipse(Point3f, Point3f, Point3f, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
 
drawFace(short, Point3i, Point3i, Point3i) - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
drawFill - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawFilledCircle(short, short, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws a ring and filled circle (halos, draw CIRCLE, draw handles)
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.___Exporter
 
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.Export3D
draws a screened circle ...
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawfillTriangle(int, int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Triangle3D
 
drawHermite(int, Point3i, Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawHermite(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawHermite(int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawHermite(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in class org.jmol.export.Export3D
 
drawHermite(int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawHermite(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Graphics3D
 
drawHLine(int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawHLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawhover - Static variable in class org.jmol.script.Token
 
drawHover - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
drawImage(Object, Object, int, int) - Method in interface org.jmol.api.ApiPlatform
 
drawImage(Object, int, int, int, int, short, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawImage(Object, Object, int, int) - Static method in class org.jmol.awt.Image
 
drawImage(Object, Object, int, int) - Method in class org.jmol.awt.Platform
 
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.export.Export3D
 
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in interface org.jmol.api.ApiPlatform
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Static method in class org.jmol.awt.Image
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
 
drawIndex - Variable in class org.jmol.symmetry.PointGroup
 
drawInfo - Variable in class org.jmol.symmetry.PointGroup
 
drawing - Static variable in class org.jmol.script.Token
 
drawLcaoCartoon(Vector3f, Vector3f, Vector3f, int) - Method in class org.jmol.shapesurface.Isosurface
 
drawLine(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLine(Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLine(short, short, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLine(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawLine(Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawLine(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawLine(Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.shape.FontLineShapeRenderer
 
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.shape.MeasuresRenderer
 
drawLine(int, int, boolean, Point3f, Point3f, Point3i, Point3i) - Method in class org.jmol.shape.MeshRenderer
 
drawLine(StringBuffer, String, float, Point3f, Point3f, String) - Static method in class org.jmol.symmetry.SymmetryOperation
 
drawLineData(List<Point3f[]>) - Method in class org.jmol.shapespecial.DrawRenderer
 
DrawMesh - Class in org.jmol.shapespecial
 
DrawMesh(String, Graphics3D, short, int) - Constructor for class org.jmol.shapespecial.DrawMesh
 
drawMode - Variable in class org.jmol.viewer.ActionManager
 
drawpicking - Static variable in class org.jmol.script.Token
 
drawPicking - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
drawPixel(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.___Exporter
 
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.__CartesianExporter
 
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
 
drawPixel(int, int, int) - Method in class org.jmol.export.Export3D
 
drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawPointer(JmolRendererInterface) - Method in class org.jmol.shape.Object2d
 
drawPoints(int, int[], int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawPoints(int, int[], int) - Method in class org.jmol.export.Export3D
 
drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
 
drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
draws a rectangle
DrawRenderer - Class in org.jmol.shapespecial
 
DrawRenderer() - Constructor for class org.jmol.shapespecial.DrawRenderer
 
drawSlicePlane(StringBuffer, int, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
drawString(String, Font3D, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws the specified string in the current font.
drawString(String, Font3D, int, int, int, int) - Method in class org.jmol.export.Export3D
draws the specified string in the current font.
drawString(String, Font3D, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
draws the specified string in the current font.
drawString(int, int, int, int, boolean, boolean, boolean, int, String) - Method in class org.jmol.shape.FontLineShapeRenderer
 
drawStringNoSlab(String, Font3D, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws the specified string in the current font.
drawStringNoSlab(String, Font3D, int, int, int) - Method in class org.jmol.export.Export3D
draws the specified string in the current font.
drawStringNoSlab(String, Font3D, int, int, int) - Method in class org.jmol.g3d.Graphics3D
draws the specified string in the current font.
drawSurface(MeshSurface, short) - Method in interface org.jmol.api.JmolRendererInterface
 
drawSurface(MeshSurface, short) - Method in class org.jmol.export.___Exporter
 
drawSurface(MeshSurface, short) - Method in class org.jmol.export._ObjExporter
 
drawSurface(MeshSurface, short) - Method in class org.jmol.export.Export3D
 
drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.___Exporter
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.__CartesianExporter
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export._MayaExporter
 
drawTicks(Point3fi, Point3fi, int, boolean) - Method in class org.jmol.shape.FontLineShapeRenderer
 
drawTicks(Point3fi, Point3fi, float, int, int, String[]) - Method in class org.jmol.shape.FontLineShapeRenderer
 
drawTriangle(Point3i, short, Point3i, short, Point3i, short, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawTriangle(Point3i, Point3i, Point3i, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawTriangle(Point3i, short, Point3i, short, Point3i, short, int) - Method in class org.jmol.export.Export3D
 
drawTriangle(Point3i, Point3i, Point3i, int) - Method in class org.jmol.export.Export3D
 
drawTriangle(Point3i, short, Point3i, short, Point3i, short, int) - Method in class org.jmol.g3d.Graphics3D
 
drawTriangle(Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Graphics3D
 
drawTriangles - Variable in class org.jmol.shape.Mesh
 
drawType - Variable in class org.jmol.shapespecial.DrawMesh
 
drawType - Variable in class org.jmol.shapespecial.DrawRenderer
 
drawType - Variable in class org.jmol.symmetry.PointGroup
 
drawTypes - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVertexCount - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVertexCounts - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVLine(int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawVLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
DRIVER_NONE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
drivingSync - Variable in class org.jmol.viewer.StatusManager
 
drop(DropTargetDropEvent) - Method in class org.jmol.export.JmolFileDropper
 
dropActionChanged(DropTargetDragEvent) - Method in class org.jmol.export.JmolFileDropper
 
dropper - Variable in class org.jmol.applet.Jmol
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
Dsn6BinaryReader - Class in org.jmol.jvxl.readers
 
Dsn6BinaryReader(SurfaceGenerator, String, String) - Constructor for class org.jmol.jvxl.readers.Dsn6BinaryReader
 
dSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
dssp - Static variable in class org.jmol.script.Token
 
dsspcalchydrogen - Static variable in class org.jmol.script.Token
 
dsspCalcHydrogen - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dtype - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
DUMMY_ATOM - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
dump() - Method in class org.jmol.bspt.Bspf
 
dump() - Method in class org.jmol.bspt.Bspt
 
dump(int, StringBuffer) - Method in class org.jmol.bspt.Element
 
dump(int, StringBuffer) - Method in class org.jmol.bspt.Leaf
 
dump(int, StringBuffer) - Method in class org.jmol.bspt.Node
 
dump() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
dumpAll() - Static method in class org.jmol.symmetry.SpaceGroup
 
dumpAllSeitz() - Static method in class org.jmol.symmetry.SpaceGroup
 
dumpArray(String, float[][], int, int, int, int) - Static method in class org.jmol.util.ArrayUtil
 
dumpCanonicalSeitz(Matrix4f) - Static method in class org.jmol.symmetry.SymmetryOperation
 
dumpCanonicalSeitzList() - Method in class org.jmol.symmetry.SpaceGroup
 
dumpDipoles(String) - Method in class org.jmol.shapespecial.Dipoles
 
dumpInfo(int) - Method in class org.jmol.quantum.MOCalculation
 
dumpInfo() - Method in class org.jmol.symmetry.HallInfo
 
dumpInfo() - Method in class org.jmol.symmetry.HallInfo.RotationTerm
 
dumpInfo(SymmetryInterface) - Method in class org.jmol.symmetry.SpaceGroup
 
dumpInfo() - Method in class org.jmol.symmetry.SymmetryOperation
 
dumpInfo(boolean) - Method in class org.jmol.symmetry.UnitCell
 
dumpIntArray(int[], int) - Static method in class org.jmol.util.ArrayUtil
 
dumpLine(Point3f, Tuple3f, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
dumpLine2(Point3f, Point3f, String, float, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
dumpList - Static variable in class org.jmol.popup.SimplePopup
 
dumpPoint(Point3f, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
dumpRingKeys(StringBuffer, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
 
dumpSeitz(Matrix4f) - Static method in class org.jmol.symmetry.SymmetryOperation
 
dumpStacks(String) - Method in class org.jmol.script.ScriptMathProcessor
 
dumpStructure(String[][]) - Method in class org.jmol.popup.MainPopupResourceBundle
 
dumpSummary(char[]) - Method in class org.jmol.modelsetbio.AminoPolymer
 
dumpTags(String, BitSet, int) - Method in class org.jmol.modelsetbio.AminoPolymer
 
dumpWords() - Method in class org.jmol.popup.MainPopupResourceBundle
 
dVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
dx - Variable in class org.jmol.bspt.CubeIterator
 
dx - Variable in class org.jmol.shape.Frank
 
dx - Variable in class org.jmol.shape.SticksRenderer
 
dx - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
dxB - Variable in class org.jmol.g3d.Cylinder3D
 
dxBf - Variable in class org.jmol.g3d.Cylinder3D
 
dxStep - Variable in class org.jmol.shape.SticksRenderer
 
DXY - Variable in class org.jmol.quantum.MOCalculation
 
dxyz - Variable in class org.jmol.g3d.Sphere3D
 
DXZ - Variable in class org.jmol.quantum.MOCalculation
 
dy - Variable in class org.jmol.bspt.CubeIterator
 
dy - Variable in class org.jmol.shape.Frank
 
dy - Variable in class org.jmol.shape.SticksRenderer
 
dyB - Variable in class org.jmol.g3d.Cylinder3D
 
dyBf - Variable in class org.jmol.g3d.Cylinder3D
 
dynamicmeasurements - Static variable in class org.jmol.script.Token
 
dynamicMeasurements - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dyStep - Variable in class org.jmol.shape.SticksRenderer
 
DYZ - Variable in class org.jmol.quantum.MOCalculation
 
dz - Variable in class org.jmol.bspt.CubeIterator
 
dzB - Variable in class org.jmol.g3d.Cylinder3D
 
dzBf - Variable in class org.jmol.g3d.Cylinder3D
 

E

e - Variable in class org.jmol.util.Eigen
Arrays for internal storage of eigenvalues.
e0 - Variable in class org.jmol.minimize.forcefield.ForceField
 
E_ANG_PER_DEBYE - Static variable in class org.jmol.shapespecial.Dipoles
 
E_MINUS_D - Static variable in class org.jmol.quantum.MepCalculation
 
E_MINUS_D_OVER_2 - Static variable in class org.jmol.quantum.MepCalculation
 
EANGLE - Static variable in class org.jmol.minimize.forcefield.ForceField
 
EBOND - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
ec - Variable in class org.jmol.shapespecial.Dots
 
eccentricity - Static variable in class org.jmol.script.Token
 
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityRatio - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityRatio - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityScale - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityScale - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
echo(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
echo - Static variable in class org.jmol.script.Token
 
Echo - Class in org.jmol.shape
 
Echo() - Constructor for class org.jmol.shape.Echo
 
echoMessage(String) - Method in class org.jmol.viewer.Viewer
 
EchoRenderer - Class in org.jmol.shape
 
EchoRenderer() - Constructor for class org.jmol.shape.EchoRenderer
 
echoShapeActive - Variable in class org.jmol.modelset.ModelSet
 
eCounts - Variable in class org.jmol.symmetry.PointGroup
 
ed - Static variable in class org.jmol.script.Token
 
EDGE_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
edgeCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgeCount - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
edgeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgeDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
edgeFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
 
edgeFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgeFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
 
edgeFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgePointIndexes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edges - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
edges - Static variable in class org.jmol.script.Token
 
edges - Static variable in class org.jmol.util.BoxInfo
 
EDGES_ALL - Static variable in class org.jmol.shapespecial.Polyhedra
 
EDGES_FRONT - Static variable in class org.jmol.shapespecial.Polyhedra
 
EDGES_NONE - Static variable in class org.jmol.shapespecial.Polyhedra
 
edgeTypeTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVector - Variable in class org.jmol.jvxl.data.VolumeData
 
edgeVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexes - Static variable in class org.jmol.util.TriangleData
 
edgeVertexes - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
edgeVertexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPlanesHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPlanesLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointers - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointersHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointersLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
editArea - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
editButton - Variable in class org.jmol.console.JmolConsole
 
editor - Variable in class org.jmol.console.ScriptEditor
 
EDITOR_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
editorAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
editorDoc - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
 
editorScrollPane - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
EditorTextPane - Variable in class org.jmol.console.ScriptEditor.EditorDocument
 
edsurlcutoff - Static variable in class org.jmol.script.Token
 
edsUrlCutoff - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
edsurlformat - Static variable in class org.jmol.script.Token
 
edsUrlFormat - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
edsUrlOptions - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
EELECTROSTATIC - Static variable in class org.jmol.minimize.forcefield.ForceField
 
EfvetReader - Class in org.jmol.jvxl.readers
 
EfvetReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.EfvetReader
 
eig_val - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
eig_vec - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
eig_vec_compressed - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
eigen - Variable in class org.jmol.quantum.NciCalculation
 
Eigen - Class in org.jmol.util
Eigenvalues and eigenvectors of a real (n x n) symmetric matrix.
Eigen(int) - Constructor for class org.jmol.util.Eigen
 
Eigen(double[][]) - Constructor for class org.jmol.util.Eigen
 
eightPiSquared100 - Static variable in class org.jmol.shapebio.BioShape
 
electronEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
eleLeft - Variable in class org.jmol.bspt.Node
 
Element - Class in org.jmol.bspt
the internal tree is made up of elements ...
Element() - Constructor for class org.jmol.bspt.Element
 
element - Static variable in class org.jmol.script.Token
 
elementCharMasks - Static variable in class org.jmol.adapter.smarter.Atom
Bits which indicate whether or not an element symbol is valid.
elementContext - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
elementCounts - Variable in class org.jmol.util.JmolMolecule
 
elementNameFromNumber(int) - Static method in class org.jmol.util.Elements
 
elementNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
elementNames - Static variable in class org.jmol.util.Elements
 
elementNumber - Variable in class org.jmol.adapter.smarter.Atom
 
elementNumber - Variable in class org.jmol.smiles.SmilesAtom
 
elementNumberFromSymbol(String, boolean) - Static method in class org.jmol.util.Elements
 
elementNumberMax - Static variable in class org.jmol.util.Elements
one larger than the last elementNumber, same as elementSymbols.length
elementNumberMax - Variable in class org.jmol.util.JmolMolecule
 
elements - Variable in class org.jmol.symmetry.PointGroup
 
Elements - Class in org.jmol.util
 
Elements() - Constructor for class org.jmol.util.Elements
 
elementsPresent - Variable in class org.jmol.modelset.ModelCollection
 
elementSymbol - Variable in class org.jmol.adapter.smarter.Atom
 
elementSymbolFromNumber(int) - Static method in class org.jmol.util.Elements
 
elementSymbols - Static variable in class org.jmol.util.Elements
The default elementSymbols.
elemisono - Static variable in class org.jmol.script.Token
 
elemno - Static variable in class org.jmol.script.Token
 
eleRight - Variable in class org.jmol.bspt.Node
 
eleRoot - Variable in class org.jmol.bspt.Bspt
 
ellipseNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
ellipsoid - Variable in class org.jmol.adapter.smarter.Atom
 
ellipsoid() - Method in class org.jmol.script.ScriptEvaluator
 
ellipsoid - Static variable in class org.jmol.script.Token
 
ellipsoid - Variable in class org.jmol.shapespecial.Ellipsoids
 
ellipsoidarcs - Static variable in class org.jmol.script.Token
 
ellipsoidArcs - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidaxes - Static variable in class org.jmol.script.Token
 
ellipsoidAxes - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidaxisdiameter - Static variable in class org.jmol.script.Token
 
ellipsoidAxisDiameter - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidball - Static variable in class org.jmol.script.Token
 
ellipsoidBall - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoiddotcount - Static variable in class org.jmol.script.Token
 
ellipsoidDotCount - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoiddots - Static variable in class org.jmol.script.Token
 
ellipsoidDots - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidfill - Static variable in class org.jmol.script.Token
 
ellipsoidFill - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
ellipsoids - Variable in class org.jmol.modelset.AtomCollection
 
Ellipsoids - Class in org.jmol.shapespecial
 
Ellipsoids() - Constructor for class org.jmol.shapespecial.Ellipsoids
 
ellipsoids - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
Ellipsoids.Ellipsoid - Class in org.jmol.shapespecial
 
Ellipsoids.Ellipsoid(String, int) - Constructor for class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
ellipsoidShades - Static variable in class org.jmol.g3d.Sphere3D
 
EllipsoidsRenderer - Class in org.jmol.shapespecial
 
EllipsoidsRenderer() - Constructor for class org.jmol.shapespecial.EllipsoidsRenderer
 
elsecmd - Static variable in class org.jmol.script.Token
 
elseif - Static variable in class org.jmol.script.Token
 
embed1 - Static variable in class org.openscience.chimetojmol.ChimePanel
 
embed2 - Static variable in class org.openscience.chimetojmol.ChimePanel
 
EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JmolConstants
 
embeddedCrystal - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
embedScript(String) - Static method in class org.jmol.viewer.JmolConstants
 
empty - Variable in class org.jmol.viewer.SelectionManager
 
emptyBitmap - Static variable in class org.jmol.util.FastBitSet
 
emptySet - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
emptySet - Static variable in class org.jmol.util.FastBitSet
 
enableButton(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
enableButtons(JList) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
enableMenu(Object, boolean) - Method in class org.jmol.popup.SimplePopup
 
enableMenuItem(Object, boolean) - Method in class org.jmol.popup.SimplePopup
 
encapsulateData(String, Object) - Static method in class org.jmol.util.Escape
 
encode() - Method in class org.jmol.export.image.ImageEncoder
 
ENCODE_ALPHA - Static variable in class org.jmol.export.image.PngEncoder
Constant specifying that alpha channel should be encoded.
encodeAlpha - Variable in class org.jmol.export.image.PngEncoder
 
encodeColor(short) - Static method in class org.jmol.shape.Shape
 
encodeDone() - Method in class org.jmol.export.image.GifEncoder
 
encodeDone() - Method in class org.jmol.export.image.ImageEncoder
 
encodeDone() - Method in class org.jmol.export.image.PpmEncoder
 
encodeFinish() - Method in class org.jmol.export.image.ImageEncoder
 
encodePixels(int, int, int, int, int[], int, int) - Method in class org.jmol.export.image.GifEncoder
 
encodePixels(int, int, int, int, int[], int, int) - Method in class org.jmol.export.image.ImageEncoder
 
encodePixels(int, int, int, int, int[], int, int) - Method in class org.jmol.export.image.PpmEncoder
 
encodePixelsWrapper(int, int, int, int, int[], int, int) - Method in class org.jmol.export.image.ImageEncoder
 
encodeRadiusParameter(int, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
encodeStart(int, int) - Method in class org.jmol.export.image.GifEncoder
 
encodeStart(int, int) - Method in class org.jmol.export.image.ImageEncoder
 
encodeStart(int, int) - Method in class org.jmol.export.image.PpmEncoder
 
encodeTransColor(byte, short, boolean) - Static method in class org.jmol.shape.Shape
 
encoding - Variable in class org.jmol.export.image.ImageEncoder
 
end - Static variable in class org.jmol.script.Token
 
END_ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
END_INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
END_SEQ_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
endcap - Variable in class org.jmol.shape.FontLineShapeRenderer
 
endcaps - Variable in class org.jmol.g3d.Cylinder3D
 
endcaps - Variable in class org.jmol.shape.SticksRenderer
 
ENDCAPS_FLAT - Static variable in class org.jmol.g3d.Graphics3D
 
ENDCAPS_NONE - Static variable in class org.jmol.g3d.Graphics3D
 
ENDCAPS_OPEN - Static variable in class org.jmol.g3d.Graphics3D
 
ENDCAPS_OPENEND - Static variable in class org.jmol.g3d.Graphics3D
 
ENDCAPS_SPHERICAL - Static variable in class org.jmol.g3d.Graphics3D
 
endcapShadeIndex - Variable in class org.jmol.g3d.Cylinder3D
 
endChainID - Variable in class org.jmol.adapter.smarter.Structure
 
endCheck - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
endCheck - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
endCoord - Variable in class org.jmol.shapespecial.Dipoles
 
endDegrees - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader.MolproHandler
 
endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
endFlag - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
 
endifcmd - Static variable in class org.jmol.script.Token
 
endIndexPending - Variable in class org.jmol.shapebio.RocketsRenderer
 
endInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
 
endMinimization() - Method in class org.jmol.minimize.Minimizer
 
endMotion() - Method in class org.jmol.viewer.TransformManager.MotionThread
 
endOfData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
endOfLine - Variable in class org.jmol.script.ScriptCompiler
 
endPos - Variable in class org.jmol.export.image.PngEncoder
 
endPositions - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
endRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
endRendering() - Method in class org.jmol.g3d.Graphics3D
 
endSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
 
energy - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
energy - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
energy - Variable in class org.jmol.minimize.forcefield.Calculation
 
ENERGY - Static variable in class org.jmol.minimize.forcefield.ForceField
 
energy - Variable in class org.jmol.modelset.HBond
 
energy - Static variable in class org.jmol.script.Token
 
energy - Variable in class org.jmol.viewer.StateManager.Connection
 
energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyBond(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyBond(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyES(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyES(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyFull(boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyKey - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
Type of energy calculated, e.g., E(RB+HF-PW91).
energyKey - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
The type of energy last calculated.
energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyStrBnd(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyStrBnd(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyString - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
Calculated energy with units (if possible).
energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyUnits - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
energyUnits - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
energyValue - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
The last calculated energy value.
energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
ensureLength(Object, int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(String[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(float[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(int[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(short[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(byte[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureSufficientBits(int[], int) - Static method in class org.jmol.util.FastBitSet
 
ensureSufficientWords(int[], int) - Static method in class org.jmol.util.FastBitSet
 
enterListener - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
EnterListener - Interface in org.openscience.jmol.app.jmolpanel
 
enterMeasurementMode(int) - Method in class org.jmol.viewer.ActionManager
 
enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
enterPressed() - Method in interface org.openscience.jmol.app.jmolpanel.EnterListener
 
enthalpy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
entries - Variable in class org.jmol.util.Int2IntHash
 
entryCount - Variable in class org.jmol.util.Int2IntHash
 
entryName - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
entryType - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
EnumAnimationMode - Enum in org.jmol.constant
Enum for animation mode.
EnumAnimationMode(String) - Constructor for enum org.jmol.constant.EnumAnimationMode
 
EnumAxesMode - Enum in org.jmol.constant
Enum for axes mode.
EnumAxesMode(int) - Constructor for enum org.jmol.constant.EnumAxesMode
 
EnumCallback - Enum in org.jmol.constant
 
EnumCallback(String) - Constructor for enum org.jmol.constant.EnumCallback
 
EnumHBondType - Enum in org.jmol.constant
Enum for hydrogen bonding donor/acceptor type
EnumHBondType() - Constructor for enum org.jmol.constant.EnumHBondType
 
EnumPalette - Enum in org.jmol.constant
Enum for animation mode.
EnumPalette(String, int) - Constructor for enum org.jmol.constant.EnumPalette
 
EnumQuantumShell - Enum in org.jmol.constant
Enum for quantum shells.
EnumQuantumShell(String, String, int, int) - Constructor for enum org.jmol.constant.EnumQuantumShell
 
EnumStereoMode - Enum in org.jmol.constant
 
EnumStereoMode(String, boolean) - Constructor for enum org.jmol.constant.EnumStereoMode
 
EnumStructure - Enum in org.jmol.constant
 
EnumStructure(int, String, int) - Constructor for enum org.jmol.constant.EnumStructure
 
EnumVdw - Enum in org.jmol.constant
 
EnumVdw(int, String, String) - Constructor for enum org.jmol.constant.EnumVdw
 
EnvelopeCalculation - Class in org.jmol.geodesic
 
EnvelopeCalculation(AtomDataServer, int, short[]) - Constructor for class org.jmol.geodesic.EnvelopeCalculation
 
envelopeRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
envelopeRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
EOF - Static variable in class org.jmol.export.image.GifEncoder
 
EOFCode - Variable in class org.jmol.export.image.GifEncoder
 
EOL - Static variable in class org.jmol.script.ScriptCompiler
 
eol(char) - Method in class org.jmol.script.ScriptCompiler
 
eol(char, int) - Static method in class org.jmol.script.ScriptCompiler
 
EOOP - Static variable in class org.jmol.minimize.forcefield.ForceField
 
equalCount - Variable in class org.jmol.script.ScriptMathProcessor
 
equals(Object) - Method in class org.jmol.modelset.Atom
 
equals(Object) - Method in class org.jmol.util.FastBitSet
 
equivalentAtomSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
The number of equivalent atom sets.
equivalentAtomSets - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
The number of equivalent atom sets.
errCount - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
error(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
error - Variable in class org.jmol.script.ParallelProcessor
 
error(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
error(int, String) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
error(int, String, String) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
error(String, String) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR(int) - Method in class org.jmol.script.ScriptCompiler
 
ERROR(int, String) - Method in class org.jmol.script.ScriptCompiler
 
error - Variable in class org.jmol.script.ScriptEvaluator
 
error(int, int) - Method in class org.jmol.script.ScriptEvaluator
 
error(int) - Method in class org.jmol.script.ScriptEvaluator
 
error(int, String) - Method in class org.jmol.script.ScriptEvaluator
 
error(int, String, String) - Method in class org.jmol.script.ScriptEvaluator
 
error(int, String, String, String) - Method in class org.jmol.script.ScriptEvaluator
 
error(int, String, String, String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
error - Static variable in class org.jmol.script.Token
 
error(String) - Method in class org.jmol.util.DefaultLogger
 
error(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
error(String) - Static method in class org.jmol.util.Logger
Writes a log at ERROR level.
error(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at ERROR level with detail on exception.
error(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level.
error(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level with detail on exception.
ERROR_axisExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_backgroundModelError - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_badContext - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_badMillerIndices - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_badRGBColor - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_booleanExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_booleanOrNumberExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_booleanOrWhateverExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_colorExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_colorOrPaletteRequired - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_commandExpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_commandExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_coordinateExpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_coordinateOrNameOrExpressionRequired - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_drawObjectNotDefined - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_endOfCommandUnexpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_endOfExpressionExpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_endOfStatementUnexpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_expressionExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_expressionOrIntegerExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_filenameExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_fileNotFoundException - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_FLAG - Static variable in class org.jmol.util.CommandHistory
 
ERROR_identifierOrResidueSpecificationExpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_incompatibleArguments - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_insufficientArguments - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_integerExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_integerOutOfRange - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_invalidArgument - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_invalidAtomSpecification - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_invalidChainSpecification - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_invalidExpressionToken - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_invalidModelSpecification - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_invalidParameterOrder - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_keywordExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_missingEnd - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_moCoefficients - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_moIndex - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_moModelError - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_moOccupancy - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_moOnlyOne - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_multipleModelsDisplayedNotOK - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_multipleModelsNotOK - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_noData - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_noPartialCharges - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_noUnitCell - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_numberExpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_numberExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_numberMustBe - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_numberOrVariableNameExpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_numberOutOfRange - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_objectNameExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_planeExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_propertyNameExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_residueSpecificationExpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_spaceGroupNotFound - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_stringExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_stringOrIdentifierExpected - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_tokenExpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_tokenUnexpected - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_tooManyPoints - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_tooManyScriptLevels - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedAtomProperty - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedBondProperty - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedCommand - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedExpression - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedExpressionToken - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_unrecognizedObject - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedParameterWarning - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedShowParameter - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_unrecognizedToken - Static variable in class org.jmol.script.ScriptCompilationTokenParser
 
ERROR_what - Static variable in class org.jmol.script.ScriptEvaluator
 
ERROR_writeWhat - Static variable in class org.jmol.script.ScriptEvaluator
 
errorLine - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
errorMessage - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
errorMessage - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
errorMessage - Variable in class org.jmol.script.ScriptContext
 
errorMessage - Variable in class org.jmol.script.ScriptEvaluator
 
errorMessage - Variable in class org.jmol.viewer.Viewer
 
errorMessageUntranslated - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
errorMessageUntranslated - Variable in class org.jmol.script.ScriptContext
 
errorMessageUntranslated - Variable in class org.jmol.script.ScriptEvaluator
 
errorMessageUntranslated - Variable in class org.jmol.viewer.Viewer
 
errorMsg - Variable in class org.jmol.export.image.AviCreator
 
errorString(int, String, String, boolean) - Static method in class org.jmol.script.ScriptCompilationTokenParser
 
errorString(int, String, String, String, boolean) - Static method in class org.jmol.script.ScriptEvaluator
 
errorType - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
errorType - Variable in class org.jmol.script.ScriptContext
 
errorType - Variable in class org.jmol.script.ScriptEvaluator
 
esCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
escapable - Static variable in class org.jmol.util.Escape
 
escape() - Method in class org.jmol.script.ScriptVariable
 
Escape - Class in org.jmol.util
 
Escape() - Constructor for class org.jmol.util.Escape
 
escape(Tuple3f) - Static method in class org.jmol.util.Escape
must be its own, because of the possibility of being null
escape(Object) - Static method in class org.jmol.util.Escape
 
escape(String) - Static method in class org.jmol.util.Escape
 
escape(ArrayList<ScriptVariable>) - Static method in class org.jmol.util.Escape
 
escape(Map<String, Object>) - Static method in class org.jmol.util.Escape
 
escape(float[], boolean) - Static method in class org.jmol.util.Escape
 
escape(float[][], boolean) - Static method in class org.jmol.util.Escape
 
escape(float[][][], boolean) - Static method in class org.jmol.util.Escape
 
escape(String[], boolean) - Static method in class org.jmol.util.Escape
 
escape(BitSet, boolean) - Static method in class org.jmol.util.Escape
 
escape(String, List<Object[]>, Object, boolean, String) - Static method in class org.jmol.util.XmlUtil
 
escapeArray(Object) - Static method in class org.jmol.util.Escape
 
escapeColor(int) - Static method in class org.jmol.util.Escape
 
escapeHTML(String) - Static method in class org.jmol.i18n.GT
 
escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
 
escapeNice(String) - Static method in class org.jmol.util.Escape
 
escapeXml(Object) - Static method in class org.jmol.util.Escape
 
espCharges - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
espressoContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
EspressoReader - Class in org.jmol.adapter.readers.xtal
 
EspressoReader() - Constructor for class org.jmol.adapter.readers.xtal.EspressoReader
 
ESTRBND - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eta - Static variable in class org.jmol.script.Token
 
ETORSION - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eval(String) - Method in interface org.jmol.api.JmolStatusListener
 
eval(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
eval - Variable in class org.jmol.script.ScriptMathProcessor
 
eval - Variable in class org.jmol.viewer.ActionManager
 
eval - Variable in class org.jmol.viewer.Viewer
 
eval(ScriptContext, ShapeManager) - Method in class org.jmol.viewer.Viewer
 
eval(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
evalError(String, String) - Method in class org.jmol.script.ScriptEvaluator
 
evalFile(String) - Method in class org.jmol.api.JmolSimpleViewer
 
evalFile(String) - Method in class org.jmol.viewer.Viewer
 
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.atomdata.AtomDataServer
 
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.script.ScriptEvaluator
 
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.viewer.Viewer
 
evalString(String) - Method in class org.jmol.api.JmolSimpleViewer
 
evalString(String) - Method in class org.jmol.viewer.Viewer
 
evalStringQuiet(String) - Method in class org.jmol.api.JmolViewer
 
evalStringQuiet(String) - Method in class org.jmol.viewer.Viewer
 
evalStringQuiet(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
evalStringWaitStatus(String, String, String) - Method in class org.jmol.viewer.Viewer
 
evalStringWaitStatus(String, String, String, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
evaluateArray(ScriptVariable[], boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateBin(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateColor(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateCompare(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateCompiledScript(boolean, boolean, boolean, boolean, StringBuffer) - Method in class org.jmol.script.ScriptEvaluator
 
evaluateConnected(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateContact(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateContext(Viewer, ScriptContext, ShapeManager) - Static method in class org.jmol.script.ScriptEvaluator
 
evaluateCross(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateData(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateDot(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateExpression(Viewer, Object, boolean) - Static method in class org.jmol.script.ScriptEvaluator
a general-use method to evaluate a "SET" type expression.
evaluateExpression(Object) - Method in class org.jmol.viewer.Viewer
 
evaluateExpressionAsVariable(Object) - Method in class org.jmol.viewer.Viewer
 
evaluateFind(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateFunction(int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateGetProperty(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateHelix(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateLabel(int, ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateList(int, ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateLoad(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateMath(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateMeasure(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluatePlane(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluatePoint(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluatePrompt(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateQuaternion(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateRandom(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateReplace(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateRowCol(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateScript(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateSort(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateString(int, ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateSubstructure(ScriptVariable[], int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateSymop(ScriptVariable[], boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateUserFunction(String, ScriptVariable[], int, boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
evaluateVolume(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateWithin(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateWrite(ScriptVariable[]) - Method in class org.jmol.script.ScriptMathProcessor
 
EVDW - Static variable in class org.jmol.minimize.forcefield.ForceField
 
Event - Class in org.jmol.api
 
Event() - Constructor for class org.jmol.api.Event
 
eventNames - Static variable in class org.jmol.multitouch.ActionManagerMT
 
EX - Variable in class org.jmol.quantum.MOCalculation
 
EXACT_OFFSET_FLAG - Static variable in class org.jmol.shape.Labels
 
excludeAtoms(BitSet, boolean) - Method in class org.jmol.viewer.SelectionManager
 
excludeAtoms(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
excludedTriangleCount - Variable in class org.jmol.jvxl.data.JvxlData
 
excludedTriangleCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
excludedVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
excludedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
excludeMaximumSet() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
excludeMinimumSet() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
excludePartialCubes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
excludeSelectionSet(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
execThread - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
execute(String) - Method in class org.jmol.console.AppletConsole
 
execute(String) - Method in class org.jmol.console.JmolConsole
 
execute(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
executeCommand(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
executeCommandAsThread(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
executeScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
executionPaused - Variable in class org.jmol.script.ScriptContext
 
executionPaused - Variable in class org.jmol.script.ScriptEvaluator
 
executionStepping - Variable in class org.jmol.script.ScriptContext
 
executionStepping - Variable in class org.jmol.script.ScriptEvaluator
 
executor - Variable in class org.jmol.viewer.Viewer
 
exit - Static variable in class org.jmol.script.Token
 
exitAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
exitjmol - Static variable in class org.jmol.script.Token
 
exitJmol() - Method in class org.jmol.viewer.Viewer
 
exitMeasurementMode() - Method in class org.jmol.viewer.ActionManager
 
exitUponCompletion - Variable in class org.openscience.jmol.app.JmolApp
 
expdta() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
explicitContours - Variable in class org.jmol.shapesurface.Isosurface
 
explicitID - Variable in class org.jmol.shape.MeshCollection
 
Export3D - Class in org.jmol.export
Provides high-level graphics primitives for 3D graphics export.
Export3D() - Constructor for class org.jmol.export.Export3D
 
EXPORT_CARTESIAN - Static variable in class org.jmol.g3d.Graphics3D
 
EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JmolConstants
 
EXPORT_NOT - Static variable in class org.jmol.g3d.Graphics3D
 
EXPORT_RAYTRACER - Static variable in class org.jmol.g3d.Graphics3D
 
exportAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
exportActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
exportDone(JComponent, Transferable, int) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
exporter - Variable in class org.jmol.export.Export3D
 
exportName - Variable in class org.jmol.export.Export3D
 
exportPass - Variable in class org.jmol.shape.MeshRenderer
 
exportSurface(short) - Method in class org.jmol.shape.MeshRenderer
 
exportType - Variable in class org.jmol.export.___Exporter
 
exportType - Variable in class org.jmol.shape.ShapeRenderer
 
expression - Static variable in class org.jmol.script.Token
 
EXPRESSION_KEY - Static variable in class org.jmol.script.ScriptEvaluator
 
expressionBegin - Static variable in class org.jmol.script.Token
 
expressionEnd - Static variable in class org.jmol.script.Token
 
expressionResult - Variable in class org.jmol.script.ScriptEvaluator
 
extendLadder(int, int) - Method in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
extendRuns(EnumStructure[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
extension - Variable in class org.jmol.export.dialog.Dialog
 
extensions - Variable in class org.jmol.export.dialog.Dialog
 
extents - Variable in class org.jmol.jvxl.readers.JaguarReader
 
externalContainer - Variable in class org.jmol.console.JmolConsole
 
extractCommandOption(String) - Method in class org.jmol.script.ScriptEvaluator
 
extractData(String, int, int, int) - Static method in class org.jmol.util.Parser
 
extractLatticeInfo(String) - Method in class org.jmol.symmetry.HallInfo
 
extractProperty(Object, ScriptVariable[], int) - Static method in class org.jmol.viewer.PropertyManager
 
extractRotationInfo(String, int, char) - Method in class org.jmol.symmetry.HallInfo
 
extractTag(String, String, String, boolean) - Static method in class org.jmol.util.XmlReader
 
extractVectorInfo(String) - Method in class org.jmol.symmetry.HallInfo
 
EY - Variable in class org.jmol.quantum.MOCalculation
 
EZ - Variable in class org.jmol.quantum.MOCalculation
 

F

F_ADDRESS_BITS_PER_WORD - Static variable in class org.jmol.util.FastBitSet
miguel 8 Feb 2010 Below are implementations of bitmap functionality on top of arrays.
F_BIT_INDEX_MASK - Static variable in class org.jmol.util.FastBitSet
 
F_BITS_PER_WORD - Static variable in class org.jmol.util.FastBitSet
 
F_INT_ALL_BITS_SET - Static variable in class org.jmol.util.FastBitSet
 
FACE_COUNT_MAX - Static variable in class org.jmol.shapespecial.Polyhedra
 
facecenteroffset - Static variable in class org.jmol.script.Token
 
faceCenterOffset - Variable in class org.jmol.shapespecial.Polyhedra
 
faceId(int, int, int) - Method in class org.jmol.shapespecial.Polyhedra
 
faceMap - Variable in class org.jmol.shapespecial.DotsRenderer
 
facePoints - Static variable in class org.jmol.util.BoxInfo
 
facePt1 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
 
facePt2 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
 
facePt3 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
 
faces - Variable in class org.jmol.export.MeshData.Data
 
faceVertexesArrays - Static variable in class org.jmol.geodesic.Geodesic
 
faceVertexesIcosahedron - Static variable in class org.jmol.geodesic.Geodesic
 
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
fact1 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
factoredLengths - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
factorType - Variable in class org.jmol.atomdata.RadiusData
 
FALSE - Static variable in class org.jmol.viewer.SelectionManager
 
falsifyMesh() - Method in class org.jmol.shapebio.BioShape
 
falsifyNearbyMesh(int) - Method in class org.jmol.shapebio.BioShape
 
FastBitSet - Class in org.jmol.util
 
FastBitSet() - Constructor for class org.jmol.util.FastBitSet
 
FastBitSet(int) - Constructor for class org.jmol.util.FastBitSet
 
FastBitSet(FastBitSet) - Constructor for class org.jmol.util.FastBitSet
 
fatal(String) - Method in class org.jmol.util.DefaultLogger
 
fatal(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
fatal(String) - Static method in class org.jmol.util.Logger
Writes a log at FATAL level.
fatal(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at FATAL level with detail on exception.
fatal(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at FATAL level.
fatal(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level with detail on exception.
fatalError(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
fc(float) - Static method in class org.jmol.symmetry.SymmetryOperation
 
fc - Variable in class org.openscience.jmol.app.webexport.Molecules
 
fc - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
fc - Variable in class org.openscience.jmol.app.webexport.Test
 
fc - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
fcoord(Tuple3f) - Method in interface org.jmol.api.SymmetryInterface
 
fcoord(Tuple3f) - Method in class org.jmol.symmetry.Symmetry
 
fcoord(Tuple3f) - Static method in class org.jmol.symmetry.SymmetryOperation
 
fd_oldFileName - Variable in class org.jmol.export.JmolFileDropper
 
FD_PROPERTY_INLINE - Static variable in class org.jmol.export.JmolFileDropper
 
fd_propSupport - Variable in class org.jmol.export.JmolFileDropper
 
fdup(String, int, int) - Static method in class org.jmol.util.TextFormat
fdup duplicates p or q formats for formatCheck and the format() function.
ff - Variable in class org.jmol.minimize.forcefield.Calculations
 
ff - Variable in class org.jmol.minimize.Minimizer
 
FF - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
fFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
FFParam - Class in org.jmol.minimize.forcefield
 
FFParam() - Constructor for class org.jmol.minimize.forcefield.FFParam
 
ffParams - Variable in class org.jmol.minimize.forcefield.Calculations
 
ffTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
fid - Variable in class org.jmol.g3d.Font3D
 
fid - Variable in class org.jmol.shape.Text
 
fid - Variable in class org.jmol.shape.UccageRenderer
 
fidPrevious - Variable in class org.jmol.shape.LabelsRenderer
 
fids - Variable in class org.jmol.shape.Labels
 
field - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
fieldCount - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
fieldCount - Variable in class org.jmol.util.CifDataReader
 
fieldOf - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
fieldProperty(int) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
fieldTypes - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
file - Variable in class org.jmol.export.history.HistoryFile
The location of the history file.
file() - Method in class org.jmol.script.ScriptEvaluator
 
file - Static variable in class org.jmol.script.Token
 
file - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
fileButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
FileButton - Variable in class org.openscience.jmol.app.webexport.Test
 
filecachedirectory - Static variable in class org.jmol.script.Token
 
filecaching - Static variable in class org.jmol.script.Token
 
FileChooser - Class in org.jmol.export.dialog
JFileChooser with possibility to fix size and location
FileChooser() - Constructor for class org.jmol.export.dialog.FileChooser
 
fileChooser - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
fileCoordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileDotModel - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
fileField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
fileHasUnitCell - Variable in class org.jmol.popup.SimplePopup
 
fileHeader - Variable in class org.jmol.modelset.ModelLoader
 
fileHeader - Variable in class org.jmol.util.CifDataReader
 
fileIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
fileIndex - Variable in class org.jmol.modelset.Model
 
fileList - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
FileManager - Class in org.jmol.viewer
 
FileManager(Viewer) - Constructor for class org.jmol.viewer.FileManager
 
fileManager - Variable in class org.jmol.viewer.Viewer
 
FileManager.ArrayDataReader - Class in org.jmol.viewer
ArrayDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with String[] arrays without any further adaptation.
FileManager.ArrayDataReader(String[]) - Constructor for class org.jmol.viewer.FileManager.ArrayDataReader
 
FileManager.DataReader - Class in org.jmol.viewer
Just a simple abstract class to join a String reader and a String[] reader under the same BufferedReader umbrella.
FileManager.DataReader(Reader) - Constructor for class org.jmol.viewer.FileManager.DataReader
 
FileManager.DOMReader - Class in org.jmol.viewer
 
FileManager.DOMReader(Object, Map<String, Object>) - Constructor for class org.jmol.viewer.FileManager.DOMReader
 
FileManager.Encoding - Enum in org.jmol.viewer
 
FileManager.Encoding() - Constructor for enum org.jmol.viewer.FileManager.Encoding
 
FileManager.EnumFileStatus - Enum in org.jmol.viewer
 
FileManager.EnumFileStatus(int) - Constructor for enum org.jmol.viewer.FileManager.EnumFileStatus
 
FileManager.FileReader - Class in org.jmol.viewer
 
FileManager.FileReader(String, String, String, String, BufferedReader, Map<String, Object>, boolean) - Constructor for class org.jmol.viewer.FileManager.FileReader
 
FileManager.FilesReader - Class in org.jmol.viewer
open a set of models residing in different files
FileManager.FilesReader(String[], String[], String[], FileManager.DataReader[], Map<String, Object>, boolean) - Constructor for class org.jmol.viewer.FileManager.FilesReader
 
FileManager.StringDataReader - Class in org.jmol.viewer
 
FileManager.StringDataReader(String) - Constructor for class org.jmol.viewer.FileManager.StringDataReader
 
FileManager.VectorDataReader - Class in org.jmol.viewer
VectorDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with Vector arrays without any further adaptation.
FileManager.VectorDataReader(List<String>) - Constructor for class org.jmol.viewer.FileManager.VectorDataReader
 
FileMolOnly - Variable in class org.jmol.popup.SimplePopup
 
fileName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileName - Variable in class org.jmol.atomdata.AtomData
 
filename - Variable in class org.jmol.console.ScriptEditor
 
fileName - Variable in class org.jmol.export.___Exporter
 
fileName - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
fileName - Variable in class org.jmol.jvxl.readers.MsmsReader
 
fileName - Variable in class org.jmol.jvxl.readers.Parameters
 
filename - Variable in class org.jmol.script.ScriptCompiler
 
filename - Variable in class org.jmol.script.ScriptContext
 
filename - Variable in class org.jmol.script.ScriptEvaluator
 
fileName - Variable in class org.jmol.viewer.FileManager
 
fileName - Variable in class org.jmol.viewer.ModelManager
 
fileNameIn - Variable in class org.jmol.viewer.FileManager.FileReader
 
fileOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
FilePreview - Class in org.jmol.export.dialog
File previsualisation before opening
FilePreview(JFileChooser, JmolAdapter, boolean, String) - Constructor for class org.jmol.export.dialog.FilePreview
Constructor
FilePreview.FPPanel - Class in org.jmol.export.dialog
 
FilePreview.FPPanel(JmolAdapter, String) - Constructor for class org.jmol.export.dialog.FilePreview.FPPanel
 
FileReader - Class in org.openscience.jvxl
 
FileReader() - Constructor for class org.openscience.jvxl.FileReader
 
files - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
fileScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
fileType - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
fileTypeIn - Variable in class org.jmol.viewer.FileManager.FileReader
 
fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
FileTyper - Class in org.openscience.jmol.app.jmolpanel
 
FileTyper() - Constructor for class org.openscience.jmol.app.jmolpanel.FileTyper
 
fileTypesIn - Variable in class org.jmol.viewer.FileManager.FilesReader
 
FileUnitOnly - Variable in class org.jmol.popup.SimplePopup
 
fileWriter(File, JList) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
fill - Static variable in class org.jmol.script.Token
 
fillArc - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
 
fillAtomData(AtomData, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
fillAtomData(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
 
fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelCollection
 
fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
 
fillConeSceen(byte, int, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
 
fillConeSceen(byte, int, Point3f, Point3f) - Method in class org.jmol.export.Export3D
 
fillConeSceen(byte, int, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
fillConeScreen(byte, int, Point3i, Point3i, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillConeScreen(short, byte, int, Point3f, Point3f, boolean) - Method in class org.jmol.export.___Exporter
 
fillConeScreen(short, byte, int, Point3f, Point3f, boolean) - Method in class org.jmol.export.__CartesianExporter
 
fillConeScreen(short, byte, int, Point3f, Point3f, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
fillConeScreen(byte, int, Point3i, Point3i, boolean) - Method in class org.jmol.export.Export3D
 
fillConeScreen(byte, int, Point3i, Point3i, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillConicalCylinder(Point3f, Point3f, int, short, byte) - Method in class org.jmol.export.__RayTracerExporter
 
fillConicalCylinder(Point3f, Point3f, int, short, byte) - Method in class org.jmol.export._TachyonExporter
 
fillCsfArray(String, String[], int, Object) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinder(byte, int, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillCylinder(byte, int, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinder(byte, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.shape.SticksRenderer
 
fillCylinderBits(byte, int, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderBits(byte, int, Point3f, Point3f) - Method in class org.jmol.export.Export3D
 
fillCylinderBits(byte, int, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderScreen(byte, int, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderScreen(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.___Exporter
 
fillCylinderScreen(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.__CartesianExporter
 
fillCylinderScreen(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.__RayTracerExporter
 
fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillCylinderScreen(byte, int, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderScreen(byte, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderScreenMad(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.___Exporter
 
fillCylinderScreenMad(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.__CartesianExporter
 
fillCylinderScreenMad(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.__RayTracerExporter
 
fillDataBlock(String[][], int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format
fillDataBlock(String[][], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills an array with a pre-defined number of lines of token data, skipping blank lines in the process
fillEllipsoid(Point3f, Point3f[], int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in interface org.jmol.api.JmolRendererInterface
 
fillEllipsoid(Point3f, Point3f[], short, int, int, int, int, Matrix3f, double[], Matrix4f, Point3i[]) - Method in class org.jmol.export.___Exporter
 
fillEllipsoid(Point3f, Point3f[], short, int, int, int, int, Matrix3f, double[], Matrix4f, Point3i[]) - Method in class org.jmol.export.__CartesianExporter
 
fillEllipsoid(Point3f, Point3f[], short, int, int, int, int, Matrix3f, double[], Matrix4f, Point3i[]) - Method in class org.jmol.export.__RayTracerExporter
 
fillEllipsoid(Point3f, Point3f[], int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.export.Export3D
 
fillEllipsoid(Point3f, Point3f[], int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.g3d.Graphics3D
 
fillFace(short, Point3i, Point3i, Point3i) - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
fillFloatArray(String, int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills a float array with string data from a file
fillFrequencyData(int, int, int, boolean[], boolean, int, int, int[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
Extracts a block of frequency data from a file.
fillHermite(int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillHermite(int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
fillHermite(int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
 
fillOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
fillQuadrilateral(Point3f, Point3f, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
 
fillQuadrilateral(Point3i, short, short, Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
 
fillQuadrilateral(Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.export.Export3D
 
fillQuadrilateral(Point3i, short, short, Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.export.Export3D
 
fillQuadrilateral(Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
fillQuadrilateral(Point3i, short, short, Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.g3d.Graphics3D
 
fillRaster(int, int, boolean, boolean, int) - Method in class org.jmol.g3d.Triangle3D
 
fillRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fills background rectangle for label
fillRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
fills background rectangle for label
fillRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fills background rectangle for label
fillSphere(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphere(int, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphere(int, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphere(short, int, Point3f) - Method in class org.jmol.export.___Exporter
 
fillSphere(short, int, Point3f) - Method in class org.jmol.export.__CartesianExporter
 
fillSphere(short, int, Point3f) - Method in class org.jmol.export.__RayTracerExporter
 
fillSphere(int, int, int, int) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphere(int, Point3i) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphere(int, Point3f) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphere(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSphere(int, Point3i) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSphere(int, Point3f) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(Point3f, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short, float) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(short, Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.export.___Exporter
 
fillTriangle(short, Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.export.__CartesianExporter
 
fillTriangle(short, Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3f, Point3f, Point3f) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short, float) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short, float) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(int, int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangle(Point3i, Point3i, Point3i, boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangle(Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangle(Point3i, Point3i, Point3i, float, boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangle(boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangles - Variable in class org.jmol.shape.Mesh
 
fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filter - Variable in class org.jmol.export.image.PngEncoder
 
filter - Static variable in class org.jmol.script.Token
 
filter1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filter2 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
FILTER_LAST - Static variable in class org.jmol.export.image.PngEncoder
 
FILTER_NONE - Static variable in class org.jmol.export.image.PngEncoder
Constants for filters
FILTER_SUB - Static variable in class org.jmol.export.image.PngEncoder
 
FILTER_UP - Static variable in class org.jmol.export.image.PngEncoder
 
filterAltLoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAtom(Atom, int) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
filterAtom(Atom, int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
filterAtom(Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAtomType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterChain - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterData(boolean, float) - Method in interface org.jmol.api.VolumeDataInterface
 
filterData(boolean, float) - Method in class org.jmol.jvxl.data.VolumeData
 
filterElement - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterEveryNth - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterGroup3 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterIsNot - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
filterMO() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
filterN - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterReject(String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterSub(byte[], int, int) - Method in class org.jmol.export.image.PngEncoder
Perform "sub" filtering on the given row.
filterTokens - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
filterUp(byte[], int, int) - Method in class org.jmol.export.image.PngEncoder
Perform "up" filtering on the given row.
fin() - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
finalize() - Method in class org.jmol.applet.Jmol.MyStatusListener
 
finalize() - Method in class org.jmol.viewer.Viewer
 
finalizeGroupBuild() - Method in class org.jmol.modelset.ModelLoader
 
finalizeHydrogens() - Method in interface org.jmol.api.JmolBioResolver
 
finalizeHydrogens() - Method in class org.jmol.modelsetbio.Resolver
 
finalizeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
finalizeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
finalizeModels(int) - Method in class org.jmol.modelset.ModelLoader
Model numbers are considerably more complicated in Jmol 11.
finalizeOutput() - Method in interface org.jmol.api.JmolRendererInterface
 
finalizeOutput() - Method in class org.jmol.export.___Exporter
 
finalizeOutput() - Method in class org.jmol.export._IdtfExporter
 
finalizeOutput() - Method in class org.jmol.export._ObjExporter
 
finalizeOutput() - Method in class org.jmol.export._PovrayExporter
 
finalizeOutput() - Method in class org.jmol.export.Export3D
 
finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
 
finalizePdbCharges() - Method in class org.jmol.modelsetbio.Resolver
 
finalizePdbMultipleBonds() - Method in class org.jmol.modelsetbio.Resolver
 
finalizeReader() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.more.P2nReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
finalizeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
finalizeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeShapes() - Method in class org.jmol.modelset.ModelLoader
 
finalizeTrajectory(List<Point3f[]>, List<Vector3f[]>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finalizeTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finalizeTransformParameters() - Method in class org.jmol.viewer.TransformManager
 
finalizeTransformParameters() - Method in class org.jmol.viewer.Viewer
 
finalOperations - Variable in class org.jmol.symmetry.SpaceGroup
 
find(String, String, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
find(List<Measurement>, Measurement) - Static method in class org.jmol.modelset.Measurement
 
find - Static variable in class org.jmol.script.Token
 
find(Measurement) - Method in class org.jmol.shape.Measures
 
find(String, String, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
Searches for all matches of a pattern within a SMILES string.
find(String, SmilesSearch, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
 
findAdditionalAxes(int) - Method in class org.jmol.symmetry.PointGroup
 
findApplets(String, String, String, List<String>) - Static method in class org.jmol.applet.JmolAppletRegistry
 
findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
 
findAtomsInRectangle(Rectangle, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
findAtomsInRectangle(Rectangle) - Method in class org.jmol.viewer.Viewer
 
findAxis(Point3f[], int, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
 
findBestFit(int, int[]) - Static method in class org.jmol.util.TempArray
 
findBondDipole(Bond) - Method in class org.jmol.shapespecial.Dipoles
 
findCAxes() - Method in class org.jmol.symmetry.PointGroup
 
findClosest(String) - Method in class org.jmol.i18n.GT
 
findDipole(String) - Method in class org.jmol.shapespecial.Dipoles
 
findDipole(Atom, Atom, boolean) - Method in class org.jmol.shapespecial.Dipoles
 
findDipole(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
findEdge(int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
findElementsPresent() - Method in class org.jmol.modelset.ModelLoader
 
findFrequency(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Have the viewer show a particular frame with frequencies if it can be found.
findHelixes(int[][][], int, BitSet, char[], boolean, boolean, List<Bond>, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
(p.
findHelixes(int, int[][][], int, EnumStructure, int, BitSet, BitSet, char[], boolean, boolean, List<Bond>, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
 
findInversionCenter() - Method in class org.jmol.symmetry.PointGroup
 
findLeftLeaf() - Method in class org.jmol.bspt.CubeIterator
does the work
findMaxRadii() - Method in class org.jmol.modelset.AtomCollection
 
findMinMaxX(int) - Method in class org.jmol.g3d.Cylinder3D
 
findMinMaxY() - Method in class org.jmol.g3d.Cylinder3D
 
findNearestAtom(int, int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
 
findNearestAtomIndex(int, int) - Method in class org.jmol.api.JmolViewer
 
findNearestAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.modelset.AtomCollection
 
findNearestAtomIndex(int, int, BitSet) - Method in class org.jmol.modelset.ModelSet
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.AminoMonomer
 
findNearestAtomIndex(int, int, Atom[], short[], int, BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
findNearestAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.shape.Shape
 
findNearestAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.shapebio.BioShape
 
findNearestAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
 
findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
 
findNearestAtomIndex(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
findNearestLabel(int, int) - Method in class org.jmol.shape.Labels
 
findNearestShapeAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.viewer.ShapeManager
 
findNearestThreePoints(float, float, float[][], int[]) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
 
findNotAttached(int, int[][], int[], int) - Method in class org.jmol.modelset.AtomCollection
 
findPickedBond(int, int, BitSet, Point3f) - Method in class org.jmol.shape.Sticks
 
findPickedObject(int, int, boolean, BitSet) - Method in class org.jmol.shapespecial.Draw
 
findPlanes() - Method in class org.jmol.symmetry.PointGroup
 
findSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
findShorter(int, int[]) - Static method in class org.jmol.util.TempArray
 
findString - Variable in class org.jmol.jvxl.readers.KinemageReader
 
findValue(int, int, boolean, BitSet) - Method in class org.jmol.shapesurface.Isosurface
 
finish() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finish() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
finish(Object) - Method in class org.jmol.api.JmolAdapter
 
first - Variable in class org.jmol.modelset.TickInfo
 
first - Static variable in class org.jmol.script.Token
 
firstAtom - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
 
firstAtomIndex - Variable in class org.jmol.modelset.Group
 
firstAtomIndex - Variable in class org.jmol.modelset.Model
 
firstAtomIndex - Variable in class org.jmol.util.JmolMolecule
 
firstAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
 
firstAtomOffset - Variable in class org.jmol.quantum.QuantumCalculation
 
firstChar - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
firstFrameDelay - Variable in class org.jmol.viewer.AnimationManager
 
firstFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
 
firstIsotope - Static variable in class org.jmol.util.Elements
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
firstLastStep - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
firstMatchOnly - Variable in class org.jmol.smiles.SmilesSearch
 
firstModelIndex - Variable in class org.jmol.atomdata.AtomData
 
firstModelIndex - Variable in class org.jmol.viewer.AnimationManager
Animation support
firstMoleculeIndex - Variable in class org.jmol.modelset.Model
 
firstNearbyAtom - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
firstProper - Static variable in class org.jmol.symmetry.PointGroup
 
firstRealVertex - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
fixBasisLine(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
 
fixChime(String, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
fixChirality(SmilesSearch) - Method in class org.jmol.smiles.SmilesParser
 
fixDataString(String) - Static method in class org.jmol.util.Parser
 
fixed() - Method in class org.jmol.script.ScriptEvaluator
 
fixed - Static variable in class org.jmol.script.Token
 
fixedCount - Variable in class org.jmol.jvxl.readers.PmeshReader
 
fixedOrigin - Variable in class org.jmol.shape.Axes
 
fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
 
fixedRotationCenter - Variable in class org.jmol.export.___Exporter
 
fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
 
fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
 
fixedtemp - Static variable in class org.jmol.script.Token
 
fixedTranslation - Variable in class org.jmol.viewer.TransformManager
 
fixFileName(File) - Method in class org.openscience.chimetojmol.ChimePanel
 
fixFileNames(String, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
fixFileNames(String, String, char) - Method in class org.openscience.chimetojmol.ChimePanel
 
fixFileNameVariables(String, String) - Static method in class org.jmol.viewer.FileManager
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
fixIndices(int, BitSet) - Method in class org.jmol.modelset.Chain
 
fixIndices(int, BitSet) - Method in class org.jmol.modelset.Group
 
fixIndices(int, int, BitSet) - Method in class org.jmol.modelset.Model
 
fixInlineString(String, char) - Method in class org.jmol.viewer.Viewer
 
fixLabel(Atom, String) - Method in class org.jmol.shape.HoverRenderer
 
fixModelSpec(Token) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
fixName(String) - Static method in class org.jmol.util.ColorEncoder
 
fixOrbitalType() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
fixPath(String) - Static method in class org.jmol.viewer.FileManager
 
fixPeriodic(Point3f, Point3f) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
 
fixPoint(float, float) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
 
fixQ(Quaternion) - Method in class org.jmol.util.Quaternion
 
fixScript(String, String) - Method in class org.jmol.popup.SimplePopup
 
fixScriptPath(String, String) - Method in class org.jmol.script.ScriptEvaluator
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
fixSlaterTypes(int, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
fixString(String) - Static method in class org.jmol.util.Escape
 
fixTag(String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Returns a modified identifier for a tag, so that the element can be determined from it in the Atom.
fixText(String) - Method in class org.jmol.shape.Text
 
fixTitleLine(int) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
fixTitleLine(int, Map<String, Object>) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
fixUnicode(String[], int) - Static method in class org.jmol.viewer.FileManager
 
fixUnits(String) - Static method in class org.jmol.modelset.Measurement
 
fixValue(float, String, boolean) - Method in class org.jmol.modelset.Measurement
 
fixXY(float, float, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
FLAG_CANINCREMENT - Static variable in class org.jmol.script.ScriptVariable
 
FLAG_LOCALVAR - Static variable in class org.jmol.script.ScriptVariable
 
FLAG_MASK - Static variable in class org.jmol.modelset.Atom
 
FLAG_OFFSET - Static variable in class org.jmol.shape.Labels
 
flags - Variable in class org.jmol.script.ScriptVariable
 
FLAGS - Static variable in class org.jmol.shape.Labels
 
flat - Static variable in class org.jmol.script.Token
 
FLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
FLICK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
flip(int) - Method in class org.jmol.util.FastBitSet
 
flip(int, int) - Method in class org.jmol.util.FastBitSet
 
flipLighting(int) - Method in class org.jmol.shape.Mesh
 
fList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
flistValue(Token, int) - Static method in class org.jmol.script.ScriptVariable
 
floatArraySet(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
 
floatArraySet(int, int, int, int) - Method in class org.jmol.script.ScriptEvaluator
 
floatparam - Static variable in class org.jmol.script.Token
 
floatParameter(int, float, float) - Method in class org.jmol.script.ScriptEvaluator
 
floatParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
floatParameterSet(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
process a general string or set of parameters as an array of floats, allowing for relatively free form input
floatproperty - Static variable in class org.jmol.script.Token
 
floatRange - Variable in class org.jmol.shapebio.BioShape
 
floatSetting(int) - Method in class org.jmol.script.ScriptEvaluator
 
floatValue() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
flowCommand - Static variable in class org.jmol.script.Token
 
flowContext - Variable in class org.jmol.script.ScriptCompiler
 
flowControl(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
flush(Object) - Static method in class org.jmol.awt.Image
 
flush_char(OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
flushBuffer(BufferedOutputStream) - Method in class org.jmol.util.Huffman
 
flushCaches() - Static method in class org.jmol.g3d.Graphics3D
 
flushImage(Object) - Method in interface org.jmol.api.ApiPlatform
 
flushImage(Object) - Method in class org.jmol.awt.Platform
 
flushQueue(String) - Method in class org.jmol.viewer.ScriptManager
 
flushShades() - Static method in class org.jmol.g3d.Colix3D
 
flushSphereCache() - Static method in class org.jmol.g3d.Sphere3D
 
fmatSuperCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
fmt(int) - Method in class org.jmol.applet.Jmol
 
fmt(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
FoldingXyzReader - Class in org.jmol.adapter.readers.simple
This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.
FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.simple.FoldingXyzReader
 
font - Variable in class org.jmol.applet.AppletWrapper
 
Font - Class in org.jmol.awt
methods required by Jmol that access java.awt.Font private to org.jmol.awt
Font() - Constructor for class org.jmol.awt.Font
 
font - Variable in class org.jmol.g3d.Font3D
 
font(int, float) - Method in class org.jmol.script.ScriptEvaluator
 
font - Static variable in class org.jmol.script.Token
 
font - Variable in class org.jmol.shape.Text
 
Font3D - Class in org.jmol.g3d
Provides font support using a byte fid (Font ID) as an index into font table.
Font3D(ApiPlatform, byte, int, int, float, float, Object) - Constructor for class org.jmol.g3d.Font3D
 
font3d - Variable in class org.jmol.shape.FontLineShapeRenderer
 
font3d - Variable in class org.jmol.shape.FontShape
 
font3d - Variable in class org.jmol.shape.LabelsRenderer
 
font3d - Variable in class org.jmol.shape.Measures
 
font3dCurrent - Variable in class org.jmol.g3d.Graphics3D
 
font3ds - Static variable in class org.jmol.g3d.Font3D
 
FONT_ALLOCATION_UNIT - Static variable in class org.jmol.g3d.Font3D
 
FONT_FACE_MONO - Static variable in class org.jmol.g3d.Font3D
 
FONT_FACE_SANS - Static variable in class org.jmol.g3d.Font3D
 
FONT_FACE_SERIF - Static variable in class org.jmol.g3d.Font3D
 
FONT_STYLE_BOLD - Static variable in class org.jmol.g3d.Font3D
 
FONT_STYLE_BOLDITALIC - Static variable in class org.jmol.g3d.Font3D
 
FONT_STYLE_ITALIC - Static variable in class org.jmol.g3d.Font3D
 
FONT_STYLE_PLAIN - Static variable in class org.jmol.g3d.Font3D
 
fontAscent - Variable in class org.jmol.applet.AppletWrapper
 
fontcaching - Static variable in class org.jmol.script.Token
 
fontCaching - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
fontFace - Static variable in class org.jmol.applet.AppletWrapper
 
fontFace - Variable in class org.jmol.g3d.Font3D
 
FONTFACE - Static variable in class org.jmol.shape.Echo
 
FONTFACE - Static variable in class org.jmol.shape.Hover
 
fontFaces - Static variable in class org.jmol.g3d.Font3D
 
fontHeight - Variable in class org.jmol.applet.AppletWrapper
 
fontkeyCount - Static variable in class org.jmol.g3d.Font3D
 
fontkeys - Static variable in class org.jmol.g3d.Font3D
 
FontLineShape - Class in org.jmol.shape
 
FontLineShape() - Constructor for class org.jmol.shape.FontLineShape
 
FontLineShapeRenderer - Class in org.jmol.shape
 
FontLineShapeRenderer() - Constructor for class org.jmol.shape.FontLineShapeRenderer
 
fontMetrics - Variable in class org.jmol.applet.AppletWrapper
 
fontMetrics - Variable in class org.jmol.g3d.Font3D
 
fontScale - Variable in class org.jmol.shape.Text
 
fontscaling - Static variable in class org.jmol.script.Token
 
fontScaling - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
FontShape - Class in org.jmol.shape
 
FontShape() - Constructor for class org.jmol.shape.FontShape
 
fontSize - Variable in class org.jmol.applet.AppletWrapper
 
fontSize - Variable in class org.jmol.g3d.Font3D
 
fontsize - Static variable in class org.jmol.script.Token
 
FONTSIZE - Static variable in class org.jmol.shape.Echo
 
FONTSIZE - Static variable in class org.jmol.shape.Hover
 
fontSizeDivisor - Static variable in class org.jmol.applet.AppletWrapper
 
fontSizeNominal - Variable in class org.jmol.g3d.Font3D
 
fontStringWidth(Object, String) - Method in interface org.jmol.api.ApiPlatform
 
fontStringWidth(Object, String) - Method in class org.jmol.awt.Platform
 
fontStyle - Variable in class org.jmol.g3d.Font3D
 
FONTSTYLE - Static variable in class org.jmol.shape.Hover
 
fontStyles - Static variable in class org.jmol.g3d.Font3D
 
force - Variable in class org.jmol.minimize.MinAtom
 
forceautobond - Static variable in class org.jmol.script.Token
 
forceAutoBond - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
forceDisplay() - Method in class org.jmol.i18n.GT.Language
 
forceEndIf - Variable in class org.jmol.script.ScriptFlowContext
 
ForceField - Class in org.jmol.minimize.forcefield
 
ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
 
ForceFieldReader - Class in org.jmol.adapter.readers.more
 
ForceFieldReader() - Constructor for class org.jmol.adapter.readers.more.ForceFieldReader
 
ForceFieldUFF - Class in org.jmol.minimize.forcefield
 
ForceFieldUFF() - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
 
forceFlowEnd(Token) - Method in class org.jmol.script.ScriptCompiler
 
forceNoAddHydrogens - Variable in class org.jmol.script.ScriptEvaluator
 
forcePlatformAWT - Static variable in class org.jmol.g3d.Platform3D
 
forcmd - Static variable in class org.jmol.script.Token
 
FORMAL_CHARGE_COLIX_BLUE - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_COLIX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_INDEX_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_INDEX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_MAX - Static variable in class org.jmol.util.Elements
 
FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements
ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
FORMAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JmolConstants
 
formalCharge - Variable in class org.jmol.adapter.smarter.Atom
 
formalcharge - Static variable in class org.jmol.script.Token
 
formalChargeAndFlags - Variable in class org.jmol.modelset.Atom
 
format(float, String, Tuple3f) - Method in class org.jmol.modelset.LabelToken
 
format - Static variable in class org.jmol.script.Token
 
format(float, int, int, boolean, boolean) - Static method in class org.jmol.util.TextFormat
 
format(double, int, int, boolean, boolean, boolean) - Static method in class org.jmol.util.TextFormat
 
format(String, int, int, boolean, boolean) - Static method in class org.jmol.util.TextFormat
 
formatAngle(float) - Method in class org.jmol.modelset.Measurement
 
FormatBox - Variable in class org.openscience.jmol.app.webexport.Molecules
 
FormatBox - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
formatCheck(String) - Static method in class org.jmol.util.TextFormat
formatCheck checks p and q formats and duplicates if necessary "%10.5p xxxx" ==> "%10.5p%10.5p%10.5p xxxx"
formatDecimal(float, int) - Static method in class org.jmol.util.TextFormat
 
formatDistance(String) - Method in class org.jmol.modelset.Measurement
 
formatLabel(Viewer, Atom, String) - Static method in class org.jmol.modelset.LabelToken
 
formatLabel(Viewer, Atom, LabelToken[], char, int[]) - Static method in class org.jmol.modelset.LabelToken
returns a formatted string based on the precompiled label tokens
formatLabel(Viewer, Bond, LabelToken[], Map<String, Object>, int[]) - Static method in class org.jmol.modelset.LabelToken
 
formatLabel(Viewer, Measurement, String, float, String) - Static method in class org.jmol.modelset.LabelToken
 
formatMeasurement(String, String, boolean) - Method in class org.jmol.modelset.Measurement
 
formatMeasurement(String) - Method in class org.jmol.modelset.Measurement
 
formats - Variable in class org.jmol.shape.Labels
 
formatString(float, String, String) - Method in class org.jmol.modelset.Measurement
 
formatString(String, String, String) - Static method in class org.jmol.util.TextFormat
 
formatString(String, String, float) - Static method in class org.jmol.util.TextFormat
 
formatString(String, String, int) - Static method in class org.jmol.util.TextFormat
 
formatString(String, String, String, float, double, boolean) - Static method in class org.jmol.util.TextFormat
generic string formatter based on formatLabel in Atom
formatters - Static variable in class org.jmol.util.TextFormat
 
formatText() - Method in class org.jmol.shape.Text
 
formatText(String) - Method in class org.jmol.viewer.Viewer
 
formattingStrings - Static variable in class org.jmol.util.TextFormat
 
formul() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
formula - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
forPoint3 - Variable in class org.jmol.script.ScriptCompiler
 
forwardDCT(float[][]) - Static method in class org.jmol.util.DCT
 
foundDistance2() - Method in interface org.jmol.api.AtomIndexIterator
 
foundDistance2() - Method in class org.jmol.bspt.CubeIterator
After calling nextElement(), allows one to find out the value of the distance squared.
foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
foundDuringLastSync - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
fourdots - Static variable in class org.jmol.shape.SticksRenderer
 
fp8ShadeIndexUp - Variable in class org.jmol.g3d.Cylinder3D
 
fps - Static variable in class org.jmol.script.Token
 
fps - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
FPS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for the fps slider.
fpsSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
FRACT_X - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
FRACT_Y - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
FRACT_Z - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
fraction(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
fractionalOffset - Variable in class org.jmol.symmetry.UnitCell
 
fractionalPoint - Variable in class org.jmol.script.ScriptEvaluator
 
fractionalrelative - Static variable in class org.jmol.script.Token
 
fractionalRelative - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
fractionData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
fractionData - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
fractionPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
fracx - Static variable in class org.jmol.script.Token
 
fracxyz - Static variable in class org.jmol.script.Token
 
fracy - Static variable in class org.jmol.script.Token
 
fracz - Static variable in class org.jmol.script.Token
 
frame(int) - Method in class org.jmol.script.ScriptEvaluator
 
frame - Static variable in class org.jmol.script.Token
 
frame - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
frame - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
frameControl(int) - Method in class org.jmol.script.ScriptEvaluator
 
frameOffset - Variable in class org.jmol.viewer.TransformManager
 
frameOffsets - Variable in class org.jmol.viewer.TransformManager
 
frameOffsets - Variable in class org.jmol.viewer.Viewer
 
framePointer - Variable in class org.jmol.viewer.AnimationManager.AnimationThread
 
framePointer2 - Variable in class org.jmol.viewer.AnimationManager.AnimationThread
 
FramesOnly - Variable in class org.jmol.popup.SimplePopup
 
frameStep - Variable in class org.jmol.viewer.AnimationManager
 
frameTimeMillis - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
frameTitles - Variable in class org.jmol.modelset.ModelCollection
 
frank(int) - Method in class org.jmol.script.ScriptEvaluator
 
frank - Static variable in class org.jmol.script.Token
 
Frank - Class in org.jmol.shape
 
Frank() - Constructor for class org.jmol.shape.Frank
 
frankAscent - Variable in class org.jmol.shape.Frank
 
frankClicked(int, int) - Method in class org.jmol.viewer.ShapeManager
 
frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
 
frankClickedModelKit(int, int) - Method in class org.jmol.viewer.Viewer
 
frankDescent - Variable in class org.jmol.shape.Frank
 
frankList - Variable in class org.jmol.popup.JmolPopup
 
frankMargin - Static variable in class org.jmol.shape.Frank
 
frankOn - Variable in class org.jmol.viewer.Viewer
 
frankPopup - Variable in class org.jmol.popup.SimplePopup
 
FrankRenderer - Class in org.jmol.shape
 
FrankRenderer() - Constructor for class org.jmol.shape.FrankRenderer
 
frankString - Variable in class org.jmol.shape.Frank
 
frankWidth - Variable in class org.jmol.shape.Frank
 
free_ent - Variable in class org.jmol.export.image.GifEncoder
 
freeBonds - Variable in class org.jmol.modelset.BondCollection
 
freeEnum - Variable in class org.jmol.util.TempArray
 
freeEnumSize - Static variable in class org.jmol.util.TempArray
 
freePoints - Variable in class org.jmol.util.TempArray
 
freePointsSize - Static variable in class org.jmol.util.TempArray
 
freeScreens - Variable in class org.jmol.util.TempArray
 
freeScreensSize - Static variable in class org.jmol.util.TempArray
 
freeTempArrays() - Method in class org.jmol.shapebio.BioShapeRenderer
 
freeTempEnum(EnumStructure[]) - Method in class org.jmol.util.TempArray
 
freeTempEnum(EnumStructure[]) - Method in class org.jmol.viewer.Viewer
 
freeTempPoints(Point3f[]) - Method in class org.jmol.util.TempArray
 
freeTempPoints(Point3f[]) - Method in class org.jmol.viewer.Viewer
 
freeTempScreens(Point3i[]) - Method in class org.jmol.util.TempArray
 
freeTempScreens(Point3i[]) - Method in class org.jmol.viewer.Viewer
 
freeze() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
freeze() - Method in class org.jmol.modelset.ModelLoader
 
freezeModels() - Method in class org.jmol.modelset.ModelCollection
 
freqAtom0 - Variable in class org.jmol.adapter.readers.simple.AmpacReader
 
fReturn - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
from - Static variable in class org.jmol.script.Token
 
FromLinks - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
FromMenu - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
front - Static variable in class org.jmol.script.Token
 
FRONT_FLAG - Static variable in class org.jmol.shape.Labels
 
frontAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
frontedges - Static variable in class org.jmol.script.Token
 
frontlit - Static variable in class org.jmol.script.Token
 
frontonly - Static variable in class org.jmol.script.Token
 
frontOnly - Variable in class org.jmol.shape.Mesh
 
frontOnly - Variable in class org.jmol.shape.MeshRenderer
 
frontOnly - Variable in class org.jmol.shapespecial.PolyhedraRenderer
 
frontonly - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
fset0 - Variable in class org.jmol.shape.UccageRenderer
 
fSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
full - Static variable in class org.jmol.script.Token
 
fullCommand - Variable in class org.jmol.script.ScriptEvaluator
 
fullCommand - Variable in class org.jmol.shapesurface.LcaoCartoon
 
fullCubePolygon - Static variable in class org.jmol.util.TriangleData
 
fullName - Variable in class org.jmol.applet.Jmol
 
fullName - Variable in class org.jmol.viewer.Viewer
 
fullpath - Variable in class org.jmol.script.ScriptContext
 
fullPathName - Variable in class org.jmol.viewer.FileManager
 
fullPathName - Variable in class org.jmol.viewer.ModelManager
 
fullPathNameIn - Variable in class org.jmol.viewer.FileManager.FileReader
 
fullPathNamesIn - Variable in class org.jmol.viewer.FileManager.FilesReader
 
fullplane - Static variable in class org.jmol.script.Token
 
fullTrim(String) - Method in class org.jmol.util.CifDataReader
specially for names that might be multiline
fullyLit - Variable in class org.jmol.jvxl.readers.Parameters
 
fullylit - Static variable in class org.jmol.script.Token
 
func - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
func - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
func - Variable in class org.jmol.jvxl.readers.Parameters
 
function() - Method in class org.jmol.script.ScriptEvaluator
 
function - Variable in class org.jmol.script.ScriptFlowContext
 
function - Static variable in class org.jmol.script.Token
 
functionInfo - Variable in class org.jmol.jvxl.readers.Parameters
 
functionName - Variable in class org.jmol.script.ScriptContext
 
functionName - Variable in class org.jmol.script.ScriptEvaluator
 
functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
for isosurface FUNCTIONXY
functionXY(String, int, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
functionxy - Static variable in class org.jmol.script.Token
 
functionXY(String, int, int) - Method in class org.jmol.viewer.StatusManager
 
functionXY(String, int, int) - Method in class org.jmol.viewer.Viewer
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
functionXY(String, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
this is just a test method for isosurface FUNCTIONXY
functionXYZ(String, int, int, int) - Method in interface org.jmol.api.JmolStatusListener
for isosurface FUNCTIONXYZ
functionXYZ(String, int, int, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
functionxyz - Static variable in class org.jmol.script.Token
 
functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.StatusManager
 
functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.Viewer
 
functionXYZ(String, int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
funcType - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
fux - Static variable in class org.jmol.script.Token
 
fuxyz - Static variable in class org.jmol.script.Token
 
fuy - Static variable in class org.jmol.script.Token
 
fuz - Static variable in class org.jmol.script.Token
 
fValue(Token) - Static method in class org.jmol.script.ScriptVariable
 

G

g3d - Variable in class org.jmol.export.___Exporter
 
g3d - Variable in class org.jmol.export.Export3D
 
g3d - Variable in class org.jmol.g3d.Circle3D
 
g3d - Variable in class org.jmol.g3d.Cylinder3D
 
g3d - Variable in class org.jmol.g3d.Hermite3D
 
g3d - Variable in class org.jmol.g3d.Line3D
 
g3d - Variable in class org.jmol.g3d.Sphere3D
 
g3d - Variable in class org.jmol.g3d.Triangle3D
 
g3d - Variable in class org.jmol.modelset.AtomCollection
 
g3d - Variable in class org.jmol.shape.Object2d
 
g3d - Variable in class org.jmol.shape.Shape
 
g3d - Variable in class org.jmol.shape.ShapeRenderer
 
g3d - Variable in class org.jmol.viewer.ColorManager
 
g3d - Variable in class org.jmol.viewer.ShapeManager
 
g3d - Variable in class org.jmol.viewer.Viewer
 
g_init_bits - Variable in class org.jmol.export.image.GifEncoder
 
GamessReader - Class in org.jmol.adapter.readers.quantum
 
GamessReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessReader
 
gamessUKContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GamessUKReader - Class in org.jmol.adapter.readers.quantum
 
GamessUKReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUKReader
 
gamessUSContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GamessUSReader - Class in org.jmol.adapter.readers.quantum
 
GamessUSReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUSReader
 
gamma - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
gamma - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
gamma - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
gamma - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
gamma - Variable in class org.jmol.jvxl.readers.MapFileReader
 
gamma - Variable in class org.jmol.util.SimpleUnitCell
 
gaussianAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
gaussianContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
gaussianCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
gaussianCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
GaussianDialog - Class in org.openscience.jmol.app.jmolpanel
 
GaussianDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
gaussianDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
 
GaussianReader - Class in org.jmol.adapter.readers.quantum
Reader for Gaussian 94/98/03/09 output files.
GaussianReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianReader
 
gaussians - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
gaussians - Variable in class org.jmol.quantum.MOCalculation
 
GaussianWfnReader - Class in org.jmol.adapter.readers.quantum
Reader for Gaussian Wfn files -- not implemented yet
GaussianWfnReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianWfnReader
 
generalResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
generateAllOperators(HallInfo) - Method in class org.jmol.symmetry.SpaceGroup
 
generateBaseEllipse() - Method in class org.jmol.g3d.Cylinder3D
 
generateBaseEllipsePrecisely(boolean) - Method in class org.jmol.g3d.Cylinder3D
 
generateContourData(boolean, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
generateCube() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoMepReader
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateCube() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
generateOperatorsFromXyzInfo(String) - Method in class org.jmol.symmetry.SpaceGroup
 
generateOutput(String, String[], int, int) - Method in class org.jmol.api.JmolViewer
 
generateOutput(String, Graphics3D, ModelSet, String) - Method in class org.jmol.viewer.RepaintManager
 
generateOutput(String, String[], int, int) - Method in class org.jmol.viewer.Viewer
 
generateRaster(int, int, int, int[], int[], int, Rgb16[]) - Method in class org.jmol.g3d.Triangle3D
 
generateResidueSpecCode(Token) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
generateSolventCavity() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateSolventCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
generateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
GenNBOReader - Class in org.jmol.adapter.readers.quantum
NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold
GenNBOReader() - Constructor for class org.jmol.adapter.readers.quantum.GenNBOReader
 
Geodesic - Class in org.jmol.geodesic
Consolidated Geodesic from dotsRenderer 3/19/07 Bob Hanson Constructs a canonical geodesic sphere of unit radius.
Geodesic() - Constructor for class org.jmol.geodesic.Geodesic
 
geodesicCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
geodesicMap - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
GEOM_BOND_ATOM_SITE_LABEL_1 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
GEOM_BOND_ATOM_SITE_LABEL_2 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
GEOM_BOND_DISTANCE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
geomBondFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
geomOpt - Variable in class org.jmol.adapter.readers.xtal.DmolReader
 
geosurface - Static variable in class org.jmol.script.Token
 
GeoSurface - Class in org.jmol.shapespecial
 
GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
 
GeoSurfaceRenderer - Class in org.jmol.shapespecial
 
GeoSurfaceRenderer() - Constructor for class org.jmol.shapespecial.GeoSurfaceRenderer
 
gestureServer - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
gestureswipefactor - Static variable in class org.jmol.script.Token
 
gestureSwipeFactor - Variable in class org.jmol.viewer.ActionManager
 
get(int) - Method in class org.jmol.util.FastBitSet
 
get(int) - Method in class org.jmol.util.Int2IntHash
 
get(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
get2SidedNormix(Vector3f, BitSet) - Static method in class org.jmol.g3d.Graphics3D
 
get2SidedNormix(Vector3f, BitSet) - Static method in class org.jmol.g3d.Normix3D
 
get3dContour(List<Object>, float, short) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
get3dProjection(Vector3f) - Method in class org.jmol.util.Quaternion
 
get3DStraightness(String, Quaternion, Quaternion) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getAction() - Method in class org.jmol.viewer.ActionManager.Gesture
 
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Fetch the action that was created for the given command.
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
getActionFromName(String) - Static method in class org.jmol.viewer.ActionManager
 
getActionName(int) - Static method in class org.jmol.viewer.ActionManager
 
getActions() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
getActions() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getActions() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
getAdapterName() - Method in class org.jmol.api.JmolAdapter
 
getAdditionalHydrogens(BitSet, boolean, boolean, List<Atom>) - Method in class org.jmol.viewer.Viewer
 
getADPMinMax(boolean) - Method in class org.jmol.modelset.Atom
 
getAlignment(int) - Static method in class org.jmol.shape.Labels
 
getAlignment(int) - Static method in class org.jmol.shape.Object2d
 
getAllAtomInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAllAtomInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAllAxes(Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
getAllBondInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAllBondInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAllChainInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAllChainInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAllCifData() - Method in class org.jmol.util.CifDataReader
reads all Cif Data for a reader defined in the constructor
getAllData() - Method in class org.jmol.util.CompoundDocument
 
getAllData(String, String, Map<String, String>) - Method in class org.jmol.util.CompoundDocument
reads a compound document directory and saves all data in a Hashtable so that the files may be organized later in a different order.
getAllData(String, String) - Method in class org.jmol.util.CompoundDocument
 
getAllData(InputStream, String[], String, String, Map<String, String>) - Static method in class org.jmol.util.ZipUtil
reads a ZIP file and saves all data in a Hashtable so that the files may be organized later in a different order.
getAllInfo() - Method in class org.jmol.shape.Measures
 
getAllInfoAsString() - Method in class org.jmol.shape.Measures
 
getAllowedGestures(int) - Method in class org.jmol.multitouch.ActionManagerMT
 
getAllowedGestures(int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
getAllowedGestures(int) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
getAllowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
 
getAllowGestures() - Method in class org.jmol.viewer.Viewer
 
getAllPolymerInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAllPolymerInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAllProperties(ScriptVariable, String) - Method in class org.jmol.script.ScriptMathProcessor
 
getAllSettings(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getAllSettings(String) - Method in class org.jmol.viewer.Viewer
 
getAlternateLocationID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAlternateLocationID() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAlternateLocationID() - Method in class org.jmol.modelset.Atom
 
getAltLocCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getAltLocIndexInModel(int, char) - Method in class org.jmol.modelset.ModelCollection
 
getAltLocListInModel(int) - Method in class org.jmol.api.JmolViewer
 
getAltLocListInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getAltLocListInModel(int) - Method in class org.jmol.viewer.Viewer
 
getAmbientPercent() - Static method in class org.jmol.g3d.Graphics3D
 
getAminoAcidValenceAndCharge(String, String, int[]) - Static method in class org.jmol.viewer.JmolConstants
returns an array if we have special hybridization or charge
getAnglefromZ() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
 
getAngles() - Method in class org.jmol.minimize.Minimizer
 
getAngleUnits() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getAngleUnitsList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getAnimationDirection() - Method in class org.jmol.viewer.Viewer
 
getAnimationFps() - Method in class org.jmol.api.JmolViewer
 
getAnimationFps() - Method in class org.jmol.viewer.Viewer
 
getAnimationInfo() - Method in class org.jmol.viewer.AnimationManager
 
getAnimationInfo() - Method in class org.jmol.viewer.Viewer
 
getAnimationReplayMode() - Method in class org.jmol.viewer.Viewer
 
getAnisoBorU(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getApiPlatform() - Method in class org.jmol.viewer.Viewer
 
getAppConsole(JmolViewer) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
getAppConsole(JmolViewer) - Method in class org.jmol.console.AppletConsole
don't delete! used by Viewer after it gets the class by name
getAppConsole(JmolViewer) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
don't delete! used by Viewer after it gets the class by name
getAppendNew() - Method in class org.jmol.viewer.Viewer
 
getAppletContext() - Method in class org.jmol.viewer.Viewer
 
getAppletDefs(int, String, StringBuffer, JmolInstance) - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
getAppletDefs(int, String, StringBuffer, JmolInstance) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
getAppletDefs(int, String, StringBuffer, JmolInstance) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getAppletDocumentBase() - Method in class org.jmol.viewer.FileManager
 
getAppletInfo() - Method in class org.jmol.applet.AppletWrapper
 
getAppletInfo() - Method in class org.jmol.applet.Jmol
 
getAppletInfo() - Method in interface org.jmol.applet.WrappedApplet
 
getAppletInfo() - Method in class org.jmol.viewer.Viewer
 
getAppletPath(boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getApplicationInterface(String) - Static method in class org.jmol.api.Interface
 
getApplySymmetryToBonds() - Method in class org.jmol.viewer.Viewer
 
getAppropriateRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getArgb(short) - Static method in class org.jmol.g3d.Colix3D
 
getArgb(short) - Static method in class org.jmol.g3d.Graphics3D
 
getArgb() - Method in class org.jmol.g3d.Rgb16
 
getArgb(float) - Method in class org.jmol.util.ColorEncoder
 
getArgbFromPalette(float, float, float, int) - Method in class org.jmol.util.ColorEncoder
 
getArgbFromString(String) - Static method in class org.jmol.g3d.Graphics3D
accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or [red,green,blue] or a valid JavaScript color
getArgbGreyscale(short) - Static method in class org.jmol.g3d.Colix3D
 
getArgbHbondType(int) - Static method in class org.jmol.util.JmolEdge
 
getArgbParam(int) - Method in class org.jmol.script.ScriptEvaluator
 
getArgbParam(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getArgbParamLast(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getAromaticDottedBondMask() - Method in class org.jmol.shape.SticksRenderer
 
getAscent(Object) - Static method in class org.jmol.awt.Font
 
getAscent() - Method in class org.jmol.g3d.Font3D
 
getAssociatedAtoms() - Method in class org.jmol.modelset.Bond.BondSet
 
getAtom(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtom(int) - Method in class org.jmol.modelset.Chain
 
getAtom(int) - Method in class org.jmol.modelset.Measurement
 
getAtom(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getAtom(int) - Method in class org.jmol.shape.MeasuresRenderer
 
getAtom1() - Method in class org.jmol.modelset.Bond
 
getAtom1() - Method in class org.jmol.smiles.SmilesBond
 
getAtom2() - Method in class org.jmol.modelset.Bond
 
getAtom2() - Method in class org.jmol.smiles.SmilesBond
 
getAtomArgb(int) - Method in class org.jmol.api.JmolViewer
 
getAtomArgb(int) - Method in class org.jmol.viewer.Viewer
 
getAtomBits(int, Object) - Method in class org.jmol.modelset.ModelCollection
general unqualified lookup of atom set type
getAtomBits(int, Object) - Method in class org.jmol.modelset.ModelSet
general lookup for integer type -- from Eval
getAtomBits(int, Object) - Method in class org.jmol.script.ScriptEvaluator
 
getAtomBits(int, Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitSet(ScriptEvaluator, Object) - Static method in class org.jmol.script.ScriptEvaluator
a general method to evaluate a string representing an atom set.
getAtomBitSet(ScriptEvaluator, Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitSetVector(ScriptEvaluator, int, Object) - Static method in class org.jmol.script.ScriptEvaluator
just provides a vector list of atoms in a string-based expression
getAtomBitSetVector(Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.AtomCollection
general unqualified lookup of atom set type
getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.BondCollection
 
getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.ModelCollection
 
getAtomChain(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomChain(int) - Method in class org.jmol.viewer.Viewer
 
getAtomColix(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomCollectionReader(String, String, BufferedReader, Map<String, Object>, int) - Static method in class org.jmol.adapter.smarter.Resolver
the main method for reading files.
getAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
Get the estimated number of atoms contained in the file.
getAtomCount() - Method in class org.jmol.api.JmolViewer
 
getAtomCount() - Method in class org.jmol.modelset.AtomCollection
 
getAtomCount() - Method in class org.jmol.modelset.ModelLoader
 
getAtomCount() - Method in class org.jmol.viewer.Viewer
 
getAtomCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getAtomCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getAtomCountInModel(int) - Method in class org.jmol.viewer.Viewer
 
getAtomDataServer() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getAtomFromOffsetIndex(int) - Method in class org.jmol.modelsetbio.Monomer
 
getAtomGroupQuaternions(BitSet, int, char) - Method in class org.jmol.modelset.ModelCollection
 
getAtomGroupQuaternions(BitSet, int) - Method in class org.jmol.viewer.Viewer
 
getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
 
getAtomicAndIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
 
getAtomicAndIsotopeNumber() - Method in interface org.jmol.util.JmolNode
 
getAtomicCharges() - Method in class org.jmol.modelset.AtomCollection
 
getAtomicCharges() - Method in class org.jmol.viewer.Viewer
 
getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
Returns the atomic mass of the atom.
getAtomicMass(int) - Static method in class org.jmol.util.Elements
 
getAtomicNumber(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
getAtomicPotentials(String, String) - Method in class org.jmol.quantum.MepCalculation
 
getAtomicPotentials(boolean, BitSet, BitSet, String) - Method in class org.jmol.viewer.Viewer
 
getAtomicPropertyState(int, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getAtomicPropertyState(StringBuffer, byte, BitSet, String, float[]) - Method in class org.jmol.modelset.AtomCollection
 
getAtomicPropertyState(StringBuffer, byte, BitSet, String, float[]) - Method in class org.jmol.viewer.Viewer
 
getAtomID() - Method in class org.jmol.modelset.Atom
 
getAtomIdentityInfo(int, Map<String, Object>) - Method in class org.jmol.modelset.ModelCollection
 
getAtomIdentityInfo(int, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
 
getAtomIndex1() - Method in class org.jmol.modelset.Bond
 
getAtomIndex1() - Method in class org.jmol.smiles.SmilesBond
 
getAtomIndex1() - Method in class org.jmol.util.JmolEdge
 
getAtomIndex2() - Method in class org.jmol.modelset.Bond
 
getAtomIndex2() - Method in class org.jmol.smiles.SmilesBond
 
getAtomIndex2() - Method in class org.jmol.util.JmolEdge
 
getAtomIndexFromAtomNumber(int, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getAtomIndexFromAtomNumber(int) - Method in class org.jmol.viewer.Viewer
 
getAtomIndexFromPrimitiveIndex(int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
getAtomIndices(BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getAtomIndices(BitSet) - Method in class org.jmol.viewer.Viewer
 
getAtomInfo(int) - Method in class org.jmol.api.JmolViewer
 
getAtomInfo(int, String) - Method in class org.jmol.modelset.AtomCollection
 
getAtomInfo(int) - Method in class org.jmol.viewer.Viewer
 
getAtomInfoLong(int) - Method in class org.jmol.modelset.ModelCollection
 
getAtomInfoXYZ(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getAtomInfoXYZ(int, boolean) - Method in class org.jmol.viewer.Viewer
 
getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get an AtomIterator for retrieval of all atoms in the file.
getAtomLabel(int) - Method in class org.jmol.modelset.ModelSet
 
getAtomLabel(int, int, int, int, int, boolean, String) - Static method in class org.jmol.smiles.SmilesAtom
 
getAtomList(String) - Method in class org.jmol.minimize.forcefield.Calculations
 
getAtomList(String) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getAtomList(String) - Method in class org.jmol.minimize.forcefield.ForceField
 
getAtomMinMax(BitSet, BitSet[]) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getAtomModelIndex(int) - Method in class org.jmol.api.JmolViewer
 
getAtomModelIndex(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
getAtomName(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
getAtomName() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomName() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomName(int) - Method in class org.jmol.api.JmolViewer
 
getAtomName() - Method in class org.jmol.modelset.Atom
 
getAtomName(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomName() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomName() - Method in interface org.jmol.util.JmolNode
 
getAtomName(int) - Method in class org.jmol.viewer.Viewer
 
getAtomNameIndex(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomNames() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getAtomNumber(int) - Method in class org.jmol.api.JmolViewer
 
getAtomNumber() - Method in class org.jmol.modelset.Atom
 
getAtomNumber(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomNumber(int) - Method in class org.jmol.viewer.Viewer
 
getAtomPicking() - Method in class org.jmol.viewer.Viewer
 
getAtomPickingMode() - Method in class org.jmol.viewer.ActionManager
 
getAtomPoint(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getAtomPoint3f(int) - Method in class org.jmol.api.JmolViewer
 
getAtomPoint3f(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomPoint3f(int) - Method in class org.jmol.viewer.Viewer
 
getAtomPointVector(BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getAtomPointVector(BitSet) - Method in class org.jmol.viewer.Viewer
 
getAtomPropertiesLike(String) - Static method in class org.jmol.script.Token
 
getAtomQuaternion(int) - Method in class org.jmol.viewer.Viewer
 
getAtomRadius(int) - Method in class org.jmol.api.JmolViewer
 
getAtomRadius(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomRadius(int) - Method in class org.jmol.viewer.Viewer
 
getAtomRecordMOL(StringBuffer, int, Atom, Quaternion, Point3f, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getAtomResidueInfo(StringBuffer, Atom) - Static method in class org.jmol.modelset.ModelCollection
 
getAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtoms(BitSet, boolean, boolean, boolean, boolean, boolean, boolean, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getAtomsAndElements(Atom[], BitSet) - Method in class org.jmol.symmetry.PointGroup
 
getAtomsConnected(float, float, int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAtomsConnected(float, float, int, BitSet) - Method in class org.jmol.viewer.Viewer
 
getAtomSequenceCode(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomSequenceCode(int) - Method in class org.jmol.viewer.Viewer
 
getAtomSerial() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomSerial() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomSerialNumberIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the auxiliary information for a particular atomSet.
getAtomSetCenter(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAtomSetCenter(BitSet) - Method in class org.jmol.viewer.Viewer
 
getAtomSetCollection(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Create the AtomSetCollection and return it
getAtomSetCollection(Object) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollection(String, boolean, Map<String, Object>, StringBuffer) - Method in class org.jmol.viewer.Viewer
 
getAtomSetCollectionAuxiliaryInfo() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetCollectionAuxiliaryInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.api.JmolAdapter
Get the auxiliary information for this atomSetCollection.
getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Direct DOM HTML4 page reading; Egon was interested in this at one point.
getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionFromReader(String, String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
all in one -- for TestSmarterJmolAdapter
getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]
getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter
Get the name of the atom set collection, if known.
getAtomSetCollectionOrBufferedReaderFromZip(InputStream, String, String[], Map<String, Object>, boolean, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
A rather complicated means of reading a ZIP file, which could be a single file, or it could be a manifest-organized file, or it could be a Spartan directory.
getAtomSetCollectionOrBufferedReaderFromZip(InputStream, String, String[], Map<String, Object>, boolean, boolean) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionReader(String, String, BufferedReader, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
The primary file or string reader -- returns just the reader now
getAtomSetCollectionReader(String, String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
Read an atomSetCollection object from a bufferedReader and close the reader.
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.api.JmolAdapter
Associate a atomSetCollection object with an array of BufferedReader.
getAtomSetCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter
Get number of atomSets in the file.
getAtomSetIndex() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomSetIndex() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomSetIndex() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
 
getAtomSetName(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the name of an atomSet.
getAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the number identifying each atomSet.
getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.ShapeManager
 
getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.Viewer
 
getAtomSite() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomSite() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomSite() - Method in class org.jmol.modelset.Atom
 
getAtomSite() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomSite() - Method in interface org.jmol.util.JmolNode
 
getAtomsNearSurface(float, String) - Method in class org.jmol.script.ScriptEvaluator
 
getAtomsWithin(float, Point4f) - Method in class org.jmol.modelset.AtomCollection
 
getAtomsWithin(float, Point3f[], BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getAtomsWithin(float, BitSet, boolean, RadiusData) - Method in class org.jmol.modelset.ModelCollection
Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms
getAtomsWithin(float, Point3f, BitSet, int) - Method in class org.jmol.modelset.ModelCollection
 
getAtomsWithin(float, Point3f) - Method in class org.jmol.viewer.Viewer
 
getAtomsWithin(float, Point3f[], BitSet) - Method in class org.jmol.viewer.Viewer
 
getAtomsWithin(float, Point4f) - Method in class org.jmol.viewer.Viewer
 
getAtomsWithin(float, BitSet, boolean, RadiusData) - Method in class org.jmol.viewer.Viewer
 
getAtomSymmetry() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomSymmetry() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomSymmetry() - Method in class org.jmol.modelset.Atom
 
getAtomType() - Method in class org.jmol.modelset.Atom
 
getAtomTypes() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceField
 
getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
getAtomTypes() - Method in class org.jmol.minimize.Minimizer
 
getAtomTypes() - Method in class org.jmol.modelset.AtomCollection
 
getAtomUniqueID1() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapter.BondIterator
 
getAtomUniqueID2() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapter.BondIterator
 
getAtomVdwRadius(int, EnumVdw) - Method in class org.jmol.modelset.AtomCollection
 
getAttached(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getAttributes(Attributes) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
getAttributes(JSObject) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
getAutoBond() - Method in class org.jmol.api.JmolViewer
 
getAutoBond() - Method in class org.jmol.viewer.Viewer
 
getAutoFps() - Method in class org.jmol.viewer.Viewer
 
getAuxiliaryFileData() - Method in class org.jmol.export._IdtfExporter
 
getAuxiliaryFileData() - Method in class org.jmol.export._PovrayExporter
 
getAuxiliaryInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAuxiliaryInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAverageAtomPoint() - Method in class org.jmol.modelset.ModelCollection
 
getAverageAtomPoint() - Method in class org.jmol.viewer.Viewer
 
getAxesForEllipsoid(double[], Vector3f[], float[]) - Static method in class org.jmol.util.Quadric
 
getAxesMode(int) - Static method in enum org.jmol.constant.EnumAxesMode
 
getAxesMode() - Method in class org.jmol.viewer.Viewer
 
getAxesOrientationRasmol() - Method in class org.jmol.api.JmolViewer
 
getAxesOrientationRasmol() - Method in class org.jmol.viewer.Viewer
 
getAxesScale() - Method in class org.jmol.viewer.Viewer
 
getAxisAngle() - Method in class org.jmol.modelset.Measurement
 
getAxisAngle(AxisAngle4f) - Method in class org.jmol.viewer.TransformManager
 
getAxisAngle(AxisAngle4f) - Method in class org.jmol.viewer.Viewer
 
getAxisEndPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getAxisPoint(int, boolean) - Method in class org.jmol.shape.Axes
 
getAxisPoints() - Method in class org.jmol.viewer.Viewer
 
getAxisStartPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
 
getBackgroundArgb() - Method in class org.jmol.viewer.Viewer
 
getBase64(StringBuffer) - Static method in class org.jmol.util.Base64
 
getBase64(byte[]) - Static method in class org.jmol.util.Base64
 
getBasePairBits(String) - Method in class org.jmol.modelset.ModelCollection
 
getBasePairInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getBaseRing6Points(Point3f[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getBboxVertices() - Method in class org.jmol.modelset.ModelCollection
 
getBboxVertices() - Method in class org.jmol.util.BoxInfo
 
getBfactor() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getBfactor() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getBfactor100() - Method in class org.jmol.modelset.Atom
 
getBfactor100Hi() - Method in class org.jmol.modelset.AtomCollection
 
getBfactor100Hi() - Method in class org.jmol.viewer.Viewer
 
getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
 
getBFactors() - Method in class org.jmol.modelset.AtomCollection
 
getBgColixes(short[]) - Method in interface org.jmol.api.JmolRendererInterface
 
getBgColixes(short[]) - Method in class org.jmol.export.Export3D
 
getBgColixes(short[]) - Method in class org.jmol.g3d.Graphics3D
 
getBinaryStringForBytes(byte[]) - Static method in class org.jmol.util.ZipUtil
 
getBindingInfo(String) - Method in class org.jmol.viewer.ActionManager
 
getBindingInfo(String[], String) - Method in class org.jmol.viewer.binding.Binding
 
getBindingInfo(String) - Method in class org.jmol.viewer.Viewer
 
getBindings() - Method in class org.jmol.viewer.binding.Binding
 
getBioPolymer(int) - Method in class org.jmol.modelset.Model
 
getBioPolymer() - Method in class org.jmol.modelsetbio.Monomer
 
getBioPolymerCount() - Method in class org.jmol.modelset.Model
 
getBioPolymerCount() - Method in class org.jmol.modelset.ModelCollection
 
getBioPolymerCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getBioPolymerIndexInModel() - Method in class org.jmol.modelset.Group
 
getBioPolymerIndexInModel() - Method in class org.jmol.modelsetbio.Monomer
 
getBioPolymerLength() - Method in class org.jmol.modelset.Group
 
getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
 
getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
 
getBioSmiles(JmolNode[], int, BitSet, boolean, boolean, String) - Method in class org.jmol.smiles.SmilesGenerator
 
getBioStructureTypeName(boolean) - Method in enum org.jmol.constant.EnumStructure
 
getBioStructureTypeName() - Method in class org.jmol.modelset.Atom
 
getBioStructureTypeName() - Method in class org.jmol.smiles.SmilesAtom
 
getBioStructureTypeName() - Method in interface org.jmol.util.JmolNode
 
getBitSet(ScriptVariable, boolean) - Static method in class org.jmol.script.ScriptVariable
 
getBitsetIdent(BitSet, String, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getBitsetProperty(BitSet, int, Point3f, Point4f, Object, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getBitsetPropertyFloat(BitSet, int, float, float) - Method in class org.jmol.script.ScriptEvaluator
 
getBitsetPropertySelector(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getBitSets(SmilesSearch, boolean, boolean) - Method in class org.jmol.smiles.SmilesSearch
 
getBitSetTrajectories() - Method in class org.jmol.modelset.ModelSet
 
getBitSetTrajectories() - Method in class org.jmol.viewer.Viewer
 
getBond(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBond(Atom) - Method in class org.jmol.modelset.Atom
 
getBond(int) - Method in class org.jmol.smiles.SmilesAtom
Returns the bond at index number.
getBondArgb1(int) - Method in class org.jmol.api.JmolViewer
 
getBondArgb1(int) - Method in class org.jmol.viewer.Viewer
 
getBondArgb2(int) - Method in class org.jmol.api.JmolViewer
 
getBondArgb2(int) - Method in class org.jmol.viewer.Viewer
 
getBondAt(int) - Method in class org.jmol.modelset.BondCollection
 
getBondAtom1(int) - Method in class org.jmol.modelset.BondCollection
 
getBondAtom2(int) - Method in class org.jmol.modelset.BondCollection
 
getBondColix1(int) - Method in class org.jmol.modelset.BondCollection
 
getBondColix2(int) - Method in class org.jmol.modelset.BondCollection
 
getBondCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBondCount() - Method in class org.jmol.api.JmolViewer
 
getBondCount() - Method in class org.jmol.modelset.BondCollection
 
getBondCount() - Method in class org.jmol.modelset.Model
 
getBondCount() - Method in class org.jmol.smiles.SmilesAtom
 
getBondCount() - Method in class org.jmol.viewer.Viewer
For use in setting a for() construct max value
getBondCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getBondCountInModel(int) - Method in class org.jmol.modelset.BondCollection
for general use
getBondCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getBondCountInModel(int) - Method in class org.jmol.viewer.Viewer
from JmolPopup.udateModelSetComputedMenu
getBondDipoles() - Method in class org.jmol.shapespecial.Dipoles
 
getBondedAtomIndex(int) - Method in class org.jmol.modelset.Atom
 
getBondedAtomIndex(int) - Method in class org.jmol.smiles.SmilesAtom
 
getBondedAtomIndex(int) - Method in interface org.jmol.util.JmolNode
 
getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
 
getBondInfo(int) - Method in class org.jmol.modelset.ModelCollection
 
getBondInfo(JmolAdapter, String, Object) - Method in class org.jmol.modelsetbio.Resolver
 
getBondingRadiusFloat(short, int) - Static method in class org.jmol.api.JmolAdapter
 
getBondingRadiusFloat() - Method in class org.jmol.modelset.Atom
 
getBondingRadiusFloat(short, int) - Static method in class org.jmol.util.Elements
 
getBondingRadiusFloat(int, int, short[]) - Static method in class org.jmol.util.Elements
 
getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get a BondIterator for retrieval of all bonds in the file.
getBondIterator(int, BitSet) - Method in class org.jmol.modelset.BondCollection
 
getBondIterator(BitSet) - Method in class org.jmol.modelset.BondCollection
 
getBondLabelValues() - Static method in class org.jmol.modelset.LabelToken
 
getBondList() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBondList(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getBondList(Object) - Method in class org.jmol.api.JmolAdapter
 
getBondModelIndex(int) - Method in class org.jmol.api.JmolViewer
 
getBondModelIndex(int) - Method in class org.jmol.modelset.BondCollection
 
getBondModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
getBondNotTo(SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesAtom
 
getBondOrder(int) - Method in class org.jmol.api.JmolViewer
 
getBondOrder(int) - Method in class org.jmol.modelset.BondCollection
 
getBondOrder(float, float, float, float, float) - Static method in class org.jmol.modelset.BondCollection
 
getBondOrder(int) - Method in class org.jmol.viewer.Viewer
 
getBondOrderFromFloat(float) - Static method in class org.jmol.util.JmolEdge
 
getBondOrderFromString(String) - Static method in class org.jmol.script.ScriptEvaluator
 
getBondOrderFromString(String) - Static method in class org.jmol.util.JmolEdge
 
getBondOrderNameFromOrder(int) - Static method in class org.jmol.util.JmolEdge
 
getBondOrderNumberFromOrder(int) - Static method in class org.jmol.util.JmolEdge
used for formatting labels and in the connect PARTIAL command
getBondOrderString(int) - Static method in class org.jmol.smiles.SmilesBond
 
getBondPicking() - Method in class org.jmol.viewer.Viewer
 
getBondPoint3f1(int) - Method in class org.jmol.api.JmolViewer
 
getBondPoint3f1(int) - Method in class org.jmol.viewer.Viewer
 
getBondPoint3f2(int) - Method in class org.jmol.api.JmolViewer
 
getBondPoint3f2(int) - Method in class org.jmol.viewer.Viewer
 
getBondRadius(int) - Method in class org.jmol.api.JmolViewer
 
getBondRadius(int) - Method in class org.jmol.modelset.BondCollection
 
getBondRadius(int) - Method in class org.jmol.viewer.Viewer
 
getBondRecordMOL(int, StringBuffer, int, int[], boolean) - Method in class org.jmol.modelset.ModelCollection
 
getBonds() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBonds() - Method in class org.jmol.modelset.Atom
 
getBonds() - Method in class org.jmol.modelset.BondCollection
 
getBondSelectionModeOr() - Method in class org.jmol.viewer.Viewer
 
getBondsForSelectedAtoms(BitSet, boolean) - Method in class org.jmol.modelset.BondCollection
 
getBondsForSelectedAtoms(BitSet) - Method in class org.jmol.viewer.Viewer
 
getBondStereochemistry(JmolEdge, JmolNode) - Method in class org.jmol.smiles.SmilesGenerator
Retrieves the saved character based on the index of the bond.
getBondTo(int) - Method in class org.jmol.minimize.MinAtom
 
getBondTo(SmilesAtom) - Method in class org.jmol.smiles.SmilesAtom
if atom is null, return bond TO this atom (bond.getAtom2() == this) otherwise, return bond connecting this atom with that atom
getBondTolerance() - Method in class org.jmol.api.JmolViewer
 
getBondTolerance() - Method in class org.jmol.viewer.Viewer
 
getBondType() - Method in class org.jmol.smiles.SmilesBond
 
getBondTypeFromCode(char) - Static method in class org.jmol.smiles.SmilesBond
 
getBoolean(boolean) - Static method in class org.jmol.script.ScriptVariable
 
getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer
 
getBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
 
getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer
 
getBooleanValue(String, boolean) - Method in class org.jmol.applet.Jmol
 
getBoundBox(ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
 
getBoundBoxCenter() - Method in class org.jmol.api.JmolViewer
 
getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
 
getBoundBoxCenter() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCenterX() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCenterY() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCommand(boolean) - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxCommand(boolean) - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCornerVector() - Method in class org.jmol.api.JmolViewer
 
getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
 
getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxInfo() - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxInfo() - Method in class org.jmol.util.BoxInfo
 
getBoundBoxInfo() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxModels() - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxModels() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxPoints() - Method in class org.jmol.util.BoxInfo
 
getBoundBoxVertices() - Method in class org.jmol.viewer.Viewer
 
getBoundingBox() - Method in class org.jmol.shape.Mesh
 
getBoundingBox() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getBox(int) - Method in class org.jmol.shape.Labels
 
getBoxInfo(BitSet, float) - Method in class org.jmol.modelset.ModelCollection
 
getBoxInfo(BitSet, float) - Method in class org.jmol.viewer.Viewer
 
getBoxVec() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getBranch2dZ(int, int, BitSet, BitSet, Vector3f, Vector3f, Vector3f) - Method in class org.jmol.modelset.ModelLoader
 
getBranchBitSet(JmolNode[], int, BitSet, List<BitSet>, int, boolean, boolean) - Static method in class org.jmol.util.JmolMolecule
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.
getBranchBitSet(int, int) - Method in class org.jmol.viewer.Viewer
 
getBreakableContext(int) - Method in class org.jmol.script.ScriptFlowContext
 
getBrickValue(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
getBridge(int[][][][], int, int, int, int, List<AminoPolymer.Bridge>, Atom, Atom, AminoPolymer, AminoPolymer, List<Bond>, Map<String, Boolean>, boolean, Map<int[][], Boolean>) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
getBridges(Polymer[], int[][][][], List<AminoPolymer.Bridge>, List<AminoPolymer.Bridge>, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, BitSet, List<Bond>, BitSet[]) - Static method in class org.jmol.modelsetbio.AminoPolymer
(p.
getBsIgnore() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getBsOK() - Method in class org.jmol.quantum.NciCalculation
grid-based discrete SCF calculation needs to know which atoms to consider inter and which intramolecular
getBsptCount() - Method in class org.jmol.bspt.Bspf
 
getBsSelected() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getBsSurfaceClone() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getBsVoxels() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getBsVoxels() - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
getBufferedInputStream(String) - Method in interface org.jmol.atomdata.AtomDataServer
 
getBufferedInputStream(String) - Method in class org.jmol.viewer.FileManager
 
getBufferedInputStream(String) - Method in class org.jmol.viewer.Viewer
 
getBufferedReader() - Method in class org.jmol.viewer.FileManager.DataReader
 
getBufferedReaderForString(String) - Static method in class org.jmol.viewer.FileManager
 
getBufferedReaderOrBinaryDocument(int, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
 
getBufferedReaderOrBinaryDocument(int, boolean) - Method in class org.jmol.viewer.FileManager.FilesReader
called by SmartJmolAdapter to request another buffered reader or binary document, rather than opening all the readers at once.
getBufferedReaderOrErrorMessageFromName(String, String[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getBufferedReaderOrErrorMessageFromName(String, String[], boolean) - Method in class org.jmol.viewer.Viewer
 
getBufferedReaderOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
 
getBytes(Image) - Static method in class org.jmol.export.image.GifEncoder
 
getBytes(Image, int) - Static method in class org.jmol.export.image.PngEncoder
 
getBytes(Image, int, int) - Static method in class org.jmol.export.image.PngEncoder
 
getBytes(Image) - Static method in class org.jmol.export.image.PpmEncoder
 
getBytes(ApiPlatform, Object, int, String) - Static method in class org.jmol.util.JpegEncoder
 
getBytes64(byte[]) - Static method in class org.jmol.util.Base64
 
getC1P() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getC2() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getC4P() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getCachedLine() - Method in class org.jmol.g3d.Line3D
 
getCallback(String) - Static method in enum org.jmol.constant.EnumCallback
 
getCameraFactors() - Method in class org.jmol.viewer.TransformManager
This method returns data needed by the VRML, X3D, and IDTF/U3D exporters It also should serve as a valuable resource for anyone adapting Jmol and wanting to know how the Jmol 11+ camera business works.
getCameraFactors() - Method in class org.jmol.viewer.Viewer
 
getCameraPosition() - Method in class org.jmol.export.__CartesianExporter
 
getCanonicalCopy(float) - Method in interface org.jmol.api.SymmetryInterface
 
getCanonicalCopy(float) - Method in class org.jmol.symmetry.Symmetry
 
getCanonicalCopy(float) - Method in class org.jmol.symmetry.UnitCell
 
getCanonicalCopy(float) - Method in class org.jmol.util.BoxInfo
 
getCanonicalCopy(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
 
getCapOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getCapSlabInfo(String) - Method in class org.jmol.shapesurface.Isosurface
 
getCapSlabObject(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getCapSlabObject(String, boolean) - Static method in class org.jmol.util.MeshSurface
legacy -- for some scripts with early isosurface slabbing
getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCarbonylOxygenAtom() - Method in class org.jmol.modelset.Group
 
getCarbonylOxygenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCartesianOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getCartesianOffset() - Method in class org.jmol.symmetry.Symmetry
 
getCartesianOffset() - Method in class org.jmol.symmetry.UnitCell
 
getCartoonBaseEdgesFlag() - Method in class org.jmol.viewer.Viewer
 
getCartoonRocketFlag() - Method in class org.jmol.viewer.Viewer
 
getCellInfos() - Method in class org.jmol.modelset.ModelCollection
 
getCellRange() - Method in interface org.jmol.api.SymmetryInterface
 
getCellRange() - Method in class org.jmol.symmetry.Symmetry
 
getCellTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
getCenter() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getCenterAndPoints(List<BitSet[]>, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getCenterAndPoints(List<Point3f>) - Static method in class org.jmol.util.Measure
 
getCenterAndPoints(List<BitSet[]>, boolean) - Method in class org.jmol.viewer.Viewer
 
getCenters() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getCenterText() - Method in class org.jmol.viewer.TransformManager
 
getChain() - Method in class org.jmol.modelset.Atom
 
getChain(char) - Method in class org.jmol.modelset.Model
 
getChain(int) - Method in class org.jmol.modelset.Model
 
getChainBits(char) - Method in class org.jmol.modelset.AtomCollection
 
getChainCaseSensitive() - Method in class org.jmol.viewer.Viewer
 
getChainCount() - Method in class org.jmol.api.JmolViewer
 
getChainCount(boolean) - Method in class org.jmol.modelset.Model
 
getChainCount(boolean) - Method in class org.jmol.modelset.ModelCollection
 
getChainCount() - Method in class org.jmol.viewer.Viewer
 
getChainCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getChainCountInModel(int, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getChainCountInModel(int) - Method in class org.jmol.viewer.Viewer
 
getChainCountInModel(int, boolean) - Method in class org.jmol.viewer.Viewer
 
getChainID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getChainID() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getChainID() - Method in class org.jmol.modelset.Atom
 
getChainID() - Method in class org.jmol.modelset.Chain
 
getChainID() - Method in class org.jmol.modelset.Group
 
getChainID() - Method in class org.jmol.smiles.SmilesAtom
 
getChainID() - Method in interface org.jmol.util.JmolNode
 
getChainInfo(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getChains() - Method in class org.jmol.modelset.Model
 
getChangeableColix(short, int) - Method in class org.jmol.g3d.Graphics3D
 
getChangeableColixIndex(short) - Static method in class org.jmol.g3d.Graphics3D
 
getChar(String, int) - Static method in class org.jmol.smiles.SmilesParser
 
getCharge() - Method in class org.jmol.smiles.SmilesAtom
Returns the charge of the atom.
getCharges() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getChemicalInfo(String, char) - Method in class org.jmol.viewer.Viewer
 
getChimeInfo(int, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getChimeInfo(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getChimeInfo(int) - Method in class org.jmol.viewer.Viewer
 
getChiralClass() - Method in class org.jmol.smiles.SmilesAtom
Returns the chiral class of the atom.
getChiralityClass(String) - Static method in class org.jmol.smiles.SmilesAtom
 
getChiralOrder() - Method in class org.jmol.smiles.SmilesAtom
Returns the chiral order of the atom.
getCifData(int) - Method in class org.jmol.viewer.Viewer
 
getCifLoopData() - Method in class org.jmol.util.CifDataReader
 
getCircleData() - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a circle.
getCircleResource() - Method in class org.jmol.export._IdtfExporter
 
getClickabilityFlags() - Method in class org.jmol.modelset.Atom
 
getClickableSet() - Method in class org.jmol.modelset.AtomCollection
 
getClickableSet() - Method in class org.jmol.viewer.Viewer
 
getClickCount(int) - Static method in class org.jmol.viewer.binding.Binding
 
getClipboardText() - Method in interface org.jmol.api.JmolImageCreatorInterface
 
getClipboardText() - Method in class org.jmol.export.image.ImageCreator
 
getClipboardText() - Static method in class org.jmol.export.image.ImageSelection
Get the String residing on the clipboard.
getClipboardTextStatic() - Static method in class org.jmol.export.image.ImageCreator
 
getClosestNormal(IsosurfaceMesh, Point3f, Point3f, Vector3f) - Method in class org.jmol.shapesurface.Isosurface
 
getClosestPoint(IsosurfaceMesh, int, Point3f, Point3f, Vector3f) - Method in class org.jmol.shapesurface.Isosurface
 
getCmd(int) - Method in class org.jmol.shapesurface.Isosurface
 
getCmlBondOrder(int) - Static method in class org.jmol.util.JmolEdge
 
getCode() - Method in enum org.jmol.constant.EnumAxesMode
 
getCode() - Method in enum org.jmol.viewer.FileManager.EnumFileStatus
 
getCodeFromName(String) - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
 
getColix(int) - Static method in class org.jmol.g3d.Colix3D
 
getColix(int) - Static method in class org.jmol.g3d.Graphics3D
 
getColix(String) - Static method in class org.jmol.g3d.Graphics3D
 
getColix(Object) - Static method in class org.jmol.g3d.Graphics3D
 
getColix() - Method in class org.jmol.modelset.Atom
 
getColix() - Method in class org.jmol.modelset.Bond
 
getColix() - Method in class org.jmol.modelset.Measurement
 
getColix(short[], int, Atom) - Static method in class org.jmol.shape.Shape
 
getColix(Object) - Method in class org.jmol.viewer.Viewer
 
getColix1() - Method in class org.jmol.modelset.Bond
 
getColix2() - Method in class org.jmol.modelset.Bond
 
getColixArray(String) - Static method in class org.jmol.g3d.Graphics3D
 
getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.ColorManager
 
getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.Viewer
 
getColixBackgroundContrast() - Method in class org.jmol.viewer.Viewer
 
getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.ColorManager
 
getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.Viewer
 
getColixForPropertyValue(float) - Method in class org.jmol.viewer.ColorManager
 
getColixForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
 
getColixInherited(short, short) - Static method in class org.jmol.g3d.Graphics3D
 
getColixRubberband() - Method in class org.jmol.viewer.Viewer
 
getColixTranslucencyFractional(short) - Static method in class org.jmol.g3d.Graphics3D
 
getColixTranslucencyLevel(short) - Static method in class org.jmol.g3d.Graphics3D
 
getColixTranslucent(int) - Static method in class org.jmol.g3d.Graphics3D
 
getColixTranslucent(short, boolean, float) - Static method in class org.jmol.g3d.Graphics3D
 
getCollectionName() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getColor() - Method in enum org.jmol.constant.EnumStructure
 
getColor(String) - Method in class org.jmol.jvxl.readers.KinemageReader
 
getColor(int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getColorArgbOrGray(short) - Method in interface org.jmol.api.JmolRendererInterface
 
getColorArgbOrGray(short) - Method in class org.jmol.export.Export3D
 
getColorArgbOrGray(short) - Method in class org.jmol.g3d.Graphics3D
 
getColorArgbOrGray(short) - Method in class org.jmol.viewer.Viewer
 
getColorCommand(String, short) - Method in class org.jmol.shape.Shape
 
getColorCommand(String, byte, short) - Method in class org.jmol.shape.Shape
 
getColorEncoder() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getColorEncoder(String) - Method in class org.jmol.viewer.ColorManager
 
getColorEncoder(String) - Method in class org.jmol.viewer.Viewer
 
getColorFromName(String) - Method in class org.jmol.applet.AppletWrapper
 
getColorIndex(float) - Method in class org.jmol.util.ColorEncoder
 
getColorIndexFromPalette(float, float, float, int, boolean) - Method in class org.jmol.util.ColorEncoder
 
getColorKey() - Method in class org.jmol.util.ColorEncoder
 
getColorList(int, short[], int, BitSet, Map<Short, Integer>) - Method in class org.jmol.export.___Exporter
input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color index
getColorPhaseIndex(String) - Static method in class org.jmol.jvxl.readers.SurfaceReader
 
getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
 
getColorRange(int) - Method in class org.jmol.script.ScriptEvaluator
 
getColorScheme(String, boolean, boolean) - Method in class org.jmol.util.ColorEncoder
 
getColorScheme() - Method in class org.jmol.util.ColorEncoder
 
getColorSchemeArray(int) - Method in class org.jmol.util.ColorEncoder
 
getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
 
getColorSchemeList(String) - Method in class org.jmol.viewer.ColorManager
 
getColorSchemeList(String) - Method in class org.jmol.viewer.Viewer
 
getColorSchemeName() - Method in class org.jmol.util.ColorEncoder
 
getColorSchemeName(int) - Method in class org.jmol.util.ColorEncoder
 
getColorTriad(int) - Method in class org.jmol.script.ScriptEvaluator
 
getColumnClass(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getColumnCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getColumnName(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getCommand(int, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
used for recall of commands in the application console
getCommand() - Method in class org.jmol.util.CommandHistory
Calculates the command to return.
getCommand() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
getCommandDown() - Method in class org.jmol.util.CommandHistory
Retrieves the following command from the top of the list, updates list position.
getCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Generates a commandline from the options set for povray path etc and sets in the textField.
getCommands(Map<String, BitSet>) - Static method in class org.jmol.viewer.StateManager
 
getCommands(Map<String, BitSet>, Map<String, BitSet>) - Static method in class org.jmol.viewer.StateManager
 
getCommands(Map<String, BitSet>, Map<String, BitSet>, String) - Static method in class org.jmol.viewer.StateManager
 
getCommands(Map<String, BitSet>, StringBuffer, String, String) - Static method in class org.jmol.viewer.StateManager
 
getCommandSet(String) - Static method in class org.jmol.script.Token
retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
getCommandUp() - Method in class org.jmol.util.CommandHistory
Retrieves the following command from the bottom of the list, updates list position.
getCompressionLevel() - Method in class org.jmol.export.image.PngEncoder
Retrieve compression level
getConeData() - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a cone.
getConeMesh(Point3f, Matrix3f, short) - Static method in class org.jmol.export.___Exporter
 
getConeResource() - Method in class org.jmol.export._IdtfExporter
 
getConformation(int, int, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getConformation(BitSet, int) - Method in class org.jmol.modelset.Polymer
 
getConformation(BitSet, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getConformation(Atom[], BitSet, int) - Method in class org.jmol.modelsetbio.Monomer
clear out bits that are not associated with the nth conformation counting for each residue from the beginning of the file listing
getConformation(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
getConnectionPoints() - Method in class org.jmol.shapespecial.DrawRenderer
 
getConstraintList() - Method in class org.jmol.minimize.forcefield.Calculations
 
getContext(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getContextTrace(StringBuffer, boolean) - Method in class org.jmol.script.ScriptContext
 
getContextVariableAsVariable(String) - Method in class org.jmol.script.ScriptEvaluator
 
getContextVariables() - Method in class org.jmol.script.ScriptEvaluator
 
getContextVariables() - Method in class org.jmol.viewer.Viewer
 
getContourList(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getContourPoint(Point3f[], int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
getContourPoint(Point3f[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
getContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
create a set of contour data.
getContourType() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getContourValues() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getContractionNormalization(int, int) - Method in class org.jmol.quantum.MOCalculation
 
getContrastingBlackOrWhite(Color) - Method in class org.jmol.applet.AppletWrapper
 
getControlPoint(int, Vector3f) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
getControlPoint(int, Vector3f) - Method in class org.jmol.modelsetbio.BioPolymer
 
getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
getControlPoints(float) - Method in class org.jmol.modelsetbio.BioPolymer
 
getCoordinateMap(Tuple3f[], int[], BitSet) - Method in class org.jmol.export.__CartesianExporter
 
getCoordinatesAreFractional() - Method in interface org.jmol.api.SymmetryInterface
 
getCoordinatesAreFractional() - Method in class org.jmol.symmetry.Symmetry
 
getCoordinateState(BitSet) - Method in class org.jmol.viewer.Viewer
 
getCorrelationMaps(String, JmolNode[], int, BitSet, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getCorrelationMaps(String, JmolNode[], int, BitSet, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
getCount() - Method in class org.jmol.modelset.Measurement
 
getCountPlusIndices() - Method in class org.jmol.modelset.Measurement
 
getCovalentBondCount() - Method in class org.jmol.modelset.Atom
 
getCovalentBondCount() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of bonds of this atom.
getCovalentBondCount() - Method in interface org.jmol.util.JmolNode
 
getCovalentBondOrder(int) - Static method in class org.jmol.util.JmolEdge
 
getCovalentBondsForAtoms(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getCovalentHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getCovalentHydrogenCount() - Method in interface org.jmol.util.JmolNode
 
getCovalentlyConnectedBitSet(JmolNode[], JmolNode, BitSet, boolean, boolean, List<BitSet>, BitSet) - Static method in class org.jmol.util.JmolMolecule
 
getCovalentOrder() - Method in class org.jmol.modelset.Bond
 
getCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
 
getCovalentOrder() - Method in class org.jmol.util.JmolEdge
 
getCovalentRadiusFloat() - Method in class org.jmol.modelset.Atom
 
getCreatingImage() - Method in class org.jmol.viewer.Viewer
 
getCriticalPoints(Point3f[], Point3f) - Static method in class org.jmol.util.BoxInfo
 
getCrossHairMinMax() - Method in class org.jmol.viewer.ShapeManager
 
getCrossHairMinMax() - Method in class org.jmol.viewer.Viewer
 
getCrossLink(int, List<Integer>) - Method in class org.jmol.modelsetbio.Monomer
 
getCrossLink(int, List<Integer>, Group) - Method in class org.jmol.modelsetbio.Monomer
 
getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.modelset.Atom
 
getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.modelset.Group
 
getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.modelsetbio.Monomer
 
getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.smiles.SmilesAtom
 
getCrossLinkLeadAtomIndexes(List<Integer>) - Method in interface org.jmol.util.JmolNode
 
getCubeIterator(int) - Method in class org.jmol.bspt.Bspf
 
getCurrentAtomSetIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getCurrentBondCount() - Method in class org.jmol.modelset.Atom
 
getCurrentColorRange() - Method in class org.jmol.viewer.Viewer
 
getCurrentFileAsString() - Method in class org.jmol.viewer.Viewer
 
getCurrentModelIndex() - Method in class org.jmol.viewer.Viewer
 
getCurrentSolventProbeRadius() - Method in class org.jmol.viewer.Viewer
 
getCurrentStep() - Method in class org.jmol.minimize.forcefield.ForceField
 
getCurrentUnitCell() - Method in class org.jmol.viewer.Viewer
 
getCurrentX() - Method in class org.jmol.viewer.ActionManager
 
getCurrentY() - Method in class org.jmol.viewer.ActionManager
 
getCursor() - Method in class org.jmol.viewer.Viewer
 
getCursorX() - Method in class org.jmol.viewer.Viewer
 
getCursorY() - Method in class org.jmol.viewer.Viewer
 
getCutoff() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getCylinderData(boolean) - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a cylinder.
getCylinderResource(boolean) - Method in class org.jmol.export._IdtfExporter
 
getData() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
getData(String, String) - Method in class org.jmol.api.JmolViewer
 
getData(Viewer, int, int, BioPolymer, char, char, int, BitSet, BitSet, boolean, boolean, boolean, boolean, boolean, boolean, float, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getData(String) - Method in class org.jmol.script.ScriptCompiler
 
getData() - Method in class org.jmol.util.CifDataReader
general reader for loop data fills loopData with fieldCount fields
getData(String) - Method in class org.jmol.viewer.DataManager
 
getData(String) - Method in class org.jmol.viewer.Viewer
 
getData(String, String) - Method in class org.jmol.viewer.Viewer
 
getDataBlock() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getDataFloat(String) - Method in class org.jmol.viewer.DataManager
 
getDataFloat(String, int) - Method in class org.jmol.viewer.DataManager
 
getDataFloat(String) - Method in class org.jmol.viewer.Viewer
 
getDataFloat(String, int) - Method in class org.jmol.viewer.Viewer
 
getDataFloat2D(String) - Method in class org.jmol.viewer.DataManager
 
getDataFloat2D(String) - Method in class org.jmol.viewer.Viewer
 
getDataFloat3D(String) - Method in class org.jmol.viewer.DataManager
 
getDataFloat3D(String) - Method in class org.jmol.viewer.Viewer
 
getDataSeparator() - Method in class org.jmol.viewer.Viewer
 
getDataState(StringBuffer, StringBuffer, String) - Method in class org.jmol.viewer.DataManager
 
getDE(MinAtom, int, int, double) - Method in class org.jmol.minimize.forcefield.ForceField
 
getDE(float[], int, int, int, int, boolean) - Method in class org.jmol.util.MeshSurface
 
getDebugFooter(int, double) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDebugFooter(int, double) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getDebugLine(int, Calculation) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getDebugScript() - Method in class org.jmol.viewer.Viewer
 
getDef(String) - Method in class org.jmol.export.UseTable
Hashtable htDefs contains references to _n where n is a number.
getDefaultColix() - Method in class org.jmol.shapesurface.Isosurface
 
getDefaultColorRasmol() - Method in class org.jmol.viewer.ColorManager
 
getDefaultCount(int, boolean) - Static method in class org.jmol.smiles.SmilesAtom
 
getDefaultDirectory(String) - Method in class org.jmol.viewer.FileManager
 
getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
 
getDefaultDrawArrowScale() - Method in class org.jmol.viewer.Viewer
 
getDefaultLargePDBRendering(StringBuffer, int) - Method in class org.jmol.modelset.Model
 
getDefaultLattice() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getDefaultLattice() - Method in class org.jmol.viewer.Viewer
 
getDefaultLoadFilter() - Method in class org.jmol.viewer.Viewer
 
getDefaultLoadScript() - Method in class org.jmol.viewer.Viewer
 
getDefaultMadFromOrder(int) - Method in class org.jmol.modelset.BondCollection
When creating a new bond, determine bond diameter from order
getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
 
getDefaultParam(int) - Static method in class org.jmol.viewer.PropertyManager
 
getDefaultRadiusData() - Method in class org.jmol.viewer.Viewer
 
getDefaultState() - Method in class org.jmol.shape.Labels
 
getDefaultStructure(BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
 
getDefaultStructure(BitSet, BitSet) - Method in class org.jmol.viewer.Viewer
 
getDefaultStructureDSSP() - Method in class org.jmol.viewer.Viewer
 
getDefaultTranslucent() - Method in class org.jmol.viewer.Viewer
 
getDefaultVdwNameOrData(int, EnumVdw, BitSet) - Method in class org.jmol.viewer.DataManager
 
getDefaultVdwType(int) - Method in class org.jmol.modelset.ModelCollection
 
getDefaultVdwTypeNameOrData(int, EnumVdw) - Method in class org.jmol.viewer.Viewer
 
getDefinedState(StringBuffer, boolean) - Method in class org.jmol.modelset.ModelSet
 
getDegrees(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
 
getDegrees(int, int) - Method in class org.jmol.viewer.ActionManager
 
getDelayMaximum() - Method in class org.jmol.viewer.Viewer
 
getDeletedAtoms() - Method in class org.jmol.viewer.SelectionManager
 
getDeletedAtoms() - Method in class org.jmol.viewer.Viewer
 
getDepth() - Method in interface org.jmol.api.JmolRendererInterface
gets g3d depth
getDepth() - Method in class org.jmol.export.Export3D
gets g3d depth
getDepth() - Method in class org.jmol.g3d.Graphics3D
gets g3d depth
getDescent(Object) - Static method in class org.jmol.awt.Font
 
getDescent() - Method in class org.jmol.g3d.Font3D
 
getDescription() - Method in class org.jmol.export.dialog.Dialog.TypeFilter
 
getDescription(SymmetryInterface, Point3f, Point3f, String) - Method in class org.jmol.symmetry.SymmetryOperation
 
getDescription(SymmetryOperation, String, SymmetryInterface, Point3f, Point3f, String) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getDfCoefMaps() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getDFMap(String, int, String, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
finds the position in the Jmol-required list of function types.
getDialog() - Method in class org.jmol.export.dialog.FileChooser
 
getDialogs() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getDiameter(int, int) - Method in class org.jmol.shape.FontLineShapeRenderer
 
getDictRefValue(Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
getDiffusePercent() - Static method in class org.jmol.g3d.Graphics3D
 
getDigits(String, int, int[]) - Static method in class org.jmol.smiles.SmilesParser
 
getDimensionValue(Point3f, int) - Static method in class org.jmol.bspt.Node
 
getDimensionValue(int) - Method in class org.jmol.modelset.Atom
 
getDipoleIndex(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
getDipoleIndex(int, int) - Method in class org.jmol.shapespecial.Dipoles
 
getDipoleScale() - Method in class org.jmol.viewer.Viewer
 
getDirectedNormalThroughPoints(Point3f, Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
 
getDirectory() - Method in class org.jmol.util.CompoundDocument
 
getDirectoryListing(String) - Method in class org.jmol.util.CompoundDocument
 
getDirectoryTable() - Method in class org.jmol.util.CompoundDocument
 
getDisablePopupMenu() - Method in class org.jmol.viewer.Viewer
 
getDisplay() - Method in class org.jmol.api.JmolViewer
 
getDisplay() - Method in class org.jmol.viewer.Viewer
 
getDisplayCellParameters() - Method in class org.jmol.viewer.Viewer
 
getDisplayModelIndex() - Method in class org.jmol.api.JmolViewer
 
getDisplayModelIndex() - Method in class org.jmol.viewer.Viewer
 
getDitheredNoisyShadeIndex(float, float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
getDotDensity() - Method in class org.jmol.viewer.Viewer
 
getDoTranslate() - Static method in class org.jmol.i18n.GT
 
getDotScale() - Method in class org.jmol.viewer.Viewer
 
getDotsConvexMaps() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getDotsSelectedOnlyFlag() - Method in class org.jmol.viewer.Viewer
 
getDotSurfaceFlag() - Method in class org.jmol.viewer.Viewer
 
getDouble(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
 
getDragSelected() - Method in class org.jmol.viewer.Viewer
 
getDrawCommand(DrawMesh) - Method in class org.jmol.shapespecial.Draw
 
getDrawCommand(DrawMesh, int) - Method in class org.jmol.shapespecial.Draw
 
getDrawHover() - Method in class org.jmol.viewer.Viewer
 
getDrawObjectAxis(String, int) - Method in class org.jmol.script.ScriptEvaluator
 
getDrawPicking() - Method in class org.jmol.viewer.Viewer
 
getDualHydrogenBondArray(Polymer[], int, boolean) - Static method in class org.jmol.modelsetbio.AminoPolymer
(p.
getDX(int, int) - Method in class org.jmol.viewer.ActionManager.Gesture
 
getDY(int, int) - Method in class org.jmol.viewer.ActionManager.Gesture
 
getDynamicMeasurements() - Method in class org.jmol.viewer.Viewer
 
getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
 
getEchoStateActive() - Method in class org.jmol.viewer.Viewer
 
getEdgeData() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getEdgeData() - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
getEdgePoints(Point3f[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getEdges() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getEdges() - Method in class org.jmol.modelset.Atom
 
getEdges() - Method in class org.jmol.smiles.SmilesAtom
 
getEdges() - Method in interface org.jmol.util.JmolNode
 
getEigenvalues() - Method in class org.jmol.util.Eigen
 
getEigenvectors() - Method in class org.jmol.util.Eigen
 
getEigenvectorsFloatTransposed() - Method in class org.jmol.util.Eigen
transpose V and turn into floats
getElectronDensityLoadInfo() - Method in class org.jmol.viewer.Viewer
 
getElementAndAtomCount(boolean) - Method in class org.jmol.util.JmolMolecule
 
getElementCounts() - Method in class org.jmol.symmetry.PointGroup
 
getElementName(int) - Method in class org.jmol.modelset.AtomCollection
 
getElementNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getElementNumber() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getElementNumber(String) - Static method in class org.jmol.api.JmolAdapter
 
getElementNumber() - Method in class org.jmol.modelset.Atom
 
getElementNumber(int) - Method in class org.jmol.modelset.AtomCollection
 
getElementNumber() - Method in class org.jmol.smiles.SmilesAtom
Returns the atomic number of the element or 0
getElementNumber(short) - Static method in class org.jmol.util.Elements
 
getElementNumber() - Method in interface org.jmol.util.JmolNode
 
getElementNumber(int) - Method in class org.jmol.viewer.Viewer
 
getElementsPresentBitSet(int) - Method in class org.jmol.api.JmolViewer
 
getElementsPresentBitSet(int) - Method in class org.jmol.modelset.ModelCollection
 
getElementsPresentBitSet(int) - Method in class org.jmol.viewer.Viewer
 
getElementSymbol(Atom, String) - Method in class org.jmol.adapter.readers.more.ForceFieldReader
 
getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
 
getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
 
getElementSymbol(boolean) - Method in class org.jmol.modelset.Atom
 
getElementSymbol() - Method in class org.jmol.modelset.Atom
 
getElementSymbol(int) - Method in class org.jmol.modelset.AtomCollection
 
getElementSymbol(int) - Method in class org.jmol.viewer.Viewer
 
getEllipsoid() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getEllipsoid() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getEllipsoid(float[]) - Method in interface org.jmol.api.SymmetryInterface
 
getEllipsoid(Vector3f[], float, float, float) - Method in interface org.jmol.api.SymmetryInterface
 
getEllipsoid() - Method in class org.jmol.modelset.Atom
 
getEllipsoid(int) - Method in class org.jmol.modelset.AtomCollection
 
getEllipsoid(float[]) - Method in class org.jmol.symmetry.Symmetry
 
getEllipsoid(Vector3f[], float, float, float) - Method in class org.jmol.symmetry.Symmetry
 
getEllipsoid(float[]) - Method in class org.jmol.symmetry.UnitCell
 
getEllipsoid(Vector3f[], float, float, float) - Method in class org.jmol.symmetry.UnitCell
 
getEllipsoidShade(float, float, float, int, Matrix4f) - Static method in class org.jmol.g3d.Sphere3D
 
getEmbeddedScript(String) - Static method in class org.jmol.script.ScriptCompiler
 
getEmptySet() - Static method in class org.jmol.util.FastBitSet
 
getEncodeAlpha() - Method in class org.jmol.export.image.PngEncoder
Retrieve alpha encoding status.
getEncodedOrder() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
getEncodedOrder() - Method in class org.jmol.api.JmolAdapter.BondIterator
 
getEncodedVertexData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within element
getEndChainID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getEndChainID() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getEndInsertionCode() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getEndInsertionCode() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getEnergy() - Method in class org.jmol.minimize.forcefield.Calculation
 
getEnergy(int, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergy() - Method in class org.jmol.modelset.Bond
 
getEnergy() - Method in class org.jmol.modelset.HBond
 
getEnergy(double, double, double, double) - Static method in class org.jmol.modelset.HBond
 
getEnergyDiff() - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergyOnly() - Method in class org.jmol.minimize.Minimizer
 
getEquationForQuadricWithCenter(float, float, float, Matrix3f, Vector3f, Matrix3f, double[], Matrix4f) - Static method in class org.jmol.util.Quadric
 
getErrorMessage() - Method in class org.jmol.api.JmolViewer
 
getErrorMessage() - Method in class org.jmol.script.ScriptEvaluator
 
getErrorMessage() - Method in class org.jmol.viewer.Viewer
 
getErrorMessageUntranslated() - Method in class org.jmol.api.JmolViewer
 
getErrorMessageUntranslated() - Method in class org.jmol.script.ScriptEvaluator
 
getErrorMessageUntranslated() - Method in exception org.jmol.script.ScriptEvaluator.ScriptException
 
getErrorMessageUntranslated() - Method in class org.jmol.viewer.Viewer
 
getEventName(int) - Static method in class org.jmol.multitouch.ActionManagerMT
 
getExecutionWalltime() - Method in class org.jmol.script.ScriptEvaluator
 
getExecutor() - Static method in class org.jmol.script.ParallelProcessor
 
getExecutor() - Method in class org.jmol.viewer.Viewer
 
getExitRate() - Method in class org.jmol.multitouch.ActionManagerMT
 
getExitRate() - Method in class org.jmol.viewer.ActionManager
 
getExplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getExplicitNH() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getExportDate() - Static method in class org.jmol.export.___Exporter
 
getExportDriverList() - Method in class org.jmol.viewer.Viewer
 
getExportName() - Method in interface org.jmol.api.JmolRendererInterface
 
getExportName() - Method in class org.jmol.export.Export3D
 
getExportName() - Method in class org.jmol.g3d.Graphics3D
 
getExportType() - Method in interface org.jmol.api.JmolRendererInterface
 
getExportType() - Method in class org.jmol.export.Export3D
 
getExportType() - Method in class org.jmol.g3d.Graphics3D
 
getFacePlane(int, Vector3f) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getFaces() - Method in class org.jmol.export.MeshData.Data
 
getFaces() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getFaces() - Method in class org.jmol.util.MeshSurface
 
getFacesFromCriticalPoints(Point3f[]) - Static method in class org.jmol.util.BoxInfo
 
getFaceVertexes(int) - Static method in class org.jmol.geodesic.Geodesic
 
getFaceVertexesArrays() - Static method in class org.jmol.geodesic.Geodesic
 
getFFParameters() - Method in class org.jmol.minimize.forcefield.ForceField
 
getFFParameters() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
getFile(int) - Method in class org.jmol.console.JmolConsole.FileChecker
 
getFile() - Method in class org.jmol.export.history.HistoryFile
 
getFile() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
getFileAsBytes(String, OutputStream) - Method in class org.jmol.api.JmolViewer
 
getFileAsBytes(String, OutputStream) - Method in class org.jmol.viewer.FileManager
 
getFileAsBytes(String, OutputStream) - Method in class org.jmol.viewer.Viewer
 
getFileAsImage(String, String[]) - Method in class org.jmol.viewer.FileManager
 
getFileAsImage(String, String[]) - Method in class org.jmol.viewer.Viewer
 
getFileAsString(String) - Method in class org.jmol.api.JmolViewer
 
getFileAsString(String[], int, boolean) - Method in class org.jmol.api.JmolViewer
 
getFileAsString(String) - Method in class org.jmol.util.CompoundDocument
 
getFileAsString(CompoundDocument.CmpDocDirectoryEntry, boolean) - Method in class org.jmol.util.CompoundDocument
 
getFileAsString(String) - Method in class org.jmol.viewer.Viewer
 
getFileAsString(String, int, boolean) - Method in class org.jmol.viewer.Viewer
 
getFileAsString(String[], int, boolean) - Method in class org.jmol.viewer.Viewer
 
getFileContents(File) - Method in class org.openscience.chimetojmol.ChimePanel
 
getFileData(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
getFileData(int) - Method in class org.jmol.modelset.ModelSet
 
getFileData() - Method in class org.jmol.viewer.Viewer
 
getFileDataOrErrorAsString(String[], int, boolean) - Method in class org.jmol.viewer.FileManager
 
getFileHeader(int) - Method in class org.jmol.modelset.ModelCollection
 
getFileHeader() - Method in class org.jmol.util.CifDataReader
 
getFileHeader() - Method in class org.jmol.viewer.Viewer
 
getFileInfo() - Method in class org.jmol.viewer.FileManager
 
getFileInfo(Object, String) - Static method in class org.jmol.viewer.PropertyManager
 
getFileInfo() - Method in class org.jmol.viewer.Viewer
 
getFileList() - Method in class org.openscience.chimetojmol.ChimePanel
 
getFileName() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getFileName() - Method in class org.jmol.viewer.FileManager
 
getFileName() - Method in class org.jmol.viewer.Viewer
 
getFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
 
getFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.export.dialog.Dialog
 
getFileNameFromDialog(String, int) - Method in class org.jmol.viewer.Viewer
 
getFilePath(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getFilePath(String, boolean) - Method in class org.jmol.viewer.Viewer
 
getFileReferences(String, List<String>) - Static method in class org.jmol.viewer.FileManager
 
getFiles() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
From SmarterJmolAdapter.getFileTypeName(Object atomSetCollectionOrReader) just return the file type with no exception issues
getFileType() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getFileTypeName() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Just get the resolved file type; if a file, does NOT close the reader
getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
Get the type of this file or molecular model, if known.
getFileTypeName(String) - Method in class org.jmol.viewer.FileManager
 
getFilter() - Method in class org.jmol.export.image.PngEncoder
Retrieve filtering scheme
getFirstAtomIndex(int) - Method in class org.jmol.modelset.ModelLoader
 
getFirstAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getFloat(int, int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
getFloat() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
getFloat() - Method in class org.jmol.jvxl.readers.PmeshReader
 
getFloatEncodedInt(String) - Static method in class org.jmol.script.ScriptEvaluator
Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders.
getFloatShadeIndexNormalized(float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
getFont(float) - Method in class org.jmol.shape.Frank
 
getFont3D(int, int, float, float, Platform3D) - Static method in class org.jmol.g3d.Font3D
 
getFont3D(byte) - Static method in class org.jmol.g3d.Font3D
 
getFont3D(float) - Method in class org.jmol.g3d.Graphics3D
 
getFont3D(String, float) - Method in class org.jmol.g3d.Graphics3D
 
getFont3D(String, String, float) - Method in class org.jmol.g3d.Graphics3D
 
getFont3D(String, String, float) - Method in class org.jmol.viewer.Viewer
 
getFont3DCurrent() - Method in interface org.jmol.api.JmolRendererInterface
 
getFont3DCurrent() - Method in class org.jmol.export.Export3D
 
getFont3DCurrent() - Method in class org.jmol.g3d.Graphics3D
 
getFont3DScaled(Font3D, float) - Method in interface org.jmol.api.JmolRendererInterface
 
getFont3DScaled(Font3D, float) - Method in class org.jmol.export.Export3D
 
getFont3DScaled(Font3D, float) - Method in class org.jmol.g3d.Graphics3D
 
getFontAscent(Object) - Method in interface org.jmol.api.ApiPlatform
 
getFontAscent(Object) - Method in class org.jmol.awt.Platform
 
getFontCaching() - Method in class org.jmol.viewer.Viewer
 
getFontCommand(String, Font3D) - Static method in class org.jmol.shape.Shape
 
getFontDescent(Object) - Method in interface org.jmol.api.ApiPlatform
 
getFontDescent(Object) - Method in class org.jmol.awt.Platform
 
getFontFaceID(String) - Static method in class org.jmol.g3d.Font3D
 
getFontFid(String, float) - Method in interface org.jmol.api.JmolRendererInterface
 
getFontFid(float) - Method in interface org.jmol.api.JmolRendererInterface
 
getFontFid(String, float) - Method in class org.jmol.export.Export3D
 
getFontFid(float) - Method in class org.jmol.export.Export3D
 
getFontFid(float) - Method in class org.jmol.g3d.Graphics3D
 
getFontFid(String, float) - Method in class org.jmol.g3d.Graphics3D
 
getFontMetrics(Object, Object) - Method in interface org.jmol.api.ApiPlatform
 
getFontMetrics(Object, Object) - Static method in class org.jmol.awt.Font
 
getFontMetrics(Object, Object) - Method in class org.jmol.awt.Platform
 
getFontMetrics() - Method in class org.jmol.shape.Text
 
getFontScaling() - Method in class org.jmol.viewer.Viewer
 
getFontStyleID(String) - Static method in class org.jmol.g3d.Font3D
 
getFontStyleID(String) - Static method in class org.jmol.g3d.Graphics3D
 
getForceAutoBond() - Method in class org.jmol.viewer.Viewer
 
getForceField() - Method in class org.jmol.minimize.Minimizer
 
getFormalCharge() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getFormalCharge() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getFormalCharge() - Method in class org.jmol.modelset.Atom
 
getFormalCharge() - Method in class org.jmol.smiles.SmilesAtom
 
getFormalCharge() - Method in interface org.jmol.util.JmolNode
 
getFortranFormatLengths(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
get all integers after letters negative entries are spaces (1Xn)
getFp8ShadeIndex(float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
 
getFractionalCoord(Vector3f) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
getFractionalCoord(char, boolean) - Method in class org.jmol.modelset.Atom
 
getFractionalCoord(boolean) - Method in class org.jmol.modelset.Atom
 
getFractionalOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getFractionalOffset() - Method in class org.jmol.symmetry.Symmetry
 
getFractionalOffset() - Method in class org.jmol.symmetry.UnitCell
 
getFractionalRelative() - Method in class org.jmol.viewer.Viewer
 
getFractionalUnitCoord(char) - Method in class org.jmol.modelset.Atom
 
getFractionalUnitCoord(boolean) - Method in class org.jmol.modelset.Atom
 
getFractionalUnitDistance(Point3f, Point3f, Point3f) - Method in class org.jmol.modelset.Atom
 
getFrame() - Method in interface org.jmol.console.JmolFrame
 
getFrame() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
getFrame() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
getFrame() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getFrameOffsets(BitSet) - Method in class org.jmol.modelset.ModelSet
 
getFrameOffsets() - Method in class org.jmol.viewer.Viewer
 
getFrameTitle(int) - Method in class org.jmol.modelset.ModelCollection
 
getFrameTitle() - Method in class org.jmol.viewer.Viewer
 
getFrontPlane() - Method in class org.jmol.viewer.TransformManager
 
getFrontPlane() - Method in class org.jmol.viewer.Viewer
 
getFullPathName() - Method in class org.jmol.script.ScriptEvaluator
 
getFullPathName() - Method in class org.jmol.viewer.FileManager
 
getFullPathName() - Method in class org.jmol.viewer.Viewer
 
getFullPathNameOrError(String) - Method in class org.jmol.viewer.FileManager
just check for a file as being readable.
getFullPathNameOrError(String) - Method in class org.jmol.viewer.Viewer
 
getFullPDBHeader(int) - Method in class org.jmol.modelset.ModelCollection
 
getFunction(String) - Method in class org.jmol.viewer.StateManager
 
getFunction(String) - Method in class org.jmol.viewer.Viewer
 
getFunctionCalls(String) - Method in class org.jmol.viewer.StateManager
 
getFunctionCalls(String) - Method in class org.jmol.viewer.Viewer
 
getFunctions(boolean) - Method in class org.jmol.viewer.StateManager
 
getFunctionZfromXY() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getGestureType() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
 
getGestureType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
getGhostOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getGlobalSettings(StateManager.GlobalSettings, boolean) - Method in class org.jmol.viewer.StateManager
 
getGlobalSettings() - Method in class org.jmol.viewer.Viewer
 
getGraphics(Object) - Method in interface org.jmol.api.ApiPlatform
 
getGraphics(Object) - Static method in class org.jmol.awt.Image
 
getGraphics(Object) - Method in class org.jmol.awt.Platform
 
getGraphics(Object) - Method in class org.jmol.g3d.Platform3D
 
getGraphics3D() - Method in class org.jmol.viewer.Viewer
 
getGreyscaleRendering() - Method in class org.jmol.viewer.Viewer
 
getGroup() - Method in class org.jmol.modelset.Atom
 
getGroup(int) - Method in class org.jmol.modelset.Chain
 
getGroup1(char) - Method in class org.jmol.modelset.Atom
 
getGroup1() - Method in class org.jmol.modelset.Group
 
getGroup1(char) - Method in class org.jmol.smiles.SmilesAtom
 
getGroup1(char) - Method in interface org.jmol.util.JmolNode
 
getGroup3() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getGroup3() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getGroup3(boolean) - Method in class org.jmol.modelset.Atom
 
getGroup3() - Method in class org.jmol.modelset.Group
 
getGroup3(short) - Static method in class org.jmol.modelset.Group
 
getGroup3(int) - Method in class org.jmol.modelset.ModelLoader
 
getGroup3(boolean) - Method in class org.jmol.smiles.SmilesAtom
 
getGroup3(boolean) - Method in interface org.jmol.util.JmolNode
 
getGroup3List() - Static method in class org.jmol.viewer.JmolConstants
 
getGroup3Pt(String) - Static method in class org.jmol.viewer.JmolConstants
 
getGroupAtom(Atom, int, String) - Method in class org.jmol.modelset.ModelCollection
 
getGroupBits(BitSet) - Method in class org.jmol.modelset.Atom
 
getGroupBits(BitSet) - Method in class org.jmol.smiles.SmilesAtom
 
getGroupBits(BitSet) - Method in interface org.jmol.util.JmolNode
 
getGroupCount() - Method in class org.jmol.api.JmolViewer
 
getGroupCount() - Method in class org.jmol.modelset.Chain
 
getGroupCount(boolean) - Method in class org.jmol.modelset.Model
 
getGroupCount() - Method in class org.jmol.modelset.Model
 
getGroupCount() - Method in class org.jmol.modelset.ModelCollection
 
getGroupCount() - Method in class org.jmol.viewer.Viewer
 
getGroupCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getGroupCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getGroupCountInModel(int) - Method in class org.jmol.viewer.Viewer
 
getGroupID() - Method in class org.jmol.modelset.Atom
 
getGroupID() - Method in class org.jmol.modelset.Group
 
getGroupID(String) - Static method in class org.jmol.modelset.Group
 
getGroupID(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
 
getGroupID(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
getGroupID(Location) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
getGroupIndex() - Method in class org.jmol.modelset.Atom
 
getGroupIndex() - Method in class org.jmol.modelset.Group
 
getGroupInfo(int) - Method in class org.jmol.modelset.Group
 
getGroupParameter(int) - Method in class org.jmol.modelset.Atom
 
getGroupParameter(int) - Method in class org.jmol.modelset.Group
 
getGroups() - Method in class org.jmol.modelset.ModelCollection
In versions earlier than 12.1.51, groups[] was a field of ModelCollection.
getGroups() - Method in class org.jmol.modelset.Polymer
 
getGroups() - Method in class org.jmol.modelsetbio.BioPolymer
 
getGroupsWithin(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getGroupsWithin(int, BitSet) - Method in class org.jmol.viewer.Viewer
 
getGzippedBytesAsString(byte[]) - Static method in class org.jmol.util.ZipUtil
 
getGzippedInputStream(byte[]) - Static method in class org.jmol.util.ZipUtil
 
getHallLatticeEquivalent(int) - Static method in class org.jmol.symmetry.Translation
 
getHandedness(JmolNode, JmolNode, JmolNode, JmolNode, SmilesSearch.VTemp) - Static method in class org.jmol.smiles.SmilesSearch
compares the
getHash(int) - Method in class org.jmol.script.ScriptEvaluator
 
getHaveStraightness() - Method in class org.jmol.modelset.AtomCollection
 
getHbondsAngleMin() - Method in class org.jmol.viewer.Viewer
 
getHbondsBackbone() - Method in class org.jmol.viewer.Viewer
 
getHbondsDistanceMax() - Method in class org.jmol.viewer.Viewer
 
getHbondsRasmol() - Method in class org.jmol.viewer.Viewer
 
getHbondsSolid() - Method in class org.jmol.viewer.Viewer
 
getHeader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getHeader(int) - Method in class org.jmol.adapter.smarter.LimitedLineReader
 
getHeader() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getHeight(Object) - Static method in class org.jmol.awt.Image
 
getHeight() - Method in class org.jmol.g3d.Font3D
 
getHeightUnitVector() - Method in class org.jmol.modelsetbio.Sheet
 
getHelixData(BitSet, int) - Method in class org.jmol.modelset.AtomCollection
 
getHelixData(int, char, int) - Method in class org.jmol.modelset.Group
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getHelixData(BitSet, int) - Method in class org.jmol.viewer.Viewer
 
getHelixData2(int, char, int) - Method in class org.jmol.modelsetbio.Monomer
 
getHelixStep() - Method in class org.jmol.viewer.Viewer
 
getHelixType(int) - Static method in class org.jmol.adapter.smarter.Structure
 
getHelp(String) - Method in class org.jmol.viewer.Viewer
 
getHermiteLevel() - Method in class org.jmol.viewer.Viewer
 
getHermiteList(int, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f[], int, int) - Static method in class org.jmol.g3d.Graphics3D
 
getHermiteList(int, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f[], int, int) - Static method in class org.jmol.g3d.Hermite3D
 
getHeteroList(int) - Method in class org.jmol.api.JmolViewer
 
getHeteroList(int) - Method in class org.jmol.modelset.ModelCollection
 
getHeteroList(int) - Method in class org.jmol.viewer.Viewer
 
getHexCode(short) - Static method in class org.jmol.g3d.Graphics3D
 
getHexCodes(short[]) - Static method in class org.jmol.g3d.Graphics3D
 
getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
 
getHexitValue(char) - Static method in class org.jmol.util.Escape
 
getHiddenSet() - Method in class org.jmol.viewer.SelectionManager
 
getHiddenSet() - Method in class org.jmol.viewer.Viewer
 
getHideNameInPopup() - Method in class org.jmol.viewer.Viewer
 
getHideNotSelected() - Method in class org.jmol.viewer.SelectionManager
 
getHighestOrder() - Method in class org.jmol.symmetry.PointGroup
 
getHighResolution() - Method in class org.jmol.viewer.Viewer
 
getHklPlane(Point3f) - Method in class org.jmol.script.ScriptEvaluator
 
getHoverDelay() - Method in class org.jmol.viewer.Viewer
 
getHtmlName() - Method in class org.jmol.viewer.Viewer
 
getHtmlResource(Object, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getHybridizationAndAxes(int, int, Vector3f, Vector3f, String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getHybridizationAndAxes(int, Vector3f, Vector3f, String) - Method in class org.jmol.viewer.Viewer
 
getHybridizationAndAxesD(int, Vector3f, Vector3f, String) - Method in class org.jmol.modelset.AtomCollection
dsp3 (trigonal bipyramidal, see-saw, T-shaped) or d2sp3 (square planar, square pyramidal, octahedral)
getHydrogenAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getHydrogenAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getHydrogenAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
Get the hydrogen atom count -- for ligand files
getHydrogens(JmolNode, BitSet) - Method in class org.jmol.smiles.SmilesSearch
 
getHydrophobicity() - Method in class org.jmol.modelset.Atom
 
getHydrophobicity() - Method in class org.jmol.modelset.AtomCollection
 
getHydrophobicity(int) - Static method in class org.jmol.util.Elements
 
getIAddGridPoints() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getIcon(String) - Method in class org.jmol.modelkit.ModelKitPopup
 
getIcon(String) - Method in class org.jmol.popup.SimplePopup
 
getIcon(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getIconX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getId() - Method in enum org.jmol.constant.EnumStructure
 
getId(Object) - Method in class org.jmol.popup.SimplePopup
 
getID(String, int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
getId(int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getIdentifierOrNull(String) - Method in class org.jmol.modelset.AtomCollection
overhauled by RMH Nov 1, 2006.
getIdentity() - Method in class org.jmol.minimize.MinAtom
 
getIdentity(boolean) - Method in class org.jmol.modelset.Atom
 
getIdentity() - Method in class org.jmol.modelset.Bond
 
getIdentityXYZ(boolean) - Method in class org.jmol.modelset.Atom
 
getImage(boolean) - Method in class org.jmol.viewer.Viewer
 
getImageAs(String, int, int, int, String, OutputStream) - Method in class org.jmol.api.JmolViewer
 
getImageAs(String, int, int, int, String, OutputStream) - Method in class org.jmol.viewer.Viewer
 
getImageAs(String, int, int, int, String, OutputStream, String) - Method in class org.jmol.viewer.Viewer
 
getImageBytes(String, int, String, Object, OutputStream) - Method in interface org.jmol.api.JmolImageCreatorInterface
 
getImageBytes(String, int, String, Object, OutputStream) - Method in class org.jmol.export.image.ImageCreator
 
getImageFileNameFromDialog(JmolViewer, String, String, String[], String[], int, int) - Method in interface org.jmol.api.JmolDialogInterface
 
getImageFileNameFromDialog(JmolViewer, String, String, String[], String[], int, int) - Method in class org.jmol.export.dialog.Dialog
 
getImageFontScaling() - Method in class org.jmol.viewer.Viewer
 
getImageHeight(Object) - Method in interface org.jmol.api.ApiPlatform
 
getImageHeight(Object) - Method in class org.jmol.awt.Platform
 
getImageWidth(Object) - Method in interface org.jmol.api.ApiPlatform
 
getImageWidth(Object) - Method in class org.jmol.awt.Platform
 
getImplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getImplicitHydrogenCount(Atom) - Method in class org.jmol.modelset.AtomCollection
 
getImplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getImplicitHydrogenCount() - Method in interface org.jmol.util.JmolNode
 
getIndex() - Method in class org.jmol.modelset.Atom
 
getIndex() - Method in class org.jmol.modelset.Measurement
 
getIndex(char, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getIndex(Monomer) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getIndex() - Method in class org.jmol.smiles.SmilesAtom
Returns the atom index of the atom.
getIndex() - Method in interface org.jmol.util.JmolNode
 
getIndexFromName(String) - Method in class org.jmol.shape.MeshCollection
 
getIndexFromName(String) - Method in class org.jmol.shape.Shape
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Dipoles
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Ellipsoids
 
getIndexOf(int) - Method in class org.jmol.modelset.MeasurementPending
 
getInfo() - Method in class org.jmol.modelset.Atom
 
getInfo(Map<String, Object>) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getInfo(int) - Method in class org.jmol.shape.Measures
 
getInfo() - Method in class org.jmol.shape.Mesh
 
getInfo(int, boolean, boolean, String, int, float) - Method in class org.jmol.symmetry.PointGroup
 
getInfo(String, SymmetryInterface) - Static method in class org.jmol.symmetry.SpaceGroup
 
getInfo() - Method in class org.jmol.util.Quaternion
 
getInfo(int) - Method in class org.jmol.util.SimpleUnitCell
 
getInfoAsString(String) - Method in class org.jmol.modelset.Measurement
 
getInfoAsString(int) - Method in class org.jmol.shape.Measures
 
getInfoHeight() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInfoWidth() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInfoXYZ(boolean) - Method in class org.jmol.modelset.Atom
 
getINI() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Save INI file
getInitiatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getInitiatorAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getInitiatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
 
getInlineChar() - Method in class org.jmol.viewer.Viewer
 
getInlineData(int) - Method in class org.jmol.modelset.ModelCollection
 
getInlineData(StringBuffer, String, boolean, String) - Static method in class org.jmol.viewer.DataManager
 
getInlineData(StringBuffer, String, boolean) - Static method in class org.jmol.viewer.Viewer
 
getInMotion() - Method in class org.jmol.viewer.Viewer
 
getInputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
getInputStreamOrErrorMessageFromName(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getInputStreamOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
 
getInputStreamOrPost(String, boolean, byte[], boolean, URL, String) - Static method in class org.jmol.viewer.FileManager
 
getInsertionCode() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getInsertionCode() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getInsertionCode() - Method in class org.jmol.modelset.Atom
 
getInsertionCode() - Method in class org.jmol.modelset.Group
 
getInsertionCode(int) - Static method in class org.jmol.modelset.Group
 
getInsertionCodeIndexInModel(int, char) - Method in class org.jmol.modelset.ModelCollection
 
getInsertionCodeValue(int) - Static method in class org.jmol.modelset.Group
 
getInsertionCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getInsertionListInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getInstance() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getInstance(JmolViewer, String, int, int, int) - Static method in class org.openscience.jmol.app.webexport.JmolInstance
 
getInstanceList() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInstanceName(int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInt() - Method in class org.jmol.jvxl.readers.PmeshReader
 
getInt(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
 
getInterface(String) - Static method in class org.jmol.api.Interface
 
getInterruptScript() - Method in class org.jmol.viewer.Viewer
 
getIntersection(Point4f, Point4f) - Static method in class org.jmol.util.Measure
 
getIntersection(Point3f, Vector3f, Point4f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
 
getIntersection(float, Point4f, Point3f[], List<Point3f[]>, float[], MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSurface
 
getInverseNormix(short) - Static method in class org.jmol.g3d.Graphics3D
 
getInverseNormix(short) - Static method in class org.jmol.g3d.Normix3D
 
getIonicRadii() - Method in class org.jmol.modelset.AtomCollection
 
getIsHetero() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getIsHetero() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getIsosurfaceDataRange(int, String) - Method in class org.jmol.script.ScriptEvaluator
 
getIsosurfaceJvxl(boolean, int) - Method in class org.jmol.script.ScriptEvaluator
 
getIsosurfaceKey() - Method in class org.jmol.viewer.Viewer
 
getIsosurfacePropertySmoothing(boolean) - Method in class org.jmol.viewer.Viewer
 
getIsotopeNumber() - Method in class org.jmol.modelset.Atom
 
getIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
 
getIsotopeNumber(short) - Static method in class org.jmol.util.Elements
 
getIsotopeNumber() - Method in interface org.jmol.util.JmolNode
 
getIsPositiveOnly() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getItem(int) - Static method in enum org.jmol.constant.EnumQuantumShell
 
getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelCollection
only some models can be iterated through.
getJavaConsole(Jmol) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
Each Widget must implement this function and make sure to use the appletID number to specify the target applet i.e.
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
A COPY OF THIS .JS FILE MUST BE STORED IN THE html PART OF WEBEXPORT
getJavaVendor() - Method in class org.jmol.api.JmolViewer
 
getJavaVendor() - Method in class org.jmol.viewer.Viewer
 
getJavaVersion() - Method in class org.jmol.api.JmolViewer
 
getJavaVersion() - Method in class org.jmol.viewer.Viewer
 
getJbr() - Method in class org.jmol.modelset.ModelCollection
 
getJMenu() - Method in interface org.jmol.api.JmolPopupInterface
 
getJMenu() - Method in class org.jmol.popup.JmolPopup
 
getJmol(JFrame, int, int, String) - Static method in class org.openscience.jmol.app.Jmol
 
getJmol(int, int, String) - Static method in class org.openscience.jmol.app.JmolData
 
getJmol(JmolApp, JFrame) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getJmolAtom(int) - Method in class org.jmol.smiles.SmilesSearch
 
getJmolDataFrameIndex(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getJmolDataFrameIndex(int, String) - Method in class org.jmol.viewer.Viewer
 
getJmolDataSourceFrame(int) - Method in class org.jmol.modelset.ModelCollection
 
getJmolDataSourceFrame(int) - Method in class org.jmol.viewer.Viewer
 
getJmolFrameType(int) - Method in class org.jmol.modelset.ModelCollection
 
getJmolFrameType(int) - Method in class org.jmol.viewer.Viewer
 
getJmolOrRasmolArgb(int, int) - Method in class org.jmol.viewer.ColorManager
 
getJmolPerspective() - Method in class org.jmol.export.___Exporter
 
getJmolValue(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
getJmolVersion() - Static method in class org.jmol.api.JmolViewer
 
getJmolVersion() - Static method in class org.jmol.viewer.Viewer
 
getJmolVersionInt() - Static method in class org.jmol.viewer.StateManager
 
getJones() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
getJpgImage(Viewer, int, String) - Method in interface org.jmol.api.ApiPlatform
used for JPG writing only; can be ignored
getJpgImage(ApiPlatform, Viewer, int, String) - Static method in class org.jmol.awt.Image
 
getJpgImage(Viewer, int, String) - Method in class org.jmol.awt.Platform
 
getJSliderLabelTable(JSlider) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
getJSONArray(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
 
getJustifyMeasurements() - Method in class org.jmol.viewer.Viewer
 
getJvxlData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
GetKey - Interface in org.jmol.console
 
getKey() - Method in interface org.jmol.console.GetKey
 
getKey() - Method in class org.jmol.console.KeyJCheckBox
 
getKey() - Method in class org.jmol.console.KeyJCheckBoxMenuItem
 
getKey() - Method in class org.jmol.console.KeyJMenu
 
getKey() - Method in class org.jmol.console.KeyJMenuItem
 
getKey(Object) - Static method in class org.jmol.console.KeyJMenuItem
 
getKey() - Method in class org.jmol.console.KeyJRadioButtonMenuItem
 
getKey(int) - Static method in class org.jmol.export.image.GifEncoder
 
getLabel(String) - Method in class org.jmol.console.JmolConsole
 
getLabel(LabelToken[]) - Static method in class org.jmol.modelset.LabelToken
 
getLabel(int, boolean, boolean) - Method in class org.jmol.modelset.Measurement
 
getLabel(int) - Method in class org.jmol.shape.Labels
 
getLabel() - Method in class org.jmol.symmetry.PointGroup.Operation
 
getLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getLabelString() - Method in class org.jmol.modelset.Measurement
 
getLabelWithoutMnemonic(String) - Static method in class org.jmol.console.KeyJMenuItem
 
getLanguage() - Static method in class org.jmol.i18n.GT
 
getLanguage() - Method in class org.jmol.viewer.Viewer
 
getLanguageList() - Static method in class org.jmol.i18n.GT
 
getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getLastConventional - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
getLastError() - Static method in exception org.jmol.smiles.InvalidSmilesException
 
getLastException() - Method in interface org.jmol.api.SmilesMatcherInterface
 
getLastException() - Method in class org.jmol.smiles.SmilesMatcher
 
getLastIndex() - Method in class org.jmol.modelset.Measurement
 
getLatticeCode(int) - Static method in class org.jmol.symmetry.Translation
 
getLatticeDesignation() - Method in interface org.jmol.api.SymmetryInterface
 
getLatticeDesignation() - Method in class org.jmol.symmetry.HallInfo
 
getLatticeDesignation() - Method in class org.jmol.symmetry.SpaceGroup
 
getLatticeDesignation() - Method in class org.jmol.symmetry.Symmetry
 
getLatticeDesignation(int) - Static method in class org.jmol.symmetry.Translation
 
getLatticeDesignation(char, boolean) - Static method in class org.jmol.symmetry.Translation
 
getLatticeExtension(char, boolean) - Static method in class org.jmol.symmetry.Translation
 
getLatticeIndex(char) - Static method in class org.jmol.symmetry.Translation
 
getLeadAtom(Atom) - Method in class org.jmol.modelset.Group
 
getLeadAtom() - Method in class org.jmol.modelset.Group
 
getLeadAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadColix(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
getLeadMidPoint(int, Point3f) - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadMidpoints() - Method in class org.jmol.modelset.Polymer
 
getLeadMidpoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadPoint(int, Point3f) - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadPoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeftPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getLength() - Method in class org.openscience.jvxl.MonitorInputStream
 
getLevel(int) - Static method in class org.jmol.util.Logger
Returns the text corresponding to a level.
getLigandBondInfo(JmolAdapter, Object, String) - Method in class org.jmol.modelsetbio.Resolver
reads PDB ligand CIF info and creates a bondInfo object.
getLigandInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getLigandInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getLigandModel(String) - Method in class org.jmol.viewer.Viewer
obtain CIF data for a ligand for purposes of adding hydrogens
getLightingInfo() - Method in class org.jmol.export._TachyonExporter
 
getLightSource() - Static method in class org.jmol.g3d.Graphics3D
 
getLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
getLine() - Method in class org.jmol.jvxl.readers.XplorReader
 
getLine() - Method in class org.jmol.util.XmlReader
 
getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getLinearOffset(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
getLinenumber(ScriptContext) - Method in class org.jmol.script.ScriptEvaluator
 
getList(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getList() - Method in class org.jmol.script.ScriptVariable
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
 
getLoadAtomDataTolerance() - Method in class org.jmol.viewer.Viewer
 
getLoadState(Map<String, Object>) - Method in class org.jmol.viewer.StateManager.GlobalSettings
these settings are determined when the file is loaded and are kept even though they might later change.
getLoadState(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
getLocalDirectory(JmolViewer, boolean) - Static method in class org.jmol.viewer.FileManager
 
getLocalPathForWritingFile(JmolViewer, String) - Static method in class org.jmol.viewer.FileManager
 
getLocalUrl(File) - Static method in class org.jmol.viewer.FileManager
 
getLogData() - Method in class org.jmol.minimize.forcefield.Calculations
 
getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
 
getLogFile() - Method in class org.jmol.viewer.Viewer
 
getLogGestures() - Method in class org.jmol.viewer.Viewer
 
getLogLevel() - Static method in class org.jmol.util.Logger
 
getLong(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
 
getMad() - Method in class org.jmol.modelset.Bond
 
getMadBond() - Method in class org.jmol.api.JmolViewer
 
getMadBond() - Method in class org.jmol.viewer.Viewer
 
getMadParameter() - Method in class org.jmol.script.ScriptEvaluator
 
getMappedAtoms(JmolNode, JmolNode, JmolNode[]) - Method in class org.jmol.smiles.SmilesSearch
 
getMaps - Variable in class org.jmol.smiles.SmilesSearch
 
getMarBond() - Method in class org.jmol.viewer.Viewer
 
getMarchingSquares() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getMass() - Method in class org.jmol.modelset.Atom
 
getMasses() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of a matching atom in a molecule.
getMatchingBondedAtom(int) - Method in class org.jmol.smiles.SmilesAtom
 
getMatrix() - Method in class org.jmol.util.Quaternion
 
getMatrix4f(Matrix3f, Tuple3f) - Static method in class org.jmol.script.ScriptMathProcessor
 
getMatrixFromString(String, float[], boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getMatrixFromString(String, float[], boolean) - Method in class org.jmol.symmetry.Symmetry
 
getMatrixFromString(String, float[], boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getMatrixRotate() - Method in class org.jmol.viewer.TransformManager
 
getMatrixRotate() - Method in class org.jmol.viewer.Viewer
 
getMatrixtransform() - Method in class org.jmol.viewer.TransformManager
 
getMatrixtransform() - Method in class org.jmol.viewer.Viewer
 
getMaxMathParams(int) - Static method in class org.jmol.script.Token
 
getMaxRadius() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getMaxVanderwaalsRadius() - Method in class org.jmol.modelset.AtomCollection
 
getMaxZoomPercent() - Method in class org.jmol.viewer.Viewer
 
getMeasureAllModelsFlag() - Method in class org.jmol.viewer.Viewer
 
getMeasureDistanceUnits() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getMeasureDistanceUnits() - Method in class org.jmol.viewer.Viewer
 
getMeasurement() - Method in class org.jmol.modelset.Measurement
 
getMeasurementCount() - Method in class org.jmol.api.JmolViewer
 
getMeasurementCount() - Method in class org.jmol.viewer.Viewer
 
getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer
 
getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer
 
getMeasurementInfo() - Method in class org.jmol.viewer.Viewer
 
getMeasurementInfoAsString() - Method in class org.jmol.viewer.Viewer
 
getMeasurements(Viewer) - Method in class org.jmol.modelset.MeasurementData
if this is the client, then this method can be called to get the result vector
getMeasurementScript(String, boolean) - Method in class org.jmol.modelset.Measurement
Used by MouseManager and Picking Manager to build the script
getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
 
getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
 
getMenu(String) - Method in interface org.jmol.api.JmolPopupInterface
 
getMenu(String) - Method in class org.jmol.popup.JmolPopup
 
getMenu(String) - Method in class org.jmol.popup.MainPopupResourceBundle
 
getMenu(String) - Method in class org.jmol.popup.PopupResource
 
getMenu(String) - Method in class org.jmol.viewer.Viewer
 
getMenuCurrent() - Method in class org.jmol.popup.JmolPopup
 
getMenuCurrent(StringBuffer, int, Object, String) - Method in class org.jmol.popup.JmolPopup
 
getMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Fetch the menu item that was created for the given command.
getMenuItemCount(Object) - Method in class org.jmol.popup.SimplePopup
 
getMenuListener() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
getMenuName(int) - Method in class org.jmol.viewer.Viewer
 
getMenus(boolean) - Method in interface org.jmol.api.JmolModelKitInterface
 
getMenus(boolean) - Method in class org.jmol.modelkit.ModelKit
 
getMenuText(String) - Method in class org.jmol.popup.SimplePopup
 
getMesh(String) - Method in class org.jmol.shape.MeshCollection
 
getMeshCommand(StringBuffer, int) - Method in class org.jmol.shapesurface.Isosurface
 
getMeshData(String, int[][], Tuple3f[], Tuple3f[]) - Method in class org.jmol.export._IdtfExporter
 
getMeshData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getMeshDataServer() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getMeshHeader(String, int, int, int, int, StringBuffer) - Method in class org.jmol.export._IdtfExporter
 
getMessageQueue() - Method in class org.jmol.viewer.StatusManager
 
getMessageQueue() - Method in class org.jmol.viewer.Viewer
 
getMessageStyleChime() - Method in class org.jmol.viewer.Viewer
 
getMiddle() - Method in class org.openscience.jmol.app.surfacetool.Slice
 
getMinBondDistance() - Method in class org.jmol.api.JmolViewer
 
getMinBondDistance() - Method in class org.jmol.viewer.Viewer
 
getMinimizationInfo() - Method in class org.jmol.viewer.Viewer
 
getMinimizer(boolean) - Method in class org.jmol.viewer.Viewer
 
getMiniPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getMinMax() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getMinMax(float[], boolean, int) - Static method in class org.jmol.script.ScriptEvaluator
 
getMinMax(Object, int) - Static method in class org.jmol.script.ScriptMathProcessor
 
getMinMaxMappedValues(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getMinMaxPoint(Object, int) - Static method in class org.jmol.script.ScriptMathProcessor
calculates the statistical value for x, y, and z independently
getMinMaxQuaternion(Object, int) - Static method in class org.jmol.script.ScriptMathProcessor
 
getMinPixelSelRadius() - Method in class org.jmol.viewer.Viewer
 
getMinZ(Atom[], int[]) - Method in class org.jmol.modelset.Group
 
getMissingHydrogenCount() - Method in class org.jmol.smiles.SmilesSearch
 
getMnemonic(String) - Static method in class org.jmol.console.KeyJMenuItem
 
getMoData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getModel() - Method in class org.jmol.modelset.Group
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModelAdapter() - Method in class org.jmol.api.JmolViewer
 
getModelAdapter() - Method in class org.jmol.viewer.Viewer
 
getModelAtomBitSetIncludingDeleted(BitSet) - Method in class org.jmol.modelset.ModelCollection
note -- this method returns ALL atoms, including deleted.
getModelAtomBitSetIncludingDeleted(int, boolean) - Method in class org.jmol.modelset.ModelCollection
Note that this method returns all atoms, included deleted ones.
getModelAtomProperty(Atom, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelAtomProperty(Atom, String) - Method in class org.jmol.viewer.Viewer
 
getModelAuxiliaryInfo(int) - Method in class org.jmol.api.JmolViewer
 
getModelAuxiliaryInfo(int, String) - Method in class org.jmol.api.JmolViewer
 
getModelAuxiliaryInfo(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelAuxiliaryInfo(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelAuxiliaryInfo(int) - Method in class org.jmol.viewer.Viewer
 
getModelAuxiliaryInfo(int, String) - Method in class org.jmol.viewer.Viewer
 
getModelAuxiliaryInfoBoolean(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelAuxiliaryInfoInt(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelBitSet(BitSet, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getModelBitSet(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
getModelCellRange(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelCenter() - Method in class org.jmol.export.__CartesianExporter
 
getModelCml(BitSet, int, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getModelCml(BitSet, int, boolean) - Method in class org.jmol.viewer.Viewer
 
getModelCount() - Method in class org.jmol.api.JmolViewer
 
getModelCount() - Method in class org.jmol.modelset.ModelCollection
 
getModelCount() - Method in class org.jmol.viewer.Viewer
 
getModelDipole(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelDipole() - Method in class org.jmol.viewer.Viewer
 
getModelExtract(BitSet, boolean, boolean, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelExtract(Object, boolean, String) - Method in class org.jmol.viewer.Viewer
 
getModelFileIndex() - Method in class org.jmol.modelset.Atom
 
getModelFileInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getModelFileInfo() - Method in class org.jmol.viewer.Viewer
 
getModelFileInfoAll() - Method in class org.jmol.viewer.Viewer
 
getModelFileName(int) - Method in class org.jmol.api.JmolViewer
 
getModelFileName(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelFileName(int) - Method in class org.jmol.viewer.Viewer
 
getModelFileNumber() - Method in class org.jmol.modelset.Atom
 
getModelFileNumber(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelFileNumber(int) - Method in class org.jmol.viewer.Viewer
 
getModelFileType(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelIndex() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getModelIndex() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getModelIndex() - Method in class org.jmol.modelset.Atom
 
getModelIndex() - Method in class org.jmol.modelset.Group
 
getModelIndex() - Method in class org.jmol.modelset.Model
 
getModelIndex() - Method in class org.jmol.smiles.SmilesAtom
 
getModelIndex() - Method in interface org.jmol.util.JmolNode
 
getModelInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getModelInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getModelInfoAsString() - Method in class org.jmol.modelset.ModelCollection
 
getModelInfoAsString() - Method in class org.jmol.viewer.Viewer
 
getModelKit(Viewer, Object) - Method in interface org.jmol.api.JmolModelKitInterface
 
getModelKit(Viewer, Object) - Method in class org.jmol.modelkit.ModelKit
 
getModelkitMode() - Method in class org.jmol.viewer.Viewer
 
getModelKitStateBitset(BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getModelKitStateBitSet(BitSet, BitSet) - Method in class org.jmol.viewer.Viewer
 
getModelLabel() - Method in class org.jmol.popup.JmolPopup
 
getModelName(int) - Method in class org.jmol.api.JmolViewer
 
getModelName(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelName(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumber() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
getModelNumber() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
getModelNumber(int) - Method in class org.jmol.api.JmolViewer
 
getModelNumber() - Method in class org.jmol.modelset.Atom
 
getModelNumber(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelNumber(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumberDotted(int) - Method in class org.jmol.api.JmolViewer
 
getModelNumberDotted() - Method in class org.jmol.modelset.Model
 
getModelNumberDotted(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelNumberDotted(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumberForAtomLabel(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelNumberForLabel() - Method in class org.jmol.modelset.Atom
 
getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getModelOrientation(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelProperties(int) - Method in class org.jmol.api.JmolViewer
 
getModelProperties(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelProperties(int) - Method in class org.jmol.viewer.Viewer
 
getModelProperty(int, String) - Method in class org.jmol.api.JmolViewer
 
getModelProperty(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelProperty(Viewer, String, Object) - Static method in class org.jmol.viewer.PropertyManager
 
getModelProperty(int, String) - Method in class org.jmol.viewer.Viewer
 
getModels() - Method in class org.jmol.modelset.ModelCollection
 
getModelSet() - Method in class org.jmol.modelset.Chain
 
getModelSet() - Method in class org.jmol.modelset.Group
 
getModelSet() - Method in class org.jmol.modelset.Model
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModelSet() - Method in class org.jmol.modelset.ModelLoader
 
getModelSet() - Method in class org.jmol.viewer.Viewer
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.api.JmolViewer
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.modelset.ModelCollection
 
getModelSetAuxiliaryInfo(String) - Method in class org.jmol.modelset.ModelCollection
 
getModelSetAuxiliaryInfo(String) - Method in class org.jmol.viewer.Viewer
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.viewer.Viewer
 
getModelSetAuxiliaryInfoBoolean(String) - Method in class org.jmol.modelset.ModelCollection
 
getModelSetFileName() - Method in class org.jmol.api.JmolViewer
 
getModelSetFileName() - Method in class org.jmol.viewer.ModelManager
 
getModelSetFileName() - Method in class org.jmol.viewer.Viewer
 
getModelSetName() - Method in class org.jmol.api.JmolViewer
 
getModelSetName() - Method in class org.jmol.modelset.ModelCollection
 
getModelSetName() - Method in class org.jmol.viewer.Viewer
 
getModelSetPathName() - Method in class org.jmol.api.JmolViewer
 
getModelSetPathName() - Method in class org.jmol.viewer.ModelManager
 
getModelSetPathName() - Method in class org.jmol.viewer.Viewer
 
getModelSetProperties() - Method in class org.jmol.api.JmolViewer
 
getModelSetProperties() - Method in class org.jmol.modelset.ModelCollection
 
getModelSetProperties() - Method in class org.jmol.viewer.Viewer
 
getModelSetProperty(String) - Method in class org.jmol.modelset.ModelCollection
 
getModelSetProperty(String) - Method in class org.jmol.viewer.Viewer
 
getModelSetTypeName() - Method in class org.jmol.modelset.ModelSet
 
getModelSetTypeName() - Method in class org.jmol.viewer.Viewer
 
getModelSymmetryCount(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelTitle() - Method in class org.jmol.modelset.Model
 
getModelTitle(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelTitle(int) - Method in class org.jmol.viewer.Viewer
 
getModelUndeletedAtomsBitSet(int) - Method in class org.jmol.viewer.Viewer
 
getModelUndeletedAtomsBitSet(BitSet) - Method in class org.jmol.viewer.Viewer
 
getModelUnitCell(int) - Method in class org.jmol.viewer.Viewer
 
getModeMultipleBond() - Method in class org.jmol.viewer.Viewer
 
getModifiers(int) - Static method in class org.jmol.viewer.binding.Binding
 
getMOHeader(int, String[], Map<String, Object>[], int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
getMoInfo(int) - Method in class org.jmol.modelset.ModelCollection
 
getMoInfo(int) - Method in class org.jmol.viewer.Viewer
 
getMoJvxl(int) - Method in class org.jmol.script.ScriptEvaluator
 
getMolecularFormula(String, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getMolecularFormula(String, boolean) - Method in class org.jmol.smiles.SmilesMatcher
 
getMolecularFormula(JmolNode[], BitSet, boolean) - Static method in class org.jmol.util.JmolMolecule
 
getMolecularFormula(boolean) - Method in class org.jmol.util.JmolMolecule
 
getMolecule(String, boolean) - Static method in class org.jmol.smiles.SmilesParser
 
getMoleculeBitSet(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeBitSet(int) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeBitSet(int) - Method in class org.jmol.viewer.Viewer
 
getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeIndex(int, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getMoleculeNumber(boolean) - Method in class org.jmol.modelset.Atom
 
getMolecules() - Method in class org.jmol.modelset.ModelCollection
 
getMolecules(JmolNode[], BitSet[], List<BitSet>, BitSet) - Static method in class org.jmol.util.JmolMolecule
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.
getMolName() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
getMonomerCount() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getMonomerIndex() - Method in class org.jmol.modelset.Atom
 
getMonomerIndex() - Method in class org.jmol.modelset.Group
 
getMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getMonomerIndex() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getMonomerSequenceAtoms(BitSet, BitSet) - Method in class org.jmol.modelsetbio.Monomer
 
getMoState(int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getMOString(float[]) - Static method in enum org.jmol.constant.EnumQuantumShell
 
getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
 
getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
 
getMotionFixedAtoms() - Method in class org.jmol.viewer.SelectionManager
 
getMotionFixedAtoms() - Method in class org.jmol.viewer.Viewer
 
getMoTokens(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
getMouseAction(int, int) - Static method in class org.jmol.viewer.binding.Binding
 
getMouseAction(String) - Static method in class org.jmol.viewer.binding.Binding
create an action code from a string such as "CTRL-LEFT-double click"
getMouseActionName(int, boolean) - Static method in class org.jmol.viewer.binding.Binding
 
getMouseEnabled() - Method in class org.jmol.viewer.Viewer
 
getMouseInfo() - Method in class org.jmol.viewer.ActionManager
 
getMouseInfo() - Method in class org.jmol.viewer.Viewer
 
getMouseManager(Viewer, ActionManager) - Method in interface org.jmol.api.ApiPlatform
 
getMouseManager(Viewer, ActionManager) - Method in class org.jmol.awt.Platform
 
getMoveToText(boolean) - Method in class org.jmol.viewer.StateManager.Orientation
 
getMoveToText(float, boolean) - Method in class org.jmol.viewer.TransformManager
 
getMoveToText(float) - Method in class org.jmol.viewer.Viewer
 
getMpsShapeCount() - Method in class org.jmol.shapebio.BioShapeCollection
 
getMultipleBondRadiusFactor() - Method in class org.jmol.viewer.Viewer
 
getMultipleBondSpacing() - Method in class org.jmol.viewer.Viewer
 
getMyInfo() - Method in class org.jmol.modelsetbio.Monomer
 
getN0() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN1() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN2() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN3() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN4() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN6() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getName() - Method in enum org.jmol.constant.EnumAnimationMode
 
getName() - Method in enum org.jmol.constant.EnumCallback
 
getName() - Method in enum org.jmol.constant.EnumStereoMode
 
getName() - Method in enum org.jmol.constant.EnumStructure
 
getName() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
 
getName() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
getName() - Method in class org.jmol.symmetry.PointGroup
 
getName() - Method in class org.jmol.symmetry.SpaceGroup
 
getName() - Method in class org.jmol.viewer.binding.Binding
 
getNameFromCode(int) - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
 
getNameList() - Static method in enum org.jmol.constant.EnumCallback
 
getNaturalIsotope(int) - Static method in class org.jmol.api.JmolAdapter
 
getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
 
getNavigateSurface() - Method in class org.jmol.viewer.Viewer
 
getNavigationCenter() - Method in class org.jmol.viewer.TransformManager
 
getNavigationCenter() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationCenter() - Method in class org.jmol.viewer.Viewer
 
getNavigationDepthPercent() - Method in class org.jmol.viewer.TransformManager
 
getNavigationDepthPercent() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationDepthPercent() - Method in class org.jmol.viewer.Viewer
 
getNavigationManager(Viewer, int, int) - Method in class org.jmol.viewer.TransformManager
 
getNavigationMode() - Method in class org.jmol.viewer.Viewer
 
getNavigationOffset() - Method in class org.jmol.viewer.TransformManager
 
getNavigationOffset() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationOffset() - Method in class org.jmol.viewer.Viewer
 
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager
 
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager11
 
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.Viewer
 
getNavigationPeriodic() - Method in class org.jmol.viewer.Viewer
 
getNavigationSlabOffsetPercent() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationSpeed() - Method in class org.jmol.viewer.Viewer
 
getNavigationState() - Method in class org.jmol.viewer.TransformManager
 
getNavigationState() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager
 
getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager11
 
getNavOn() - Method in class org.jmol.viewer.TransformManager
 
getNavOn() - Method in class org.jmol.viewer.Viewer
 
getNavPtHeight() - Method in class org.jmol.viewer.TransformManager11
 
getNBackbonesDisplayed() - Method in class org.jmol.modelset.Atom
 
getNBOCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
getNboCharges() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
getNBOs - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
getNboTypes() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
getNegCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getNeighbors(AtomIndexIterator) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getNeighborVertexesArrays() - Static method in class org.jmol.geodesic.Geodesic
 
getNested(int) - Method in class org.jmol.smiles.SmilesSearch
 
getNewCubeIterator(int) - Method in class org.jmol.bspt.Bspf
 
getNewDfCoefMap() - Static method in class org.jmol.api.JmolAdapter
 
getNewDfCoefMap() - Static method in enum org.jmol.constant.EnumQuantumShell
 
getNewFixedRotationCenter() - Method in class org.jmol.viewer.TransformManager
 
getNextComment() - Method in class org.jmol.script.ScriptEvaluator
 
getNextDataToken() - Method in class org.jmol.util.CifDataReader
first checks to see if the next token is an unquoted control code, and if so, returns null
getNextPreloadClassName() - Method in class org.jmol.applet.AppletWrapper
 
getNextQuotedString() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
getNextQuotedString(String, int) - Static method in class org.jmol.util.Parser
 
getNextQuotedString(String, int[]) - Static method in class org.jmol.util.Parser
 
getNextStatement() - Method in class org.jmol.script.ScriptEvaluator
when paused, indicates what statement will be next
getNextToken() - Method in class org.jmol.util.CifDataReader
 
getNextValue() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getNHPoint(Point3f, Vector3f, boolean, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNitrogenAtom() - Method in class org.jmol.modelset.Group
 
getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNitrogenHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNode(int) - Method in class org.jmol.viewer.ActionManager.Gesture
 
getNoneSelected() - Method in class org.jmol.viewer.Viewer
 
getNormal() - Method in class org.jmol.util.Quaternion
 
getNormalCount() - Method in class org.jmol.export.MeshData.Data
 
getNormalDirected(Vector3f) - Method in class org.jmol.util.Quaternion
 
getNormalFromCenter(Point3f, Point3f, Point3f, Point3f, boolean, Vector3f) - Static method in class org.jmol.util.Measure
 
getNormalizedDE() - Method in class org.jmol.minimize.forcefield.ForceField
 
getNormalMap(Tuple3f[], int, BitSet, List<String>) - Method in class org.jmol.export.__CartesianExporter
 
getNormals() - Method in class org.jmol.export.MeshData.Data
 
getNormals(Point3f[], Point4f) - Method in class org.jmol.shape.Mesh
 
getNormalThroughPoints(JmolNode, JmolNode, JmolNode, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.smiles.SmilesAromatic
 
getNormalThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
 
getNormalToLine(Point3f, Point3f, Vector3f) - Static method in class org.jmol.util.Measure
 
getNormix(Vector3f, BitSet) - Static method in class org.jmol.g3d.Graphics3D
 
getNormix(Vector3f, BitSet) - Static method in class org.jmol.g3d.Normix3D
 
getNormix(double, double, double, int, BitSet) - Static method in class org.jmol.g3d.Normix3D
 
getNormixVector(short) - Static method in class org.jmol.g3d.Graphics3D
 
getNotionalUnitcell(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getNotionalUnitcell(Object) - Method in class org.jmol.api.JmolAdapter
Get the notional unit cell.
getNotionalUnitCell() - Method in interface org.jmol.api.SymmetryInterface
 
getNotionalUnitcell() - Method in class org.jmol.modelset.ModelCollection
deprecated due to multimodel issues, but required by an interface -- do NOT remove.
getNotionalUnitCell() - Method in class org.jmol.symmetry.Symmetry
 
getNotionalUnitCell() - Method in class org.jmol.util.SimpleUnitCell
 
getNoValue() - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
getNoValue() - Method in class org.jmol.quantum.NciCalculation
 
getNPQ(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
getNPQd(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
for D orbitals, MOPAC adds 1 to n for noble gases but subtracts 1 from n for transition metals
getNPQp(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
for P orbitals, MOPAC adds 1 to n for helium only
getNPQs(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
for S orbitals, MOPAC adds 1 to n for noble gases other than helium
getNucleicPhosphorusAtom(int) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
getNumberFromCode(int) - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
 
getNumericalToken() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
getNumericParameter(String) - Method in class org.jmol.script.ScriptEvaluator
 
getNumSet() - Method in class org.jmol.modelset.MeasurementPending
 
getO2() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getO4() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getO6() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getObjectArgb(int) - Method in class org.jmol.viewer.Viewer
 
getObjectAsSections(String, String, Map<String, String>) - Method in class org.jmol.viewer.FileManager
delivers file contents and directory listing for a ZIP/JAR file into sb
getObjectBoundingBox(String) - Method in class org.jmol.script.ScriptEvaluator
 
getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptEvaluator
 
getObjectColix(int) - Method in class org.jmol.viewer.Viewer
 
getObjectIdFromName(String) - Static method in class org.jmol.viewer.StateManager
 
getObjectMad(int) - Method in class org.jmol.viewer.Viewer
 
getObjectMap(Map<String, Token>, boolean) - Method in class org.jmol.api.JmolViewer
retrieves list of draw/isosurface objects
getObjectMap(Map<String, Token>, boolean) - Method in class org.jmol.viewer.ShapeManager
 
getObjectMap(Map<String, Token>, boolean) - Method in class org.jmol.viewer.Viewer
 
getObjectNameFromId(int) - Static method in class org.jmol.viewer.StateManager
 
getObjectState(String) - Method in class org.jmol.viewer.Viewer
 
getOccupancy() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getOccupancy() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getOccupancy100() - Method in class org.jmol.modelset.Atom
 
getOctant(Point3f) - Static method in class org.jmol.util.Quadric
 
getOffset(int, int) - Static method in class org.jmol.shape.Object2d
 
getOffset(int) - Method in class org.jmol.util.CompoundDocument
 
getOffsetResidueAtom(String, int) - Method in class org.jmol.modelset.Atom
 
getOffsetResidueAtom(String, int) - Method in class org.jmol.smiles.SmilesAtom
 
getOffsetResidueAtom(String, int) - Method in interface org.jmol.util.JmolNode
 
getOffsetVertices(Point4f) - Method in class org.jmol.shape.Mesh
 
getOpenFileNameFromDialog(String, JmolViewer, String, Object, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
 
getOpenFileNameFromDialog(String, JmolViewer, String, Object, String, boolean) - Method in class org.jmol.export.dialog.Dialog
 
getOpenFileNameFromDialog(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getOperatingSystemName() - Method in class org.jmol.api.JmolViewer
 
getOperatingSystemName() - Method in class org.jmol.viewer.Viewer
 
getOperation(int) - Method in class org.jmol.symmetry.SpaceGroup
 
getOperationCount() - Method in class org.jmol.symmetry.SpaceGroup
 
getOptionInterface(String) - Static method in class org.jmol.api.Interface
 
getOptions() - Method in class org.openscience.jmol.app.JmolApp
 
getOrAddBond(Atom, Atom, int, short, BitSet, float, boolean) - Method in class org.jmol.modelset.BondCollection
 
getOrAllocateChain(Model, char) - Method in class org.jmol.modelset.ModelLoader
 
getOrderName() - Method in class org.jmol.modelset.Bond
 
getOrderNumberAsString() - Method in class org.jmol.modelset.Bond
 
getOrientation() - Method in class org.jmol.viewer.StateManager
 
getOrientation(String) - Method in class org.jmol.viewer.StateManager
 
getOrientation() - Method in class org.jmol.viewer.Viewer
 
getOrientationInfo() - Method in class org.jmol.viewer.TransformManager
 
getOrientationInfo() - Method in class org.jmol.viewer.Viewer
 
getOrientationText(int) - Method in class org.jmol.viewer.TransformManager
 
getOrientationText(int, String) - Method in class org.jmol.viewer.Viewer
 
getOriginFloat() - Method in interface org.jmol.api.VolumeDataInterface
 
getOriginFloat() - Method in class org.jmol.jvxl.data.VolumeData
 
getOriginPoint(boolean) - Method in class org.jmol.shape.Axes
 
getOrSetNewVariable(String, boolean) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getOrSetNewVariable(String, boolean) - Method in class org.jmol.viewer.Viewer
 
getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
 
getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
 
getOtherAtom(JmolNode) - Method in class org.jmol.modelset.Bond
 
getOtherAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
getOtherAtom(JmolNode) - Method in class org.jmol.smiles.SmilesBond
 
getOtherAtom(JmolNode) - Method in class org.jmol.util.JmolEdge
 
getOutputStream(String, String[]) - Method in class org.jmol.viewer.Viewer
 
getOutputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
getP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getPageAuthorName() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getPairs(BitSet, BitSet, RadiusData, int) - Method in class org.jmol.shapesurface.Contact
 
getPalette(String) - Static method in enum org.jmol.constant.EnumPalette
 
getPaletteAtoB(int, int, int) - Static method in class org.jmol.util.ColorEncoder
 
getPaletteBW() - Method in class org.jmol.util.ColorEncoder
 
getPaletteColorCount(int) - Method in class org.jmol.util.ColorEncoder
 
getPaletteID(String) - Static method in enum org.jmol.constant.EnumPalette
 
getPaletteID() - Method in class org.jmol.modelset.Atom
 
getPaletteId() - Method in class org.jmol.modelset.HBond
 
getPaletteName(byte) - Static method in enum org.jmol.constant.EnumPalette
 
getPaletteWB() - Method in class org.jmol.util.ColorEncoder
 
getPane() - Method in class org.jmol.console.JmolConsole
 
getPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getPanel() - Method in class org.openscience.jmol.app.webexport.Molecules
 
getPanel() - Method in class org.openscience.jmol.app.webexport.Orbitals
 
getPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getParameter(String) - Method in class org.jmol.api.JmolViewer
 
getParameter(String) - Method in class org.jmol.applet.Jmol
 
getParameter(String, Map<String, FFParam>) - Static method in class org.jmol.minimize.forcefield.Calculations
 
getParameter(float[], int, double, String) - Static method in class org.jmol.quantum.NciCalculation
 
getParameter(String, int) - Method in class org.jmol.script.ScriptEvaluator
 
getParameter(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
strictly a getter -- returns "" if not found
getParameter(String, boolean) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getParameter(String) - Method in class org.jmol.viewer.Viewer
 
getParameterEscaped(String) - Method in class org.jmol.script.ScriptEvaluator
 
getParameterEscaped(String, int) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getParameterEscaped(String) - Method in class org.jmol.viewer.Viewer
 
getParams() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getParamType(int) - Static method in class org.jmol.script.Token
 
getParamType(int) - Static method in class org.jmol.viewer.PropertyManager
 
getParent(Object) - Method in class org.jmol.popup.JmolPopup
 
getParent() - Method in class org.jmol.script.ScriptFlowContext
 
getParent() - Method in class org.jmol.smiles.SmilesSearch
 
getParentItem(String, Matrix4f) - Method in class org.jmol.export._IdtfExporter
 
getPartialBondDotted(int) - Static method in class org.jmol.util.JmolEdge
 
getPartialBondOrder(int) - Static method in class org.jmol.util.JmolEdge
 
getPartialBondOrderFromFloatEncodedInt(int) - Static method in class org.jmol.script.ScriptEvaluator
reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)
getPartialBondOrderFromString(String) - Static method in class org.jmol.script.ScriptEvaluator
 
getPartialCharge() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getPartialCharge() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getPartialCharge() - Method in class org.jmol.modelset.Atom
 
getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
 
getPartialCharges() - Method in class org.jmol.viewer.Viewer
 
getPartialDots() - Method in class org.jmol.viewer.Viewer
 
getPathHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Just recovers the path settings from last session.
getPdbAtomData(BitSet, OutputStringBuffer) - Method in class org.jmol.modelset.ModelCollection
 
getPdbBondInfo(int) - Static method in class org.jmol.viewer.JmolConstants
 
getPdbBondInfo(String) - Method in class org.jmol.viewer.Viewer
 
getPdbCharge(String, String) - Method in class org.jmol.modelset.ModelLoader
 
getPdbConformation(BitSet, int) - Method in class org.jmol.modelset.Model
 
getPdbData(int, String, BitSet, Object[], OutputStringBuffer) - Method in class org.jmol.modelset.ModelCollection
 
getPdbData(Viewer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Method in class org.jmol.modelset.Polymer
 
getPdbData(Viewer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
getPdbData(Viewer, BioPolymer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getPdbData(Viewer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
getPdbData(Viewer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Method in class org.jmol.modelsetbio.PhosphorusPolymer
 
getPdbData(BitSet, OutputStringBuffer) - Method in class org.jmol.viewer.Viewer
 
getPdbData(int, String, Object[]) - Method in class org.jmol.viewer.Viewer
 
getPDBHeader(int) - Method in class org.jmol.modelset.ModelCollection
 
getPDBHeader() - Method in class org.jmol.viewer.Viewer
 
getPdbScaleMatrix(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getPdbScaleMatrix(Object) - Method in class org.jmol.api.JmolAdapter
Get the PDB scale matrix.
getPdbScaleTranslate(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getPdbScaleTranslate(Object) - Method in class org.jmol.api.JmolAdapter
Get the PDB scale translation vector.
getPendingMeasurement() - Method in class org.jmol.viewer.Viewer
 
getPercentageRead() - Method in class org.openscience.jvxl.MonitorInputStream
 
getPercentVdwAtom() - Method in class org.jmol.api.JmolViewer
 
getPercentVdwAtom() - Method in class org.jmol.viewer.Viewer
 
getPerspectiveDepth() - Method in class org.jmol.api.JmolViewer
 
getPerspectiveDepth() - Method in class org.jmol.viewer.TransformManager
 
getPerspectiveDepth() - Method in class org.jmol.viewer.Viewer
 
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager
calculate the perspective factor based on z
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager10
 
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager11
 
getPhase(Point3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getPhongExponent() - Static method in class org.jmol.g3d.Graphics3D
 
getPickedPoint(Point3f, int) - Method in class org.jmol.shape.MeshCollection
 
getPickingMode(String) - Static method in class org.jmol.viewer.ActionManager
 
getPickingMode() - Method in class org.jmol.viewer.Viewer
 
getPickingModeName(int) - Static method in class org.jmol.viewer.ActionManager
 
getPickingSpinRate() - Method in class org.jmol.viewer.Viewer
 
getPickingState() - Method in class org.jmol.viewer.ActionManager
 
getPickingStyle(String) - Static method in class org.jmol.viewer.ActionManager
 
getPickingStyle() - Method in class org.jmol.viewer.ActionManager
 
getPickingStyleName(int) - Static method in class org.jmol.viewer.ActionManager
 
GetPixel(int, int) - Method in class org.jmol.export.image.GifEncoder
 
getPlane(int, float[]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
 
getPlane(int) - Method in interface org.jmol.jvxl.api.VertexDataServer
 
getPlane(int, boolean) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
getPlane(int, float[]) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getPlane() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getPlane(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getPlane(float[], boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
 
getPlane(int) - Method in class org.jmol.shapesurface.Isosurface
 
getPlane(Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
getPlane(String) - Static method in class org.openscience.jvxl.Jvxl
 
getPlaneIntersection(int, Point4f, float, int, int) - Method in class org.jmol.modelset.ModelCollection
 
getPlaneIntersection(int, Point4f, float, int) - Method in class org.jmol.viewer.Viewer
 
getPlaneNormals(JmolNode, JmolNode, JmolNode, JmolNode, SmilesSearch.VTemp) - Static method in class org.jmol.smiles.SmilesSearch
 
getPlaneProcessed(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneProjection(Point3f, Point4f, Point3f, Vector3f) - Static method in class org.jmol.util.Measure
 
getPlaneShade(int, int, double[]) - Method in class org.jmol.g3d.Sphere3D
 
getPlaneThroughPoint(Point3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
 
getPlaneThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
 
getPlaneValue(int) - Method in class org.jmol.quantum.NciCalculation
We always have four raw planes in hand; we just need to know which three to use in any particular case.
getPoint() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
getPoint(int, Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
getPoint(String, int, int[], boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
 
getPoint(Map<String, Object>) - Method in class org.jmol.viewer.ActionManager
 
getPoint3f(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getPoint4f(int) - Method in class org.jmol.script.ScriptEvaluator
 
getPointArc() - Method in class org.jmol.modelset.Measurement
 
getPointArray(int, int) - Method in class org.jmol.script.ScriptEvaluator
 
getPointCount() - Method in class org.jmol.viewer.ActionManager.Gesture
 
getPointCount(int, int) - Method in class org.jmol.viewer.ActionManager.Gesture
 
getPointer(int) - Static method in class org.jmol.shape.Object2d
 
getPointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getPointers(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
 
getPointGroup(PointGroup, Atom[], BitSet, boolean, float, float) - Static method in class org.jmol.symmetry.PointGroup
 
getPointGroupAsString(BitSet, boolean, String, int, float) - Method in class org.jmol.modelset.ModelSet
 
getPointGroupAsString(boolean, String, int, float) - Method in class org.jmol.viewer.Viewer
 
getPointGroupInfo(int, boolean, boolean, String, int, float) - Method in interface org.jmol.api.SymmetryInterface
 
getPointGroupInfo(BitSet) - Method in class org.jmol.modelset.ModelSet
 
getPointGroupInfo(int, boolean, boolean, String, int, float) - Method in class org.jmol.symmetry.Symmetry
 
getPointGroupInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getPointGroupName() - Method in interface org.jmol.api.SymmetryInterface
 
getPointGroupName() - Method in class org.jmol.symmetry.Symmetry
 
getPointGroupTolerance(int) - Method in class org.jmol.viewer.Viewer
 
getPointIndex(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
getPointOrBitsetOperation(Token, ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
 
getPointOrPlane(int, boolean, boolean, boolean, boolean, int, int) - Method in class org.jmol.script.ScriptEvaluator
 
getPointP(int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getPoints() - Method in class org.jmol.modelset.Measurement
 
getPointVector(Token, int) - Method in class org.jmol.script.ScriptEvaluator
 
getPolygonColorData(int, short[], BitSet) - Static method in class org.jmol.shapesurface.Isosurface
 
getPolymerCount() - Method in class org.jmol.api.JmolViewer
 
getPolymerCount() - Method in class org.jmol.viewer.Viewer
 
getPolymerCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getPolymerCountInModel(int) - Method in class org.jmol.viewer.Viewer
 
getPolymerIndexInModel() - Method in class org.jmol.modelset.Atom
 
getPolymerInfo(BitSet) - Method in class org.jmol.modelset.Polymer
 
getPolymerInfo(BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPolymerLeadMidPoints(int, int) - Method in class org.jmol.api.JmolViewer
 
getPolymerLeadMidPoints(int, int) - Method in class org.jmol.modelset.ModelCollection
 
getPolymerLeadMidPoints(int, int) - Method in class org.jmol.viewer.Viewer
 
getPolymerLength() - Method in class org.jmol.modelset.Atom
 
getPolymerPointsAndVectors(BitSet, List<Point3f[]>) - Method in class org.jmol.modelset.ModelCollection
 
getPolymerPointsAndVectors(int, BitSet, List<Point3f[]>, boolean, float) - Method in class org.jmol.modelset.Polymer
 
getPolymerPointsAndVectors(int, BitSet, List<Point3f[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPolymerPointsAndVectors(BitSet, List<Point3f[]>) - Method in class org.jmol.viewer.Viewer
 
getPolymerSequenceAtoms(int, int, BitSet, BitSet) - Method in class org.jmol.modelset.Polymer
 
getPolymerSequenceAtoms(int, int, BitSet, BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPopInHeight() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getPopInWidth() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getPopupMenu() - Method in class org.jmol.viewer.Viewer
 
getPort() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
getPosCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getPosition(Object) - Method in class org.jmol.popup.JmolPopup
 
getPosition() - Method in class org.jmol.util.BinaryDocument
 
getPosition() - Method in class org.openscience.jvxl.MonitorInputStream
 
getPositionMin() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getPrecedence(int) - Static method in class org.jmol.script.Token
 
getPrefixToken() - Method in class org.jmol.script.ScriptCompiler
 
getPreserveState() - Method in class org.jmol.viewer.Viewer
This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
getPrivateKey() - Method in class org.jmol.export.Export3D
 
getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
 
getProperties() - Method in class org.jmol.export.history.HistoryFile
 
getProperty(String, String, Object) - Method in class org.jmol.api.JmolSimpleViewer
 
getProperty(String, int) - Method in interface org.jmol.api.MinimizerInterface
 
getProperty(String) - Method in class org.jmol.applet.Jmol
 
getProperty(String, String) - Method in class org.jmol.applet.Jmol
 
getProperty(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
getProperty(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
 
getProperty(String, String) - Method in class org.jmol.export.history.HistoryFile
Get the value of a property
getProperty(String, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getProperty(String, int) - Method in class org.jmol.minimize.Minimizer
 
getProperty() - Method in class org.jmol.script.ScriptEvaluator
 
getproperty - Static variable in class org.jmol.script.Token
 
getProperty(String, int) - Method in class org.jmol.shape.Axes
 
getProperty(String, Object[]) - Method in class org.jmol.shape.Echo
 
getProperty(String, int) - Method in class org.jmol.shape.Labels
 
getProperty(String, int) - Method in class org.jmol.shape.Measures
 
getProperty(String, Object[]) - Method in class org.jmol.shape.MeshCollection
 
getProperty(String, int) - Method in class org.jmol.shape.MeshCollection
 
getProperty(String, Object[]) - Method in class org.jmol.shape.Shape
 
getProperty(String, int) - Method in class org.jmol.shape.Shape
 
getProperty(String, int) - Method in class org.jmol.shape.Sticks
 
getProperty(String, Object[]) - Method in class org.jmol.shapespecial.Dipoles
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
 
getProperty(String, Object[]) - Method in class org.jmol.shapespecial.Draw
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
 
getProperty(String, Object[]) - Method in class org.jmol.shapespecial.Ellipsoids
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
 
getProperty(String, Object[]) - Method in class org.jmol.shapesurface.Isosurface
 
getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
 
getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getProperty(String, boolean) - Static method in class org.jmol.util.Logger
 
getProperty(Viewer, String, String, Object) - Static method in class org.jmol.viewer.PropertyManager
 
getProperty(Object) - Method in class org.jmol.viewer.ShapeManager
 
getProperty(String, String, String) - Method in class org.jmol.viewer.Viewer
 
getProperty(String, String, Object) - Method in class org.jmol.viewer.Viewer
 
getPropertyAsJSON(String) - Method in class org.jmol.applet.Jmol
 
getPropertyAsJSON(String, String) - Method in class org.jmol.applet.Jmol
 
getPropertyAsJSON(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
getPropertyAsJSON(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
 
getPropertyAsObject(Viewer, String, Object, String) - Static method in class org.jmol.viewer.PropertyManager
 
getPropertyAsString(String) - Method in class org.jmol.applet.Jmol
 
getPropertyAsString(String, String) - Method in class org.jmol.applet.Jmol
 
getPropertyAsString(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
getPropertyAsString(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
 
getPropertyColorRange() - Method in class org.jmol.viewer.ColorManager
 
getPropertyColorScheme() - Method in class org.jmol.viewer.Viewer
 
getPropertyCount(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
getPropertyName(int) - Static method in class org.jmol.viewer.PropertyManager
 
getPropertyNumber(String) - Static method in class org.jmol.viewer.PropertyManager
 
getPropertyTensors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
getProteinStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructure(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getProteinStructure() - Method in class org.jmol.modelsetbio.Monomer
 
getProteinStructureState(BitSet, boolean, boolean, int) - Method in class org.jmol.modelset.ModelCollection
 
getProteinStructureState() - Method in class org.jmol.viewer.Viewer
 
getProteinStructureSubType() - Method in class org.jmol.modelset.Atom
 
getProteinStructureSubType() - Method in class org.jmol.modelset.Group
 
getProteinStructureSubType() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructureTag() - Method in class org.jmol.modelset.Atom
 
getProteinStructureTag() - Method in class org.jmol.modelset.Group
 
getProteinStructureTag() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getProteinStructureType(String) - Static method in enum org.jmol.constant.EnumStructure
In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
getProteinStructureType() - Method in class org.jmol.modelset.Atom
 
getProteinStructureType() - Method in class org.jmol.modelset.Group
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
 
getQuality(String) - Method in class org.jmol.export.dialog.Dialog
 
getQuantumShell(String) - Static method in enum org.jmol.constant.EnumQuantumShell
 
getQuantumShellTag(int) - Static method in enum org.jmol.constant.EnumQuantumShell
 
getQuantumShellTagID(String) - Static method in class org.jmol.api.JmolAdapter
 
getQuantumShellTagID(String) - Static method in enum org.jmol.constant.EnumQuantumShell
 
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.api.JmolAdapter
 
getQuantumShellTagIDSpherical(String) - Static method in enum org.jmol.constant.EnumQuantumShell
 
getQuardricZ(double, double, double[], double[]) - Static method in class org.jmol.util.Quadric
 
getQuaternion(int, char) - Method in class org.jmol.modelset.AtomCollection
 
getQuaternion(char) - Method in class org.jmol.modelset.Group
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getQuaternionArray(Object) - Static method in class org.jmol.script.ScriptMathProcessor
 
getQuaternionFrame(Atom[]) - Method in class org.jmol.modelset.Group
 
getQuaternionFrame(Point3f, Tuple3f, Tuple3f) - Static method in class org.jmol.util.Quaternion
 
getQuaternionFrame(Vector3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Quaternion
 
getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.Monomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getQuaternionParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
getQuaternionStraightness(String, Quaternion, Quaternion) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getQuotedString(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
getRadius() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getRadius() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getRadius() - Method in class org.jmol.modelset.Atom
 
getRadius() - Method in class org.jmol.modelset.Bond
 
getRadius(int) - Static method in class org.jmol.shapespecial.Ellipsoids
 
getRadiusVdwJmol(Atom) - Method in class org.jmol.modelset.AtomCollection
 
getRange(BitSet) - Method in class org.jmol.modelset.Polymer
 
getRange(BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
getRangeGroups(int, BitSet, BitSet) - Method in class org.jmol.modelset.Polymer
 
getRangeGroups(int, BitSet, BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
getRasmolHydrogenBonds(Model, BitSet, BitSet, List<Bond>, boolean, int, boolean) - Method in class org.jmol.modelset.BondCollection
 
getRasMolRadius() - Method in class org.jmol.modelset.Atom
 
getRasmolScale() - Static method in class org.jmol.util.ColorEncoder
 
getRasmolSetting(int) - Method in class org.jmol.viewer.Viewer
 
getRawNormal(Quaternion) - Static method in class org.jmol.util.Quaternion
 
getReaderClassBase(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getReaderFromType(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getReadingTimeMillis() - Method in class org.openscience.jvxl.MonitorInputStream
 
getRefreshing() - Method in class org.jmol.viewer.Viewer
 
getRegistryInfo() - Method in interface org.jmol.api.JmolStatusListener
 
getRegistryInfo() - Method in class org.jmol.applet.Jmol.MyStatusListener
 
getRegistryInfo() - Method in class org.jmol.viewer.StatusManager
 
getRegistryInfo() - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
getRelationship(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getRelationship(String, String) - Method in class org.jmol.smiles.SmilesMatcher
 
getRenderableBitSet() - Method in class org.jmol.viewer.ShapeManager
 
getRenderableBitSet() - Method in class org.jmol.viewer.Viewer
 
getRenderer(int, Graphics3D) - Method in class org.jmol.viewer.RepaintManager
 
getRenderHeight() - Method in interface org.jmol.api.JmolRendererInterface
gets g3d height
getRenderHeight() - Method in class org.jmol.export.Export3D
gets g3d height
getRenderHeight() - Method in class org.jmol.g3d.Graphics3D
gets g3d height
getRendering() - Method in class org.jmol.shape.Mesh
 
getRenderWidth() - Method in interface org.jmol.api.JmolRendererInterface
gets g3d width
getRenderWidth() - Method in class org.jmol.export.Export3D
gets g3d width
getRenderWidth() - Method in class org.jmol.g3d.Graphics3D
gets g3d width
getRepaintWait() - Method in class org.jmol.viewer.Viewer
 
getResidueLabels() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getResiduePointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getResno() - Method in class org.jmol.modelset.Atom
 
getResno() - Method in class org.jmol.modelset.Group
 
getResno() - Method in class org.jmol.smiles.SmilesAtom
 
getResno() - Method in interface org.jmol.util.JmolNode
 
getResource(Object, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getResource(Object, String, boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getResourceStream(String) - Static method in class org.openscience.chimetojmol.ChimePanel
 
getResourceString(Object, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getResult(boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
getRibbonAspectRatio() - Method in class org.jmol.viewer.Viewer
 
getRibbonBorder() - Method in class org.jmol.viewer.Viewer
 
getRingCache(int, int, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
 
getRingKey(int, int) - Static method in class org.jmol.smiles.SmilesGenerator
 
getRingPointer(int) - Static method in class org.jmol.smiles.SmilesParser
 
getRmsd(Point3f[][], Quaternion) - Static method in class org.jmol.util.Measure
 
getRnd(float) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getRocketBarrelFlag() - Method in class org.jmol.viewer.Viewer
 
getRotateBondIndex() - Method in class org.jmol.viewer.Viewer
 
getRotateXyzText() - Method in class org.jmol.viewer.TransformManager
 
getRotateZyzText(boolean) - Method in class org.jmol.viewer.TransformManager
 
getRotation(Matrix3f) - Method in class org.jmol.viewer.TransformManager
 
getRotation(Matrix3f) - Method in class org.jmol.viewer.Viewer
 
getRotationCenter() - Method in class org.jmol.viewer.TransformManager
 
getRotationCenter() - Method in class org.jmol.viewer.Viewer
 
getRotationInfo(String, int, char) - Method in class org.jmol.symmetry.HallInfo.RotationTerm
 
getRotationMatrix(Point3f, Point3f, float) - Method in class org.jmol.export.___Exporter
 
getRotationMatrix(Point3f, Point3f, float, Point3f, Point3f) - Method in class org.jmol.export.___Exporter
 
getRotationQuaternion() - Method in class org.jmol.viewer.TransformManager
 
getRotationQuaternion() - Method in class org.jmol.viewer.Viewer
 
getRotationRadius() - Method in class org.jmol.api.JmolViewer
 
getRotationRadius() - Method in class org.jmol.viewer.TransformManager
 
getRotationRadius() - Method in class org.jmol.viewer.Viewer
 
getRotationText() - Method in class org.jmol.viewer.TransformManager
 
getRowCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getRubberBand() - Method in class org.jmol.viewer.ActionManager
 
getRubberBandSelection() - Method in class org.jmol.viewer.Viewer
 
getSavedCoordinates(String) - Method in class org.jmol.viewer.StateManager
 
getSavedCoordinates(String) - Method in class org.jmol.viewer.Viewer
 
getSavedOrienationText(String) - Method in class org.jmol.viewer.Viewer
 
getSavedOrientationText(String) - Method in class org.jmol.viewer.StateManager
 
getSavedState(String) - Method in class org.jmol.viewer.StateManager
 
getSavedState(String) - Method in class org.jmol.viewer.Viewer
 
getSavedStructure(String) - Method in class org.jmol.viewer.StateManager
 
getSavedStructure(String) - Method in class org.jmol.viewer.Viewer
 
getSaveFileNameFromDialog(JmolViewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
 
getSaveFileNameFromDialog(JmolViewer, String, String) - Method in class org.jmol.export.dialog.Dialog
 
getScalePixelsPerAngstrom(boolean) - Method in class org.jmol.viewer.Viewer
 
getScalePixelsPerMicron() - Method in class org.jmol.shape.Object2d
 
getSchemeIndex(String) - Static method in class org.jmol.util.ColorEncoder
 
getScreenDim() - Method in class org.jmol.viewer.Viewer
 
getScreenHeight() - Method in class org.jmol.api.JmolViewer
 
getScreenHeight() - Method in class org.jmol.viewer.Viewer
 
getScreenImage(Object) - Method in class org.jmol.api.JmolViewer
 
getScreenImage() - Method in class org.jmol.g3d.Graphics3D
 
getScreenImage(Object) - Method in class org.jmol.viewer.Viewer
 
getScreenNormal(Point3f, Vector3f, float) - Method in class org.jmol.export.__RayTracerExporter
 
getScreenWidth() - Method in class org.jmol.api.JmolViewer
 
getScreenWidth() - Method in class org.jmol.viewer.Viewer
 
getScript() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getScript() - Method in class org.jmol.script.ScriptEvaluator
 
getScript() - Method in class org.jmol.shape.Object2d
 
getScriptBitSets(String, BitSet[]) - Method in class org.jmol.shapesurface.Isosurface
 
getScriptButtonPercent() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getScriptContext() - Method in class org.jmol.script.ScriptEvaluator
 
getScriptCount() - Method in class org.jmol.viewer.ScriptManager
 
getScriptDelay() - Method in class org.jmol.viewer.Viewer
 
getScriptEditor() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
getScriptEditor() - Method in class org.jmol.console.JmolConsole
 
getScriptID(ScriptContext) - Method in class org.jmol.script.ScriptEvaluator
 
getScriptItem(boolean, boolean) - Method in class org.jmol.viewer.ScriptManager
 
getScriptParams() - Method in class org.jmol.jvxl.readers.Parameters
 
getSearch(String, int, BitSet) - Method in class org.jmol.minimize.Minimizer
 
getSearch(SmilesSearch, String, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
 
getSectorAllocationTable() - Method in class org.jmol.util.CompoundDocument
 
getSectorData(StringBuffer, byte[], int, int, boolean, ZipUtil.GZipData) - Method in class org.jmol.util.CompoundDocument
 
getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getSelectAllModels() - Method in class org.jmol.viewer.Viewer
 
getSelectedAtomIterator(BitSet, boolean, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
 
getSelectedAtomIterator(BitSet, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getSelectedAtomIterator(BitSet, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getSelectedGroupCount() - Method in class org.jmol.modelset.Chain
 
getSelectedGroupCountWithinChain() - Method in class org.jmol.modelset.Atom
 
getSelectedGroupIndex() - Method in class org.jmol.modelset.Group
 
getSelectedGroupIndexWithinChain() - Method in class org.jmol.modelset.Atom
 
getSelectedMonomerCount() - Method in class org.jmol.modelset.Group
 
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.BioPolymer
 
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.Monomer
 
getSelectedMonomerCountWithinPolymer() - Method in class org.jmol.modelset.Atom
 
getSelectedMonomerIndex() - Method in class org.jmol.modelset.Group
 
getSelectedMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getSelectedMonomerIndexWithinPolymer() - Method in class org.jmol.modelset.Atom
 
getSelectionCount() - Method in class org.jmol.api.JmolViewer
 
getSelectionCount() - Method in class org.jmol.viewer.SelectionManager
 
getSelectionCount() - Method in class org.jmol.viewer.Viewer
 
getSelectionHaloEnabled() - Method in class org.jmol.modelset.ModelSet
 
getSelectionHaloEnabled(boolean) - Method in class org.jmol.viewer.Viewer
 
getSelectionSet(String) - Method in class org.jmol.viewer.ActionManager
 
getSelectionSet(boolean) - Method in class org.jmol.viewer.SelectionManager
 
getSelectionSet(boolean) - Method in class org.jmol.viewer.Viewer
 
getSelectionSubset() - Method in class org.jmol.viewer.SelectionManager
 
getSelectionSubset() - Method in class org.jmol.viewer.Viewer
 
getSeqcode() - Method in class org.jmol.modelset.Atom
 
getSeqcode() - Method in class org.jmol.modelset.Group
 
getSeqcode(int, char) - Static method in class org.jmol.modelset.Group
 
getSeqCode(Token) - Static method in class org.jmol.script.ScriptEvaluator
 
getSeqcodeBits(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getSeqcodeString() - Method in class org.jmol.modelset.Atom
 
getSeqcodeString() - Method in class org.jmol.modelset.Group
 
getSeqcodeString(int) - Static method in class org.jmol.modelset.Group
 
getSeqNumber() - Method in class org.jmol.modelset.Atom
 
getSeqNumber() - Method in class org.jmol.modelset.Group
 
getSequence() - Method in class org.jmol.modelset.Polymer
 
getSequence() - Method in class org.jmol.modelsetbio.BioPolymer
 
getSequence() - Method in class org.jmol.viewer.ActionManager
 
getSequenceBits(String, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getSequenceBits(String, BitSet) - Method in class org.jmol.viewer.Viewer
 
getSequenceCode(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
getSequenceNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getSequenceNumber() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getSequenceNumber(int) - Static method in class org.jmol.modelset.Group
 
getSerialID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getSerialID() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getSetAxesTypeMad(int) - Method in class org.jmol.script.ScriptEvaluator
 
getSetHistory(int) - Method in class org.jmol.api.JmolViewer
 
getSetHistory(int) - Method in class org.jmol.util.CommandHistory
Options include: all Integer.MAX_VALUE n prev n >= 1 next -1 set max to -2 - n n <= -3 just clear -2 clear and turn off; return "" 0 clear and turn on; return "" Integer.MIN_VALUE;
getSetHistory(int) - Method in class org.jmol.viewer.Viewer
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
getSettableTokFromString(String) - Static method in class org.jmol.script.Token
 
getSettings(String) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getShadeIndex(Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
getShadeIndex(short) - Method in class org.jmol.g3d.Normix3D
 
getShadeIndex(float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
getShadeIndexNormalized(float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
getShades(int, boolean) - Static method in class org.jmol.g3d.Colix3D
 
getShades(short) - Static method in class org.jmol.g3d.Colix3D
 
getShades(short) - Method in class org.jmol.g3d.Graphics3D
 
getShades(int, boolean) - Static method in class org.jmol.g3d.Shade3D
 
getShadesGreyscale(short) - Static method in class org.jmol.g3d.Colix3D
 
getShape(int) - Method in class org.jmol.viewer.ShapeManager
 
getShapeClassName(int) - Static method in class org.jmol.viewer.JmolConstants
 
getShapeCommands(Map<String, BitSet>, Map<String, BitSet>) - Static method in class org.jmol.shape.Shape
 
getShapeCommands(Map<String, BitSet>, Map<String, BitSet>, String) - Static method in class org.jmol.shape.Shape
 
getShapeDetail() - Method in class org.jmol.shape.Shape
 
getShapeDetail() - Method in class org.jmol.shapespecial.Dipoles
 
getShapeDetail() - Method in class org.jmol.shapespecial.Draw
 
getShapeDetail() - Method in class org.jmol.shapesurface.Isosurface
 
getShapeErrorState() - Method in class org.jmol.viewer.Viewer
 
getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.ShapeManager
Returns the shape type index for a shape object given the object name.
getShapeInfo() - Method in class org.jmol.viewer.ShapeManager
 
getShapeInfo() - Method in class org.jmol.viewer.Viewer
 
getShapeManager() - Method in class org.jmol.viewer.Viewer
 
getShapeNameParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
getShapeProperty(int, String) - Method in class org.jmol.script.ScriptEvaluator
 
getShapeProperty(int, String, Object[]) - Method in class org.jmol.script.ScriptEvaluator
 
getShapeProperty(int, String, int) - Method in class org.jmol.script.ScriptEvaluator
 
getShapeProperty(int, String, int) - Method in class org.jmol.viewer.ShapeManager
 
getShapeProperty(int, String, Object[]) - Method in class org.jmol.viewer.ShapeManager
 
getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
 
getShapeProperty(int, String, Object[]) - Method in class org.jmol.viewer.Viewer
 
getShapeProperty(int, String, int) - Method in class org.jmol.viewer.Viewer
 
getShapePropertyAsInt(int, String) - Method in class org.jmol.viewer.Viewer
 
getShapes() - Method in class org.jmol.viewer.ShapeManager
 
getShapeState() - Method in class org.jmol.shape.AtomShape
 
getShapeState() - Method in class org.jmol.shape.Axes
 
getShapeState() - Method in class org.jmol.shape.Balls
 
getShapeState() - Method in class org.jmol.shape.Echo
 
getShapeState() - Method in class org.jmol.shape.FontLineShape
 
getShapeState() - Method in class org.jmol.shape.FontShape
 
getShapeState() - Method in class org.jmol.shape.Halos
 
getShapeState() - Method in class org.jmol.shape.Hover
 
getShapeState() - Method in class org.jmol.shape.Labels
 
getShapeState() - Method in class org.jmol.shape.Measures
 
getShapeState() - Method in class org.jmol.shape.Shape
 
getShapeState() - Method in class org.jmol.shape.Sticks
 
getShapeState() - Method in class org.jmol.shape.Uccage
 
getShapeState() - Method in class org.jmol.shapebio.BioShapeCollection
 
getShapeState() - Method in class org.jmol.shapespecial.Dipole
 
getShapeState() - Method in class org.jmol.shapespecial.Dipoles
 
getShapeState() - Method in class org.jmol.shapespecial.Dots
 
getShapeState() - Method in class org.jmol.shapespecial.Draw
 
getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
 
getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
 
getShapeState() - Method in class org.jmol.shapespecial.Vectors
 
getShapeState() - Method in class org.jmol.shapesurface.Isosurface
 
getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
 
getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
 
getShapeState(StringBuffer, boolean) - Method in class org.jmol.viewer.ShapeManager
 
getShapeState(StringBuffer, boolean) - Method in class org.jmol.viewer.Viewer
 
getShapeType(int) - Method in class org.jmol.script.ScriptEvaluator
 
getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JmolConstants
 
getShapeVisibilityFlags() - Method in class org.jmol.modelset.Atom
 
getShapeVisibilityFlags() - Method in class org.jmol.modelset.Bond
 
getSheetSmoothing() - Method in class org.jmol.viewer.Viewer
 
getSheetStructures(Polymer[], List<AminoPolymer.Bridge>, List<AminoPolymer.Bridge>, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, char[][], BitSet[], boolean, boolean) - Static method in class org.jmol.modelsetbio.AminoPolymer
"sheet =: a set of one or more ladders connected by shared residues" (p.
getShellEnumeration(int) - Static method in class org.jmol.api.JmolAdapter
 
getShellOrder(int) - Static method in class org.jmol.quantum.MOCalculation
 
getShortSectorAllocationTable() - Method in class org.jmol.util.CompoundDocument
 
getShortStringData(int, int, boolean) - Method in class org.jmol.util.CompoundDocument
 
getShowAxes() - Method in class org.jmol.api.JmolViewer
 
getShowAxes() - Method in class org.jmol.viewer.Viewer
 
getShowBbcage() - Method in class org.jmol.api.JmolViewer
 
getShowBbcage() - Method in class org.jmol.viewer.Viewer
 
getShowFrank() - Method in class org.jmol.viewer.Viewer
 
getShowHiddenSelectionHalos() - Method in class org.jmol.viewer.Viewer
 
getShowHydrogens() - Method in class org.jmol.api.JmolViewer
 
getShowHydrogens() - Method in class org.jmol.viewer.Viewer
 
getShowMeasurementLabels() - Method in class org.jmol.viewer.Viewer
 
getShowMeasurements() - Method in class org.jmol.api.JmolViewer
 
getShowMeasurements() - Method in class org.jmol.viewer.Viewer
 
getShowMultipleBonds() - Method in class org.jmol.viewer.Viewer
 
getShowNavigationPoint() - Method in class org.jmol.viewer.Viewer
 
getShowUnitCell() - Method in class org.jmol.viewer.Viewer
 
getSignature() - Method in class org.jmol.script.ScriptFunction
 
getSize(int) - Method in class org.jmol.shape.AtomShape
 
getSize(int) - Method in class org.jmol.shape.Shape
 
getSize(Group) - Method in class org.jmol.shape.Shape
 
getSize(Group) - Method in class org.jmol.shapebio.BioShapeCollection
 
getSize(int) - Method in class org.jmol.shapespecial.Dots
 
getSlab() - Method in interface org.jmol.api.JmolRendererInterface
gets g3d slab
getSlab() - Method in class org.jmol.export.Export3D
gets g3d slab
getSlab() - Method in class org.jmol.g3d.Graphics3D
gets g3d slab
getSlabByAtom() - Method in class org.jmol.viewer.Viewer
 
getSlabByMolecule() - Method in class org.jmol.viewer.Viewer
 
getSlabColor() - Method in class org.jmol.util.MeshSurface
 
getSlabDepthPlane(boolean) - Method in class org.jmol.viewer.TransformManager
 
getSlabEnabled() - Method in class org.jmol.viewer.Viewer
 
getSlabInfo() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getSlabObject(int, Object, boolean, Object) - Static method in class org.jmol.util.MeshSurface
 
getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
 
getSlabTranslucency() - Method in class org.jmol.util.MeshSurface
 
getSlabType() - Method in class org.jmol.util.MeshSurface
 
getSlabWithinRange(float, float) - Static method in class org.jmol.util.MeshSurface
 
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstDSpherical(int, double, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
spherical scaling factors specifically for x2-y2 and z2 orbitals see http://openmopac.net/Manual/real_spherical_harmonics.html dz2 sqrt((1/2p)(5/8))(2cos2(q) -sin2(q)) sqrt(5/16p)(3z2-r2)/r2 dxz sqrt((1/2p)(15/4))(cos(q)sin(q))cos(f) sqrt(15/4p)(xz)/r2 dyz sqrt((1/2p)(15/4))(cos(q)sin(q))sin(f) sqrt(15/4p)(yz)/r2 dx2-y2 sqrt((1/2p)(15/16))sin2(q)cos2(f) sqrt(15/16p)(x2-y2)/r2 dxy sqrt((1/2p)(15/16))sin2(q)sin2(f) sqrt(15/4p)(xy)/r2 The fact() method returns sqrt(15/4p) for both z2 and x2-y2.
getSlice() - Method in class org.openscience.jmol.app.surfacetool.Slice
 
getSliceAngleXY() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSliceMiddle() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSlicePosition() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSliceThickness() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSmallMoleculeMaxAtoms() - Method in class org.jmol.viewer.Viewer
 
getSmartAromatic() - Method in class org.jmol.viewer.Viewer
 
getSmartsMatch(String, BitSet) - Method in class org.jmol.api.JmolViewer
 
getSmartsMatch(String, BitSet) - Method in class org.jmol.viewer.Viewer
 
getSmiles(JmolNode[], int, BitSet, boolean, boolean, boolean, String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSmiles(JmolNode[], int, BitSet) - Method in class org.jmol.smiles.SmilesGenerator
 
getSmiles(StringBuffer, JmolNode, boolean, boolean) - Method in class org.jmol.smiles.SmilesGenerator
 
getSmiles(JmolNode[], int, BitSet, boolean, boolean, boolean, String) - Method in class org.jmol.smiles.SmilesMatcher
 
getSmiles(int, int, BitSet, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
returns the SMILES string for a sequence or atom set does not include attached protons on groups
getSmilesComponent(JmolNode, BitSet, boolean) - Method in class org.jmol.smiles.SmilesGenerator
creates a valid SMILES string from a model.
getSmilesCorrelation(BitSet, BitSet, String, List<Point3f>, List<Point3f>, Matrix4f, List<BitSet>, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getSmilesMatcher() - Method in class org.jmol.viewer.Viewer
 
getSmilesMatches(String, String, BitSet, BitSet, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getSolventOn() - Method in class org.jmol.viewer.Viewer
 
getSolventPoints(int, int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getSolventProbeRadius() - Method in class org.jmol.viewer.Viewer
 
getSourceActions(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
getSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupInfo(String, SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupInfo(int, String, int, Point3f, Point3f, String) - Method in class org.jmol.modelset.ModelCollection
 
getSpaceGroupInfo(String, SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupInfo(String) - Method in class org.jmol.viewer.Viewer
 
getSpaceGroupName() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupName() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperation(int) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperation(int) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperationCount() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperationCount() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupXyz(int, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupXyz(int, boolean) - Method in class org.jmol.symmetry.Symmetry
 
getSpartanDirs(String) - Static method in class org.jmol.adapter.smarter.Resolver
read the output file from the Spartan directory and decide from that what files need to be read and in what order - usually M0001 or a set of Profiles.
getSpartanFileList(String, String[]) - Static method in class org.jmol.adapter.smarter.Resolver
returns the list of files to read for every Spartan spardir.
getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
 
getSpecialAtomName(int) - Static method in class org.jmol.viewer.JmolConstants
 
getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
 
getSpecName(String) - Method in class org.jmol.modelset.AtomCollection
 
getSpecNameOrNull(String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getSpecular() - Static method in class org.jmol.g3d.Graphics3D
 
getSpecularExponent() - Static method in class org.jmol.g3d.Graphics3D
 
getSpecularPercent() - Static method in class org.jmol.g3d.Graphics3D
 
getSpecularPower() - Static method in class org.jmol.g3d.Graphics3D
 
getSpecularState() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getSpecularState() - Method in class org.jmol.viewer.Viewer
 
getSpeedPixelsPerMillisecond(int, int) - Method in class org.jmol.viewer.ActionManager.Gesture
 
getSphereData() - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a sphere.
getSphereResource() - Method in class org.jmol.export._IdtfExporter
 
getSphereShape(int) - Static method in class org.jmol.g3d.Sphere3D
 
getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
 
getSpinAxis(String, int) - Method in class org.jmol.shapespecial.Draw
 
getSpinCenter(String, int, int) - Method in class org.jmol.shapespecial.Draw
 
getSpinOn() - Method in class org.jmol.viewer.TransformManager
 
getSpinOn() - Method in class org.jmol.viewer.Viewer
 
getSpinState(boolean) - Method in class org.jmol.viewer.TransformManager
 
getSpinState() - Method in class org.jmol.viewer.Viewer
 
getSsbondsBackbone() - Method in class org.jmol.viewer.Viewer
 
getStandardLabelFormat(int) - Method in class org.jmol.viewer.Viewer
 
getStandardPdbHydrogenCount(int) - Static method in class org.jmol.viewer.JmolConstants
 
getStandardStringData(int, int, boolean) - Method in class org.jmol.util.CompoundDocument
 
getStartChainID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStartChainID() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getStartInsertionCode() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStartInsertionCode() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getState() - Method in interface org.jmol.api.JmolGestureServerInterface
 
getState(StringBuffer, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
getState(int) - Method in class org.jmol.shape.Measures
 
getState(String) - Method in class org.jmol.shape.Mesh
 
getState() - Method in class org.jmol.shape.Text
 
getState() - Method in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
getState(StringBuffer) - Method in class org.jmol.util.ColorEncoder
 
getState(StringBuffer) - Method in class org.jmol.viewer.AnimationManager
 
getState(StringBuffer) - Method in class org.jmol.viewer.ColorManager
 
getState(StringBuffer) - Method in class org.jmol.viewer.FileManager
 
getState(StringBuffer) - Method in class org.jmol.viewer.SelectionManager
 
getState(StringBuffer) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getState(StringBuffer) - Method in class org.jmol.viewer.TransformManager
 
getStateInfo() - Method in class org.jmol.api.JmolViewer
 
getStateInfo() - Method in class org.jmol.viewer.Viewer
 
getStateInfo(String, int, int) - Method in class org.jmol.viewer.Viewer
 
getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.ApiPlatform
 
getStaticGraphics(Object, boolean) - Static method in class org.jmol.awt.Image
 
getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
 
getStatusChanged(String) - Method in class org.jmol.viewer.StatusManager
 
getStatusChanged(String) - Method in class org.jmol.viewer.Viewer
 
getStatusList() - Method in class org.jmol.viewer.StatusManager
 
getStatusManager() - Method in class org.jmol.viewer.Viewer
 
getStereoFlag(JmolNode, JmolNode[], int, SmilesSearch.VTemp) - Static method in class org.jmol.smiles.SmilesGenerator
 
getStereoImage(EnumStereoMode) - Method in class org.jmol.viewer.Viewer
 
getStereoMode(String) - Static method in enum org.jmol.constant.EnumStereoMode
 
getStereoRotationMatrix(boolean) - Method in class org.jmol.viewer.TransformManager
 
getStraightness(float) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getStrandCount() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStrandCount() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getStrandCount(int) - Method in class org.jmol.viewer.Viewer
 
getStream(InputStream) - Static method in class org.jmol.util.ZipUtil
 
getStreamAsBytes(BufferedInputStream, OutputStream) - Static method in class org.jmol.viewer.FileManager
 
getStrFormat() - Method in class org.jmol.modelset.Measurement
 
getString(String) - Method in class org.jmol.i18n.GT
 
getString(String, Object[]) - Method in class org.jmol.i18n.GT
 
getString() - Method in class org.jmol.modelset.Measurement
 
getString(Viewer, String, String) - Method in class org.jmol.modelset.Measurement
 
getString(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getString(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
 
getStringDetail() - Method in class org.jmol.modelset.Measurement
 
getStringObjectAsVariable(String, String) - Method in class org.jmol.script.ScriptEvaluator
 
getStringParameter(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getStringX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getStrucNo() - Method in class org.jmol.modelset.Atom
 
getStrucNo() - Method in class org.jmol.modelset.Group
 
getStrucNo() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getStructure() - Method in class org.jmol.modelset.Group
 
getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getStructure(String) - Method in class org.jmol.popup.PopupResource
 
getStructureCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getStructureID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStructureID() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getStructureId() - Method in class org.jmol.modelset.Atom
 
getStructureId() - Method in class org.jmol.modelset.Group
 
getStructureId() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getStructureId() - Method in class org.jmol.modelsetbio.Monomer
 
getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get a StructureIterator.
getStructureList() - Method in class org.jmol.modelset.ModelCollection
 
getStructureList() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getStructureList() - Method in class org.jmol.viewer.Viewer
 
getStructureMidPoint(int) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getStructures() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getStructureState() - Method in class org.jmol.viewer.Viewer
 
getStructureType() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStructureType() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getStrutDefaultRadius() - Method in class org.jmol.viewer.Viewer
 
getStrutLengthMaximum() - Method in class org.jmol.viewer.Viewer
 
getStrutsMultiple() - Method in class org.jmol.viewer.Viewer
 
getStrutSpacingMinimum() - Method in class org.jmol.viewer.Viewer
 
getSubPattern(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
 
getSubstructureSet(String, JmolNode[], int, BitSet, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSubstructureSet(String, JmolNode[], int, BitSet, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
Returns a bitset matching the pattern within atoms.
getSubstructureSetArray(String, JmolNode[], int, BitSet, BitSet, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSubstructureSetArray(String, JmolNode[], int, BitSet, BitSet, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
Returns a vector of bitsets indicating which atoms match the pattern.
getSubstructureType() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getSubstructureType() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getSupported(String, boolean) - Method in class org.jmol.i18n.GT
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
The list of files returned by this function should contain the full path to each file.
getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfaceData() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getSurfaceData() - Method in class org.jmol.jvxl.readers.PmeshReader
 
getSurfaceData() - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
getSurfaceDistance100() - Method in class org.jmol.modelset.Atom
 
getSurfaceDistance100(int) - Method in class org.jmol.modelset.AtomCollection
 
getSurfaceDistanceMax() - Method in class org.jmol.modelset.AtomCollection
 
getSurfaceDistanceMax() - Method in class org.jmol.viewer.Viewer
 
getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.IsoSolventReader
TEST: alternative EXACT position of fraction for spherical MarchingCubes FOR: ttest.xyz: 2 isosurface molecular test showing discontinuities C -2.70 0 0 C 2.75 0 0 RESULT: LINEAR (points slightly within R): $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.06620391572324] isosurfaceVolume = [41.639681683494324] NONLINEAR: $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.11873783245028] isosurfaceVolume = [41.727027252180655] MSMS: msms -if ttest.xyzrn -of ttest -density 5 MSMS 2.6.1 started on Local PC Copyright M.F.
getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getSurfacePointIndexAndFraction(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean, float[]) - Method in interface org.jmol.jvxl.api.VertexDataServer
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
getSurfacePointIndexAndFraction(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean, float[]) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfacePointIndexAndFraction(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean, float[]) - Method in class org.jmol.shapesurface.Isosurface
 
getSurfaces() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
 
getSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
getSurfaceSets() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getSymbol(String) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getSymmetry() - Method in class org.jmol.viewer.Viewer
 
getSymmetryInfo(BitSet, String, int, Point3f, Point3f, String, int) - Method in class org.jmol.modelset.ModelCollection
 
getSymmetryInfo(BitSet, String, int, Point3f, Point3f, String, int) - Method in class org.jmol.viewer.Viewer
 
getSymmetryInfoAsString(int) - Method in class org.jmol.modelset.ModelCollection
 
getSymmetryInfoAsString() - Method in class org.jmol.modelset.ModelCollection
 
getSymmetryInfoAsString() - Method in class org.jmol.viewer.Viewer
 
getSymmetryInfoString() - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryInfoString() - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryOperation(int, String, int, Point3f, Point3f, String, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getSymmetryOperation(String, int, Point3f, Point3f, boolean) - Method in class org.jmol.viewer.Viewer
 
getSymmetryOperationDescription(int, SymmetryInterface, Point3f, Point3f, String) - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryOperationDescription(int, SymmetryInterface, Point3f, Point3f, String) - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryOperations() - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryOperations() - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryOperatorList() - Method in class org.jmol.modelset.Atom
 
getSymmetryTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
getSymTemp(boolean) - Method in class org.jmol.modelset.ModelCollection
 
getSyncMode() - Method in class org.jmol.viewer.StatusManager
 
getTabulatedPotential(Atom) - Method in class org.jmol.quantum.MepCalculation
 
getTaintedAtoms(byte) - Method in class org.jmol.modelset.AtomCollection
 
getTaintedAtoms(byte) - Method in class org.jmol.viewer.Viewer
 
getTargetValence() - Method in class org.jmol.modelset.Atom
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getTerminatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
 
getTestFlag(int) - Method in class org.jmol.viewer.Viewer
 
getText() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
getText() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
getText() - Method in class org.jmol.console.AppletConsole
 
getText() - Method in class org.jmol.console.JmolConsole
 
getText() - Method in class org.jmol.console.ScriptEditor
 
getText() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
getText() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getText3D(int, int, Graphics3D, String, Font3D, boolean) - Static method in class org.jmol.g3d.Text3D
 
getTextureName(short) - Method in class org.jmol.export._ObjExporter
Returns the name to be used for the texture associated with the given colix.
getTextWrapper - Static variable in class org.jmol.i18n.GT
 
getTextWrapper() - Static method in class org.jmol.i18n.GT
 
getTheta() - Method in class org.jmol.util.Quaternion
 
getThetaDirected(Point4f) - Method in class org.jmol.util.Quaternion
 
getThetaDirected(Vector3f) - Method in class org.jmol.util.Quaternion
 
getThetaRadians() - Method in class org.jmol.util.Quaternion
 
getThicknessMax() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getTickInfo() - Method in class org.jmol.modelset.Measurement
 
getTimeDifference(int) - Method in class org.jmol.viewer.ActionManager.Gesture
 
getTitle() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getToken() - Method in class org.jmol.script.ScriptCompilationTokenParser
gets the next token and sets global theToken and theValue
getToken(int) - Method in class org.jmol.script.ScriptEvaluator
 
getTokenFromName(String) - Static method in class org.jmol.script.Token
 
getTokenPeeked() - Method in class org.jmol.util.CifDataReader
 
getTokens(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
getTokens() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokens(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokens(String, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokens() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
getTokens(String) - Static method in class org.jmol.util.Parser
 
getTokens(String, int) - Static method in class org.jmol.util.Parser
 
getTokensFloat(String, float[], int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokensLike(String) - Static method in class org.jmol.script.Token
 
getTokFromName(String) - Static method in class org.jmol.script.Token
 
getToPlaneParameter() - Method in class org.jmol.jvxl.data.VolumeData
 
getTorsionAngleRadians(double[], double[], double[], double[], Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
getTorsions() - Method in class org.jmol.minimize.Minimizer
 
getTraceAlpha() - Method in class org.jmol.viewer.Viewer
 
getTrajectoryCount() - Method in class org.jmol.modelset.ModelCollection
 
getTrajectoryIndex(int) - Method in class org.jmol.modelset.ModelCollection
 
getTrajectoryInfo() - Method in class org.jmol.modelset.ModelSet
 
getTrajectoryInfo() - Method in class org.jmol.viewer.Viewer
 
getTrajectoryStep(Point3f[]) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
getTrajectoryStep(Point3f[], boolean) - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
getTransferData(DataFlavor) - Method in class org.jmol.export.image.ImageSelection
 
getTransferData(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
getTransferDataFlavors() - Method in class org.jmol.export.image.ImageSelection
 
getTransferDataFlavors() - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
getTransformedVectors() - Method in class org.jmol.g3d.Normix3D
 
getTransformedVertexVectors() - Method in interface org.jmol.api.JmolRendererInterface
 
getTransformedVertexVectors() - Method in class org.jmol.export.Export3D
 
getTransformedVertexVectors() - Method in class org.jmol.g3d.Graphics3D
 
getTransformMatrix4(List<Point3f>, List<Point3f>, Matrix4f, Point3f) - Static method in class org.jmol.util.Measure
 
getTransformText() - Method in class org.jmol.viewer.TransformManager
 
getTransformText() - Method in class org.jmol.viewer.Viewer
 
getTranslation(String) - Method in class org.jmol.i18n.GT
 
getTranslationScript() - Method in class org.jmol.viewer.TransformManager
 
getTranslationScript() - Method in class org.jmol.viewer.Viewer
 
getTranslationXPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslationXPercent() - Method in class org.jmol.viewer.Viewer
 
getTranslationYPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslationYPercent() - Method in class org.jmol.viewer.Viewer
 
getTranslationZPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslationZPercent() - Method in class org.jmol.viewer.Viewer
 
getTranslucentLabel(short) - Static method in class org.jmol.shape.Shape
 
getTranslucentLevel(int) - Method in class org.jmol.script.ScriptEvaluator
 
getTriangleData(Point3f, Point3f, Point3f) - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a triangle.
getTriangleResource(String, Point3f, Point3f, Point3f) - Method in class org.jmol.export._IdtfExporter
 
getTriangles() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getTrimmedLine() - Method in class org.jmol.g3d.Line3D
Cohen-Sutherland line clipping used to check visibility.
getTrueAtomCount() - Method in class org.jmol.modelset.Model
 
getType() - Method in interface org.jmol.api.JmolDialogInterface
 
getType(Atom) - Static method in enum org.jmol.constant.EnumHBondType
 
getType() - Method in class org.jmol.export.dialog.Dialog
 
getType() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
getType() - Method in class org.jmol.modelset.Polymer
 
getType(int) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
 
getUndeletedGroupAtomBits(BitSet) - Method in class org.jmol.viewer.Viewer
 
getUnescapedStringLiteral() - Method in class org.jmol.script.ScriptCompiler
 
getUniqueID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getUniqueID() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getUniqueID() - Method in class org.jmol.modelsetbio.Monomer
 
getUnit() - Method in class org.jmol.minimize.forcefield.Calculations
 
getUnit() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getUnitCell(int) - Method in class org.jmol.modelset.ModelCollection
 
getUnitCellAsArray(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellAsArray(boolean) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellAsArray(boolean) - Method in class org.jmol.util.SimpleUnitCell
 
getUnitCellInfo(int) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfo() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfo(int) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellInfo() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellInfo(int) - Method in class org.jmol.viewer.Viewer
 
getUnitCellInfoText() - Method in class org.jmol.modelset.ModelCollection
 
getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
 
getUnitCellMultiplier() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellMultiplier() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellMultiplier() - Method in class org.jmol.symmetry.UnitCell
 
getUnitCellVertices() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellVertices() - Method in class org.jmol.symmetry.Symmetry
 
getUnits() - Method in class org.jmol.minimize.forcefield.ForceField
 
getUnitsymmetryInfo() - Method in class org.jmol.symmetry.Symmetry
 
getUnitsymmetryInfo(int) - Method in class org.jmol.symmetry.Symmetry
 
getUnscaledTransformMatrix() - Method in class org.jmol.api.JmolViewer
 
getUnscaledTransformMatrix() - Method in class org.jmol.viewer.TransformManager
 
getUnscaledTransformMatrix() - Method in class org.jmol.viewer.Viewer
 
getUnzippedBufferedReaderOrErrorMessageFromName(String, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getUseMolecular() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getUseNumberLocalization() - Method in class org.jmol.viewer.Viewer
 
getUserDirectory() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
 
getUserVariable(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getValAsObj() - Method in class org.jmol.script.ScriptVariable
 
getValence() - Method in class org.jmol.modelset.Atom
 
getValence() - Method in class org.jmol.modelset.Bond
 
getValence() - Method in class org.jmol.smiles.SmilesAtom
 
getValence() - Method in class org.jmol.smiles.SmilesBond
 
getValence() - Method in interface org.jmol.util.JmolNode
 
getValue(String, String) - Method in class org.jmol.applet.Jmol
 
getValue(int, int, int, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
for readers only
getValue(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getValue(int, int, int, int, float[]) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
 
getValue(float, float) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getValue() - Method in class org.jmol.modelset.Measurement
 
getValue(double, boolean) - Method in class org.jmol.quantum.NciCalculation
 
getValue(int, int, int, int) - Method in class org.jmol.shapesurface.Isosurface
 
getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
getValue(int, int, int) - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
getValueAt(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
getValueAtPoint(Point3f, BitSet) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getValueAtPoint(Point3f) - Method in class org.jmol.quantum.MepCalculation
 
getValueLowerCase(String, String) - Method in class org.jmol.applet.Jmol
 
getValues() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getVanderwaalsMar(int, EnumVdw) - Static method in class org.jmol.util.Elements
 
getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
 
getVanderwaalsMar(int, EnumVdw) - Method in class org.jmol.viewer.Viewer
 
getVanderwaalsRadiusFloat(Viewer, EnumVdw) - Method in class org.jmol.modelset.Atom
 
getVariable(Object) - Static method in class org.jmol.script.ScriptVariable
 
getVariableList(Map<String, ScriptVariable>, int, boolean, boolean) - Static method in class org.jmol.viewer.StateManager
 
getVariableList() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getVariableList() - Method in class org.jmol.viewer.Viewer
 
getVdwClashRadius(ContactPair, double, double, double, double) - Static method in class org.jmol.shapesurface.Contact
well, heh, heh...
getVdwLabel() - Method in enum org.jmol.constant.EnumVdw
 
getVdwType(String) - Static method in enum org.jmol.constant.EnumVdw
 
getVdwType(EnumVdw) - Method in class org.jmol.modelset.Atom
 
getVdwType2(String) - Static method in enum org.jmol.constant.EnumVdw
 
getVector(short) - Static method in class org.jmol.g3d.Normix3D
 
getVector(int) - Method in class org.jmol.util.Quaternion
 
getVector(int, float) - Method in class org.jmol.util.Quaternion
 
getVectorsAndOrigin() - Method in class org.jmol.jvxl.readers.MapFileReader
 
getVectorScale() - Method in class org.jmol.viewer.Viewer
 
getVectorX() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getVectorX() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getVectorY() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getVectorY() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getVectorZ() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getVectorZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getVertex(short, short) - Static method in class org.jmol.geodesic.Geodesic
 
getVertexCount() - Method in class org.jmol.export.MeshData.Data
 
getVertexCount(int) - Static method in class org.jmol.geodesic.Geodesic
 
getVertexIndexFromNumber(int) - Method in class org.jmol.shape.Mesh
 
getVertexList(DrawMesh, int, int) - Static method in class org.jmol.shapespecial.Draw
 
getVertexSource() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getVertexValues(boolean) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getVertexVector(int) - Static method in class org.jmol.geodesic.Geodesic
 
getVertexVectors() - Static method in class org.jmol.geodesic.Geodesic
 
getVertexVectorsCount() - Static method in class org.jmol.geodesic.Geodesic
 
getVertices() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getVertices(Mesh) - Method in class org.jmol.shape.MeshCollection
 
getVertices() - Method in class org.jmol.symmetry.UnitCell
 
getVertices() - Method in class org.jmol.util.MeshSurface
 
getVibrationCoord(char) - Method in class org.jmol.modelset.Atom
 
getVibrationCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
 
getVibrationPeriod() - Method in class org.jmol.viewer.Viewer
 
getVibrationScale() - Method in class org.jmol.viewer.Viewer
 
getVibrationVector() - Method in class org.jmol.modelset.Atom
 
getVibrationVector(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getVibrationVector(int) - Method in class org.jmol.viewer.Viewer
 
getViewer() - Method in class org.jmol.export.dialog.FilePreview.FPPanel
 
getViewer() - Method in class org.jmol.shape.Shape
 
getViewerData() - Method in class org.jmol.popup.SimplePopup
 
getVisibleFramesBitSet() - Method in class org.jmol.api.JmolViewer
 
getVisibleFramesBitSet() - Method in class org.jmol.viewer.AnimationManager
 
getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
 
getVisibleGhostBitSet() - Method in class org.jmol.shape.Mesh
 
getVisibleSet() - Method in class org.jmol.modelset.AtomCollection
 
getVisibleSet() - Method in class org.jmol.viewer.Viewer
 
getVisibleVertexBitSet() - Method in class org.jmol.shape.Mesh
 
getVolume(Viewer, EnumVdw) - Method in class org.jmol.modelset.Atom
 
getVolume() - Method in class org.jmol.util.ContactPair
 
getVolume(BitSet, String) - Method in class org.jmol.viewer.Viewer
 
getVolumeData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getVolumetricVectorLengths() - Method in interface org.jmol.api.VolumeDataInterface
 
getVolumetricVectorLengths() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxel(int, int, int, int) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getVoxelCounts() - Method in interface org.jmol.api.VolumeDataInterface
 
getVoxelCounts() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelData() - Method in interface org.jmol.api.VolumeDataInterface
 
getVoxelData() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelData(int) - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelValue(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
getWidth(Object) - Static method in class org.jmol.awt.Image
 
getWidth() - Method in class org.jmol.g3d.Text3D
 
getWidthUnitVector() - Method in class org.jmol.modelsetbio.Sheet
 
getWindow(Container) - Static method in class org.jmol.console.JmolConsole
 
getWindowBorder(String) - Method in class org.jmol.export.history.HistoryFile
 
getWindowPosition(String) - Method in class org.jmol.export.history.HistoryFile
 
getWindowSize(String) - Method in class org.jmol.export.history.HistoryFile
 
getWindowState(StringBuffer, int, int) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getWindowVisibility(String) - Method in class org.jmol.export.history.HistoryFile
 
getWingAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getWingPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
getWireframeRotation() - Method in class org.jmol.viewer.Viewer
 
getWithinDistanceVector(List<Object[]>, float, Point3f, BitSet, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
getWord(String) - Method in class org.jmol.popup.PopupResource
 
getWordContents() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
getWordContents() - Method in class org.jmol.popup.MainPopupResourceBundle
 
getWordContents() - Method in class org.jmol.popup.PopupResource
 
getWordCountFromBitCount(int) - Static method in class org.jmol.util.FastBitSet
 
getWorkingRadius(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getWorkingRadius(Atom, AtomData) - Method in class org.jmol.modelset.AtomCollection
 
getWrappedState(boolean, int, int) - Method in class org.jmol.viewer.Viewer
 
getX() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getX() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getX() - Method in class org.jmol.script.ScriptMathProcessor
 
getX(SmilesAtom, JmolNode[], int, boolean, boolean) - Method in class org.jmol.smiles.SmilesSearch
 
getXmlAttrib(String, String) - Static method in class org.jmol.util.XmlReader
 
getXmlData(String, String, boolean, boolean) - Method in class org.jmol.util.XmlReader
 
getXmlPoint(String, String) - Method in class org.jmol.util.XmlReader
 
getXMLReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
getXmlReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
getXmlType(JSObject) - Static method in class org.jmol.adapter.smarter.Resolver
 
getXmlType(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getXOffset(int) - Static method in class org.jmol.shape.Object2d
 
getXPlatformLook(JFileChooser) - Static method in class org.jmol.export.dialog.Dialog
 
getXYZ() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getXYZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getXYZ(boolean) - Method in class org.jmol.symmetry.HallInfo.RotationTerm
 
getXyz(int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
getXyz(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
 
getXYZFromMatrix(Matrix4f, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getY() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getY() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getYCCArray(ApiPlatform) - Method in class org.jmol.util.JpegInfo
 
getYOffset(int) - Static method in class org.jmol.shape.Object2d
 
getYzCount() - Method in class org.jmol.jvxl.data.VolumeData
 
getZ() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getZapName() - Method in class org.jmol.viewer.Viewer
 
getZeroBasedXyzRasmol() - Method in class org.jmol.viewer.Viewer
 
getZipDirectory(String, boolean) - Method in class org.jmol.viewer.FileManager
 
getZipDirectoryAndClose(InputStream, boolean) - Static method in class org.jmol.util.ZipUtil
 
getZipDirectoryAsString(String) - Method in class org.jmol.viewer.FileManager
 
getZipDirectoryAsStringAndClose(InputStream) - Static method in class org.jmol.util.ZipUtil
 
getZipDirectoryOrErrorAndClose(InputStream, boolean) - Static method in class org.jmol.util.ZipUtil
 
getZipEntryAsBytes(ZipInputStream) - Static method in class org.jmol.util.ZipUtil
 
getZipEntryAsString(InputStream) - Static method in class org.jmol.util.ZipUtil
 
getZipFileContents(InputStream, String[], int, boolean) - Static method in class org.jmol.util.ZipUtil
iteratively drills into zip files of zip files to extract file content or zip file directory.
getZipFileContentsAsBytes(InputStream, String[], int) - Static method in class org.jmol.util.ZipUtil
 
getZoom(int, BitSet, float) - Method in class org.jmol.script.ScriptEvaluator
 
getZoomEnabled() - Method in class org.jmol.viewer.Viewer
 
getZoomLarge() - Method in class org.jmol.viewer.Viewer
 
getZoomPercent() - Method in class org.jmol.api.JmolViewer
 
getZoomPercent() - Method in class org.jmol.viewer.Viewer
 
getZoomPercentFloat() - Method in class org.jmol.api.JmolViewer
 
getZoomPercentFloat() - Method in class org.jmol.viewer.TransformManager
 
getZoomPercentFloat() - Method in class org.jmol.viewer.Viewer
 
getZoomSetting() - Method in class org.jmol.viewer.TransformManager
 
getZoomSetting() - Method in class org.jmol.viewer.Viewer
 
getZShadePower() - Static method in class org.jmol.g3d.Graphics3D
 
geVdwBitSet() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
ghemicalMMLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GhemicalMMReader - Class in org.jmol.adapter.readers.simple
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.simple.GhemicalMMReader
 
ghostCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
ghostPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
gibbsEnergy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
gibbsEnergy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
gibbsEntropy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
GIFEncode(OutputStream, int, int, boolean, byte, int, int, byte[], byte[], byte[]) - Method in class org.jmol.export.image.GifEncoder
 
GifEncoder - Class in org.jmol.export.image
 
GifEncoder(Image, OutputStream) - Constructor for class org.jmol.export.image.GifEncoder
 
GifEncoder(Image, OutputStream, boolean) - Constructor for class org.jmol.export.image.GifEncoder
 
GifEncoder(ImageProducer, OutputStream) - Constructor for class org.jmol.export.image.GifEncoder
 
GifEncoder(ImageProducer, OutputStream, boolean) - Constructor for class org.jmol.export.image.GifEncoder
 
GifEncoder.AdaptiveColorCollection - Class in org.jmol.export.image
 
GifEncoder.AdaptiveColorCollection(int) - Constructor for class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
GifEncoder.ColorItem - Class in org.jmol.export.image
 
GifEncoder.ColorItem(int, int, int, boolean) - Constructor for class org.jmol.export.image.GifEncoder.ColorItem
 
GifEncoder.ColorVector - Class in org.jmol.export.image
 
GifEncoder.ColorVector() - Constructor for class org.jmol.export.image.GifEncoder.ColorVector
 
GifEncoder.ColorVector.CountComparator - Class in org.jmol.export.image
 
GifEncoder.ColorVector.CountComparator() - Constructor for class org.jmol.export.image.GifEncoder.ColorVector.CountComparator
 
GIFNextPixel() - Method in class org.jmol.export.image.GifEncoder
 
global - Variable in class org.jmol.viewer.Viewer
 
GLOBAL_CONECT - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_FRACTCOORD - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_ISPDB - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_SYMMETRY - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_UNITCELLS - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
globalBooleans - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
globalDoApplySymmetry - Variable in class org.jmol.adapter.readers.xtal.AimsReader
 
globalSerialID - Static variable in class org.jmol.modelsetbio.ProteinStructure
 
goButton - Variable in class org.openscience.chimetojmol.ChimePanel
 
goButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
gOffscreen - Variable in class org.jmol.g3d.Platform3D
 
GOLD - Static variable in class org.jmol.g3d.Graphics3D
 
goPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Save or else launch povray- ie do our thang!
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
gotoCmd(String) - Method in class org.jmol.script.ScriptEvaluator
 
gotocmd - Static variable in class org.jmol.script.Token
 
gotoCommand(int, boolean, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
gotoParsedLine() - Method in class org.jmol.console.ScriptEditor
 
gotoPosition(int, int) - Method in class org.jmol.console.ScriptEditor
 
gotoSector(int) - Method in class org.jmol.util.CompoundDocument
 
gotoTop() - Method in class org.jmol.console.ScriptEditor
 
grabPixels(Object, int, int, int, int) - Method in interface org.jmol.api.ApiPlatform
 
grabPixels(Object, int, int, int[]) - Method in interface org.jmol.api.ApiPlatform
used for JPG writing only; can be ignored
grabPixels(Object, int, int, int[]) - Static method in class org.jmol.awt.Image
 
grabPixels(Object, int, int, int, int) - Static method in class org.jmol.awt.Image
 
grabPixels(Object, int, int, int[]) - Method in class org.jmol.awt.Platform
 
grabPixels(Object, int, int, int, int) - Method in class org.jmol.awt.Platform
 
grad - Variable in class org.jmol.quantum.NciCalculation
 
GRADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
gradients - Variable in class org.jmol.minimize.forcefield.Calculations
 
Graphics3D - Class in org.jmol.g3d
Provides high-level graphics primitives for 3D visualization.
Graphics3D(ApiPlatform, boolean) - Constructor for class org.jmol.g3d.Graphics3D
Allocates a g3d object
Graphics3D.Pixel - Class in org.jmol.g3d
 
Graphics3D.Pixel() - Constructor for class org.jmol.g3d.Graphics3D.Pixel
 
Graphics3D.ShadePixel - Class in org.jmol.g3d
 
Graphics3D.ShadePixel() - Constructor for class org.jmol.g3d.Graphics3D.ShadePixel
 
graphicsOffscreen - Variable in class org.jmol.g3d.Platform3D
 
GRAY - Static variable in class org.jmol.g3d.Graphics3D
 
GRAY - Static variable in class org.jmol.util.ColorEncoder
 
green - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
GREEN - Static variable in class org.jmol.g3d.Graphics3D
 
greyscalerendering - Static variable in class org.jmol.script.Token
 
greyscaleRendering - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
gridpoints - Static variable in class org.jmol.script.Token
 
gRight - Variable in class org.jmol.applet.Jmol
 
GromacsReader - Class in org.jmol.adapter.readers.more
 
GromacsReader() - Constructor for class org.jmol.adapter.readers.more.GromacsReader
 
group - Variable in class org.jmol.modelset.Atom
 
Group - Class in org.jmol.modelset
 
Group(Chain, String, int, int, int) - Constructor for class org.jmol.modelset.Group
 
group - Variable in class org.jmol.popup.SimplePopup
 
group - Static variable in class org.jmol.script.Token
 
group1 - Static variable in class org.jmol.script.Token
 
group3 - Variable in class org.jmol.adapter.smarter.Atom
 
group3Count - Static variable in class org.jmol.viewer.JmolConstants
 
group3Counts - Variable in class org.jmol.modelset.ModelLoader
 
group3Counts - Variable in class org.jmol.popup.JmolPopup
 
group3List - Variable in class org.jmol.popup.JmolPopup
 
group3List - Static variable in class org.jmol.viewer.JmolConstants
 
group3Lists - Variable in class org.jmol.modelset.ModelLoader
 
group3NameCount - Static variable in class org.jmol.modelset.Group
 
group3Names - Static variable in class org.jmol.modelset.Group
 
group3Of - Variable in class org.jmol.modelset.ModelLoader
 
group3s - Variable in class org.jmol.adapter.readers.more.MdTopReader
 
GROUP_FLAG - Static variable in class org.jmol.shape.Labels
 
GROUP_PDB - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
groupCount - Variable in class org.jmol.modelset.Chain
 
groupCount - Variable in class org.jmol.modelset.Model
 
groupCount - Variable in class org.jmol.modelset.ModelLoader
 
groupID - Variable in class org.jmol.modelset.Group
 
groupID - Variable in class org.jmol.multitouch.ActionManagerMT
 
groupid - Static variable in class org.jmol.script.Token
 
GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_ARGININE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_ION_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_ION_MIN - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_LYSINE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_PROLINE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_SOLVENT_MIN - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_WATER - Static variable in class org.jmol.viewer.JmolConstants
 
groupIndex - Variable in class org.jmol.modelset.Group
 
groupindex - Static variable in class org.jmol.script.Token
 
groups - Variable in class org.jmol.modelset.Chain
 
groups - Variable in class org.jmol.modelset.ModelLoader
 
growAtomArrays(int) - Method in class org.jmol.modelset.ModelCollection
 
gScaled - Variable in class org.jmol.g3d.Rgb16
 
GT - Class in org.jmol.i18n
 
GT(String) - Constructor for class org.jmol.i18n.GT
 
GT() - Constructor for class org.jmol.i18n.GT
 
GT.Language - Class in org.jmol.i18n
 
GT.Language(String, String, String, boolean) - Constructor for class org.jmol.i18n.GT.Language
 
gto_exp - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
gui - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
guimap - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
GuiMap - Class in org.openscience.jmol.app.jmolpanel
 
GuiMap() - Constructor for class org.openscience.jmol.app.jmolpanel.GuiMap
 
guimap - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
guimap - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
gulpContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GulpReader - Class in org.jmol.adapter.readers.xtal
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
GulpReader() - Constructor for class org.jmol.adapter.readers.xtal.GulpReader
 
gxTemp - Variable in class org.jmol.quantum.NciCalculation
 
gxxTemp - Variable in class org.jmol.quantum.NciCalculation
 
gxyTemp - Variable in class org.jmol.quantum.NciCalculation
 
gxzTemp - Variable in class org.jmol.quantum.NciCalculation
 
gyTemp - Variable in class org.jmol.quantum.NciCalculation
 
gyyTemp - Variable in class org.jmol.quantum.NciCalculation
 
gyzTemp - Variable in class org.jmol.quantum.NciCalculation
 
gzTemp - Variable in class org.jmol.quantum.NciCalculation
 
gzzTemp - Variable in class org.jmol.quantum.NciCalculation
 

H

H3T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
H5T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
halfRoot5 - Static variable in class org.jmol.geodesic.Geodesic
 
hAlignNames - Static variable in class org.jmol.shape.Object2d
 
HallInfo - Class in org.jmol.symmetry
 
HallInfo(String) - Constructor for class org.jmol.symmetry.HallInfo
 
hallInfo - Variable in class org.jmol.symmetry.SpaceGroup
 
HallInfo.RotationTerm - Class in org.jmol.symmetry
 
HallInfo.RotationTerm() - Constructor for class org.jmol.symmetry.HallInfo.RotationTerm
 
HallInfo.RotationTerm(String, int, char) - Constructor for class org.jmol.symmetry.HallInfo.RotationTerm
 
hallRotationTerms - Static variable in class org.jmol.symmetry.Rotation
 
hallSymbol - Variable in class org.jmol.symmetry.HallInfo
 
hallSymbol - Variable in class org.jmol.symmetry.SpaceGroup
 
hallTranslationTerms - Static variable in class org.jmol.symmetry.Translation
 
halo - Static variable in class org.jmol.script.Token
 
Halos - Class in org.jmol.shape
 
Halos() - Constructor for class org.jmol.shape.Halos
 
HalosRenderer - Class in org.jmol.shape
 
HalosRenderer() - Constructor for class org.jmol.shape.HalosRenderer
 
halt - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
haltButton - Variable in class org.jmol.console.ScriptEditor
 
haltButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
haltExecution() - Method in class org.jmol.script.ScriptEvaluator
 
haltScriptExecution() - Method in class org.jmol.api.JmolViewer
 
haltScriptExecution() - Method in class org.jmol.viewer.Viewer
 
handleError() - Method in class org.jmol.script.ScriptCompiler
 
handleError(Error, boolean) - Method in class org.jmol.viewer.Viewer
 
handleEvent(Event) - Method in class org.jmol.applet.AppletWrapper
 
handleEvent(Event) - Method in class org.jmol.applet.Jmol
 
handleEvent(Event) - Method in interface org.jmol.applet.WrappedApplet
 
handleOldJvm10Event(int, int, int, int, long) - Method in interface org.jmol.api.ApiPlatform
 
handleOldJvm10Event(int, int, int, int, long) - Method in class org.jmol.api.JmolViewer
 
handleOldJvm10Event(int, int, int, int, long) - Method in class org.jmol.awt.Mouse
 
handleOldJvm10Event(int, int, int, int, long) - Method in class org.jmol.awt.Platform
 
handleOldJvm10Event(int, int, int, int, long) - Method in class org.jmol.viewer.Viewer
 
has(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
 
HAS_CLIENT - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
HAS_DRIVER - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
HAS_MAXGRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
hasBfactorRange - Variable in class org.jmol.modelset.AtomCollection
 
hasBfactorRange - Variable in class org.jmol.shapebio.BioShape
 
hasCalculatedHBonds(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
hasCalculatedHBonds(BitSet) - Method in class org.jmol.viewer.Viewer
 
hasColorData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
hasColorRange - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
hasContent() - Method in class org.jmol.g3d.Graphics3D
 
hasContent() - Method in class org.jmol.g3d.Platform3D
 
hasFocus(Object) - Method in interface org.jmol.api.ApiPlatform
 
hasFocus(Object) - Static method in class org.jmol.awt.Display
 
hasFocus(Object) - Method in class org.jmol.awt.Platform
 
hasFocus() - Method in class org.jmol.viewer.Viewer
 
hasGridPoints - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
hash - Static variable in class org.jmol.script.Token
 
hashCode() - Method in class org.jmol.modelset.Atom
 
hashCode() - Method in class org.jmol.util.FastBitSet
 
hasLocalArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
hasMoreElements() - Method in class org.jmol.bspt.CubeIterator
normal iterator predicate
hasMoreTokens() - Method in class org.jmol.util.CifDataReader
 
hasNext() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
hasNext() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
hasNext() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
hasNext() - Method in interface org.jmol.api.AtomIndexIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapter.BondIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
 
hasNext() - Method in interface org.jmol.modelset.BondIterator
 
hasNext() - Method in class org.jmol.modelset.BondIteratorSelected
 
hasOAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
hasPlane() - Method in class org.jmol.jvxl.data.VolumeData
 
hasProgressBar - Variable in class org.jmol.applet.Jmol
 
hasRasmolHBonds - Variable in class org.jmol.modelset.Model
 
hasRnaO2Prime - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
hasSerialArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
hasSymbol - Variable in class org.jmol.smiles.SmilesAtom
 
hasVibration() - Method in class org.jmol.modelset.Atom
 
hasWingPoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
hAtomRadius - Variable in class org.jmol.atomdata.AtomData
 
hAtoms - Variable in class org.jmol.atomdata.AtomData
 
haveAt - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
haveAtomFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
haveAtoms - Variable in class org.jmol.shapespecial.Dipole
 
haveAtomStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
 
haveAxis(int, Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
haveBFactors - Variable in class org.jmol.popup.SimplePopup
 
haveBitSetVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
haveBondStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
 
haveBorder - Variable in class org.openscience.jmol.app.JmolApp
 
haveBorder - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
haveBsDisplay - Variable in class org.jmol.shape.MeshRenderer
 
haveBsSlabDisplay - Variable in class org.jmol.shape.MeshRenderer
 
haveBsSlabGhost - Variable in class org.jmol.shape.MeshRenderer
 
haveCharges - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
haveCharges - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
haveCharges - Variable in class org.jmol.popup.SimplePopup
 
haveCircle - Variable in class org.jmol.export._IdtfExporter
 
haveCoeffMap - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
haveComments - Variable in class org.jmol.script.ScriptCompiler
 
haveCommon(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
 
haveCone - Variable in class org.jmol.export._IdtfExporter
 
haveConsole - Variable in class org.openscience.jmol.app.JmolApp
 
haveContourData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
haveControlPointScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
 
haveCylinder - Variable in class org.jmol.export._IdtfExporter
 
haveCylinderIn - Variable in class org.jmol.export._IdtfExporter
 
haveDisplay - Variable in class org.jmol.viewer.Viewer
 
haveDisplay - Variable in class org.openscience.jmol.app.JmolApp
 
haveDisplay - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
haveDocumentAccess - Variable in class org.jmol.applet.Jmol
 
haveDoubleBonds - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
haveEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
 
haveEnergy - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
haveFileSet() - Method in class org.jmol.viewer.Viewer
 
haveFrame() - Method in class org.jmol.api.JmolViewer
 
haveFrame() - Method in class org.jmol.viewer.Viewer
 
haveHeader - Variable in class org.jmol.adapter.readers.simple.MopacReader
 
haveHiddenBonds - Variable in class org.jmol.modelset.BondCollection
 
haveHsAlready - Variable in class org.jmol.modelsetbio.Resolver
 
haveInversionCenter - Variable in class org.jmol.symmetry.PointGroup
 
haveLine - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
 
haveMacros - Variable in class org.jmol.export._PovrayExporter
 
haveMappedSerials - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
haveMappedSerials - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
haveModel - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
haveModelKit() - Method in class org.jmol.modelset.ModelCollection
 
haveModelKit() - Method in class org.jmol.viewer.Viewer
 
haveModelSet() - Method in class org.jmol.viewer.Viewer
 
haveModified - Variable in class org.jmol.modelset.MeasurementPending
 
haveModified() - Method in class org.jmol.modelset.MeasurementPending
 
haveMolecule - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
haveMultiTouchInput - Variable in class org.jmol.viewer.ActionManager
 
haveNboCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
haveNboOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
haveNotifiedError - Variable in class org.jmol.applet.Jmol.MyStatusListener
 
haveNotifiedNaN - Variable in class org.jmol.viewer.TransformManager
 
haveParameters() - Method in class org.jmol.modelset.Group
 
haveParameters - Variable in class org.jmol.modelsetbio.BioPolymer
 
haveParameters() - Method in class org.jmol.modelsetbio.Monomer
 
haveParams() - Method in class org.jmol.minimize.forcefield.Calculations
 
havePartialChargeFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
havePartialCharges() - Method in class org.jmol.api.JmolViewer
 
havePartialCharges - Variable in class org.jmol.minimize.forcefield.Calculations
 
havePartialCharges() - Method in class org.jmol.viewer.Viewer
 
havePhonons - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
havePlanarContours - Variable in class org.jmol.shape.Mesh
 
havePlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
havePoints - Variable in class org.jmol.quantum.MOCalculation
 
havePoints - Variable in class org.jmol.quantum.NciCalculation
 
havePrimitiveMapping - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
haveQuads - Variable in class org.jmol.util.MeshSurface
 
haveReadColorData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
haveSelected - Variable in class org.jmol.smiles.SmilesSearch
 
haveSelection - Variable in class org.jmol.viewer.ActionManager
 
haveSequenceNumber(int) - Static method in class org.jmol.modelset.Group
 
haveSetAnisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
haveSetStructureList - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
haveSpaceBeforeSquare - Variable in class org.jmol.script.ScriptMathProcessor
 
haveSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
 
haveSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
 
haveSphere - Variable in class org.jmol.export._IdtfExporter
 
haveStraightness - Variable in class org.jmol.modelset.AtomCollection
 
haveString - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
haveSurfaceAtoms - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
haveTarget - Variable in class org.jmol.modelset.MeasurementPending
 
haveTarget() - Method in class org.jmol.modelset.MeasurementPending
 
haveTranslations - Static variable in class org.jmol.export.dialog.Dialog
 
haveTranslucentObjects() - Method in interface org.jmol.api.JmolRendererInterface
 
haveTranslucentObjects() - Method in class org.jmol.export.Export3D
 
haveTranslucentObjects - Variable in class org.jmol.g3d.Graphics3D
 
haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
 
haveUnitCell - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
haveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
haveUnitCell() - Method in interface org.jmol.api.SymmetryInterface
 
haveUnitCell() - Method in class org.jmol.symmetry.Symmetry
 
haveWarned - Variable in class org.jmol.modelset.BondCollection
 
haveXyPoints - Variable in class org.jmol.shape.Mesh
 
HBond - Class in org.jmol.modelset
 
HBond(Atom, Atom, int, short, short, float) - Constructor for class org.jmol.modelset.HBond
 
HBond(Atom, Atom, int, float) - Constructor for class org.jmol.modelset.HBond
 
hbond() - Method in class org.jmol.script.ScriptEvaluator
 
hbond - Static variable in class org.jmol.script.Token
 
hbondMin - Static variable in class org.jmol.modelset.ModelCollection
 
hbondsangleminimum - Static variable in class org.jmol.script.Token
 
hbondsAngleMinimum - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hbondsbackbone - Static variable in class org.jmol.script.Token
 
hbondsBackbone - Variable in class org.jmol.shape.SticksRenderer
 
hbondsBackbone - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hbondsdistancemaximum - Static variable in class org.jmol.script.Token
 
hbondsDistanceMaximum - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hbondsrasmol - Static variable in class org.jmol.script.Token
 
hbondsRasmol - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hbondssolid - Static variable in class org.jmol.script.Token
 
hbondsSolid - Variable in class org.jmol.shape.SticksRenderer
 
hbondsSolid - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hCount - Variable in class org.jmol.minimize.MinAtom
 
hDashes - Static variable in class org.jmol.shape.SticksRenderer
 
hdrPos - Variable in class org.jmol.export.image.PngEncoder
 
header() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
header - Variable in class org.jmol.export.history.HistoryFile
The information written to the header of the history file.
header - Variable in class org.jmol.util.CompoundDocument
 
HEADER_GAMESS_OCCUPANCIES - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_GAMESS_ORIGINAL - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_GAMESS_UK_MO - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_NONE - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
headerContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
headOffsetVector - Variable in class org.jmol.shapespecial.VectorsRenderer
 
headScale - Variable in class org.jmol.shapespecial.VectorsRenderer
 
headWidthPixels - Variable in class org.jmol.shapespecial.DipolesRenderer
 
headWidthPixels - Variable in class org.jmol.shapespecial.VectorsRenderer
 
heavyAtomIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
height - Variable in class org.jmol.export.Export3D
 
height - Variable in class org.jmol.export.image.GifEncoder
 
Height - Variable in class org.jmol.export.image.GifEncoder
 
height - Variable in class org.jmol.export.image.ImageEncoder
 
height - Variable in class org.jmol.export.image.PngEncoder
 
height - Variable in class org.jmol.g3d.Graphics3D
 
height - Variable in class org.jmol.g3d.Sphere3D
 
height - Variable in class org.jmol.g3d.Text3D
 
height - Variable in class org.jmol.util.Dimension
 
height - Variable in class org.jmol.util.Rectangle
 
height - Variable in class org.jmol.viewer.TransformManager
 
height - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
heightOffscreen - Variable in class org.jmol.g3d.Platform3D
 
heightUnitVector - Variable in class org.jmol.modelsetbio.Sheet
 
Helix - Class in org.jmol.modelsetbio
 
Helix(AlphaPolymer, int, int, int, EnumStructure) - Constructor for class org.jmol.modelsetbio.Helix
 
helix - Static variable in class org.jmol.script.Token
 
helix310 - Static variable in class org.jmol.script.Token
 
HELIX_CLASS - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
helixalpha - Static variable in class org.jmol.script.Token
 
helixpi - Static variable in class org.jmol.script.Token
 
helixstep - Static variable in class org.jmol.script.Token
 
helixStep - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
help() - Method in class org.jmol.script.ScriptEvaluator
 
help - Static variable in class org.jmol.script.Token
 
helpButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
helpButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
HelpDialog - Class in org.openscience.jmol.app.jmolpanel
 
HelpDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
 
HelpDialog(JFrame, URL) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
If url is null, then the default help url is taken.
HelpDialog.PageLoader - Class in org.openscience.jmol.app.jmolpanel
temporary class that loads synchronously (although later than the request so that a cursor change can be done).
HelpDialog.PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
 
helppath - Static variable in class org.jmol.script.Token
 
helpPath - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hemisphereOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
hermite3d - Variable in class org.jmol.export.Export3D
 
hermite3d - Variable in class org.jmol.g3d.Graphics3D
 
Hermite3D - Class in org.jmol.g3d
Implementation of hermite curves for drawing smoothed curves that pass through specified points.
Hermite3D(JmolRendererInterface) - Constructor for class org.jmol.g3d.Hermite3D
 
hermitelevel - Static variable in class org.jmol.script.Token
 
hermiteLevel - Variable in class org.jmol.shapebio.BioShapeRenderer
 
hermiteLevel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hess - Variable in class org.jmol.quantum.NciCalculation
 
het() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
hetatmData - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
optional nonloop format -- see 1jsa.cif
hetero - Static variable in class org.jmol.script.Token
 
hetnam() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
hi - Variable in class org.jmol.util.ColorEncoder
 
hidden - Static variable in class org.jmol.script.Token
 
hidden - Variable in class org.jmol.shape.Object2d
 
hide - Static variable in class org.jmol.script.Token
 
hide(ModelSet, BitSet, Boolean, boolean) - Method in class org.jmol.viewer.SelectionManager
 
hidenameinpopup - Static variable in class org.jmol.script.Token
 
hideNameInPopup - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hidenavigationpoint - Static variable in class org.jmol.script.Token
 
hideNavigationPoint - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hidenotselected - Static variable in class org.jmol.script.Token
 
hideNotSelected - Variable in class org.jmol.viewer.SelectionManager
 
HIGH - Static variable in class org.jmol.util.ColorEncoder
 
highlight - Static variable in class org.jmol.script.Token
 
highlight(BitSet) - Method in class org.jmol.viewer.Viewer
 
highlightBond(int, boolean) - Method in class org.jmol.viewer.Viewer
 
highresolution - Static variable in class org.jmol.script.Token
 
highResolutionFlag - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hintflags - Variable in class org.jmol.export.image.ImageEncoder
 
history(int) - Method in class org.jmol.script.ScriptEvaluator
 
history - Static variable in class org.jmol.script.Token
 
historyButton - Variable in class org.jmol.console.JmolConsole
 
historyDisabled - Variable in class org.jmol.script.ScriptEvaluator
 
HistoryFile - Class in org.jmol.export.history
The history file contains data from previous uses of Jmol.
HistoryFile(File, String) - Constructor for class org.jmol.export.history.HistoryFile
Creates a history file.
historyFile - Variable in class org.openscience.jmol.app.JmolApp
 
historyFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
historyFile - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
historyFile - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
historylevel - Static variable in class org.jmol.script.Token
 
histWinName - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
hkl - Static variable in class org.jmol.script.Token
 
hklParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
hmSymbol - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAbbr - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAbbrShort - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAlternative - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolExt - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolFull - Variable in class org.jmol.symmetry.SpaceGroup
 
hNames - Variable in class org.jmol.modelsetbio.Resolver
 
holdRepaint - Variable in class org.jmol.viewer.RepaintManager
 
homeAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
homePosition() - Method in class org.jmol.api.JmolViewer
 
homePosition(boolean) - Method in class org.jmol.viewer.TransformManager
 
homePosition() - Method in class org.jmol.viewer.Viewer
 
homo - Static variable in class org.jmol.script.Token
 
HOTPINK - Static variable in class org.jmol.g3d.Graphics3D
 
hover() - Method in class org.jmol.script.ScriptEvaluator
 
hover - Static variable in class org.jmol.script.Token
 
Hover - Class in org.jmol.shape
 
Hover() - Constructor for class org.jmol.shape.Hover
 
hoverable - Static variable in class org.jmol.viewer.ShapeManager
 
hoverActive - Variable in class org.jmol.viewer.ActionManager
 
hoverAtomIndex - Variable in class org.jmol.viewer.Viewer
 
hoverdelay - Static variable in class org.jmol.script.Token
 
hoverDelayMs - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hoverEnabled - Variable in class org.jmol.viewer.Viewer
 
hoverKey(int, int) - Method in class org.jmol.shapesurface.Isosurface
 
hoverlabel - Static variable in class org.jmol.script.Token
 
hoverOff() - Method in class org.jmol.viewer.ActionManager
 
hoverOff() - Method in class org.jmol.viewer.Viewer
 
hoverOn(int) - Method in class org.jmol.viewer.ActionManager
 
hoverOn(int, int) - Method in class org.jmol.viewer.Viewer
 
hoverOn(int, int, String) - Method in class org.jmol.viewer.Viewer
 
HoverRenderer - Class in org.jmol.shape
 
HoverRenderer() - Constructor for class org.jmol.shape.HoverRenderer
 
hoverText - Variable in class org.jmol.shape.Hover
 
hoverText - Variable in class org.jmol.viewer.Viewer
 
hoverWatcherThread - Variable in class org.jmol.viewer.ActionManager
 
HsampFactor - Variable in class org.jmol.util.JpegInfo
 
HSIZE - Static variable in class org.jmol.export.image.GifEncoder
 
hsize - Variable in class org.jmol.export.image.GifEncoder
 
htab - Variable in class org.jmol.export.image.GifEncoder
 
htAtomicPotentials - Variable in class org.jmol.quantum.MepCalculation
 
htAtomMap - Variable in class org.jmol.modelset.ModelLoader
 
htBondMap - Variable in class org.jmol.modelsetbio.Resolver
 
htBonds - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
htBooleanParameterFlags - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
htCheckbox - Variable in class org.jmol.popup.SimplePopup
 
htDefs - Variable in class org.jmol.export._IdtfExporter
 
htEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
htElementMap - Static variable in class org.jmol.util.Elements
 
htElementsInCurrentGroup - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
 
htExponents - Variable in class org.jmol.adapter.readers.quantum.DgridReader
 
htFont3d - Static variable in class org.jmol.g3d.Text3D
 
htFont3dAntialias - Static variable in class org.jmol.g3d.Text3D
 
htFormul - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htFuncMap - Variable in class org.jmol.adapter.readers.quantum.DgridReader
 
htGroup - Static variable in class org.jmol.modelset.Group
 
htGroupBonds - Variable in class org.jmol.modelsetbio.Resolver
 
htHetero - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
htHetero - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htMeasures - Variable in class org.jmol.smiles.SmilesParser
 
htMenus - Variable in class org.jmol.popup.SimplePopup
 
html - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
html - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
html - Variable in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
 
htmlAppletTemplate - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
htmlName - Variable in class org.jmol.applet.Jmol
 
htmlName - Variable in class org.jmol.viewer.Viewer
 
htModels - Variable in class org.jmol.shapesurface.MolecularOrbital
 
htMolIds - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htNested - Variable in class org.jmol.smiles.SmilesSearch
 
htNodes - Variable in class org.jmol.export._IdtfExporter
 
htNonbooleanParameterValues - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
htObjects - Variable in class org.jmol.shape.MeshCollection
 
htParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
htParams - Variable in class org.jmol.viewer.FileManager.DOMReader
 
htParams - Variable in class org.jmol.viewer.FileManager.FileReader
 
htParams - Variable in class org.jmol.viewer.FileManager.FilesReader
 
htPdbBondInfo - Variable in class org.jmol.viewer.Viewer
 
htPropertyFlagsRemoved - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
htPts - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
htRegistry - Static variable in class org.jmol.applet.JmolAppletRegistry
 
htRings - Variable in class org.jmol.smiles.SmilesGenerator
 
htRingsSequence - Variable in class org.jmol.smiles.SmilesGenerator
 
htSites - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
htSites - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htSpecialAtoms - Static variable in class org.jmol.viewer.JmolConstants
 
htSpheresRendered - Variable in class org.jmol.export._VrmlExporter
 
htSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
htUserFunctions - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
htUserVariables - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
htVertex - Static variable in class org.jmol.geodesic.Geodesic
 
Huf - Variable in class org.jmol.util.JpegEncoder
 
Huffman - Class in org.jmol.util
 
Huffman(int, int) - Constructor for class org.jmol.util.Huffman
 
HuffmanBlockEncoder(BufferedOutputStream, int[], int, int, int) - Method in class org.jmol.util.Huffman
HuffmanBlockEncoder run length encodes and Huffman encodes the quantized data.
hydrogen - Static variable in class org.jmol.script.Token
 
hydrogenAtomCount - Variable in class org.jmol.atomdata.AtomData
 
hydrogenAtomPsi(Point3f) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
hydrogenCount - Variable in class org.jmol.modelset.Model
 
hydrogensAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
hydrophobic - Static variable in class org.jmol.script.Token
 
hydrophobicities - Variable in class org.jmol.modelset.AtomCollection
 
hydrophobicities - Static variable in class org.jmol.util.Elements
 
hyperChemLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
HyperChemReader - Class in org.jmol.adapter.readers.simple
Support for .hin, HyperChem's native file format.
HyperChemReader() - Constructor for class org.jmol.adapter.readers.simple.HyperChemReader
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
 
hypot(double, double) - Static method in class org.jmol.util.Eigen
 

I

ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
ia - Variable in class org.jmol.minimize.forcefield.Calculation
 
ia - Variable in class org.jmol.minimize.forcefield.Calculations
 
iA - Variable in class org.jmol.util.MeshSurface
 
iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
 
iAtom - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
iAtom - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
iAtom - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
iatom - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
iAtom - Variable in class org.jmol.quantum.SlaterData
 
iAtomSurface - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
iAtomSurface - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
ib - Variable in class org.jmol.minimize.forcefield.Calculation
 
ib - Variable in class org.jmol.minimize.forcefield.Calculations
 
iB - Variable in class org.jmol.util.MeshSurface
 
ibond - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
iBond - Variable in class org.jmol.modelset.BondIteratorSelected
 
iBrace - Variable in class org.jmol.script.ScriptCompiler
 
ic - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
ic - Variable in class org.jmol.minimize.forcefield.Calculation
 
ic - Variable in class org.jmol.minimize.forcefield.Calculations
 
iC - Variable in class org.jmol.util.MeshSurface
 
ich - Variable in class org.jmol.util.CifDataReader
 
iChain - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
ichBrace - Variable in class org.jmol.script.ScriptCompiler
 
ichComment - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
ichCurrent - Variable in class org.jmol.adapter.smarter.LimitedLineReader
 
ichCurrent - Variable in class org.jmol.util.LimitedLineReader
 
ichCurrentCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
ichEnd - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
ichMathTerminator(String, int, int) - Static method in class org.jmol.script.ScriptCompiler
For @{....}
ichPeeked - Variable in class org.jmol.util.CifDataReader
 
ichToken - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
iCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
iCommandError - Variable in class org.jmol.script.ScriptContext
 
iCommandError - Variable in class org.jmol.script.ScriptEvaluator
 
iCutout - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
ID - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
id - Variable in enum org.jmol.constant.EnumPalette
 
id - Variable in enum org.jmol.constant.EnumQuantumShell
 
id - Variable in enum org.jmol.constant.EnumStructure
 
id - Variable in class org.jmol.export._MayaExporter
 
id - Variable in class org.jmol.minimize.forcefield.Calculation
 
id - Variable in class org.jmol.minimize.forcefield.Calculations
 
id - Variable in class org.jmol.modelset.TickInfo
 
id - Static variable in class org.jmol.script.Token
 
id - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
 
id - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
iD - Variable in class org.jmol.util.MeshSurface
 
id - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
iData - Variable in class org.jmol.minimize.forcefield.Calculation
 
ident - Variable in class org.jmol.script.ScriptFlowContext
 
identifier - Static variable in class org.jmol.script.Token
 
identify - Static variable in class org.jmol.script.Token
 
idFontFace - Variable in class org.jmol.g3d.Font3D
 
idFontStyle - Variable in class org.jmol.g3d.Font3D
 
idSpherical - Variable in enum org.jmol.constant.EnumQuantumShell
 
iE - Variable in class org.jmol.util.MeshSurface
 
ifCmd() - Method in class org.jmol.script.ScriptEvaluator
 
ifcmd - Static variable in class org.jmol.script.Token
 
ifPt - Variable in class org.jmol.script.ScriptMathProcessor
 
ifStack - Variable in class org.jmol.script.ScriptMathProcessor
 
ignore - Static variable in class org.jmol.script.Token
 
ignoreApplicationBundle - Static variable in class org.jmol.i18n.GT
 
ignoreApplicationBundle() - Static method in class org.jmol.i18n.GT
 
ignoreError - Variable in class org.jmol.script.ScriptEvaluator
 
ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreMOs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
ignoreStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
 
ignoreSymmetry - Variable in class org.jmol.adapter.smarter.Atom
 
iGroup - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
ihalf - Variable in class org.jmol.util.ColorEncoder
 
iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
 
iHaveCenterBitSet - Variable in class org.jmol.shapespecial.Polyhedra
 
iHaveDesiredModel - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveModelIndex - Variable in class org.jmol.shapesurface.Isosurface
 
iHaveModelStatement - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
iHaveQuotedString - Variable in class org.jmol.script.ScriptCompiler
 
iHaveSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveTwoEnds - Variable in class org.jmol.shapespecial.Dipoles
 
iHaveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHideBackground - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
ijkToPoint3f(int) - Method in interface org.jmol.api.SymmetryInterface
 
ijkToPoint3f(int) - Method in class org.jmol.symmetry.Symmetry
 
ijkToPoint3f(int) - Static method in class org.jmol.util.SimpleUnitCell
 
ijkToPoint3f(int, Point3f, int) - Static method in class org.jmol.util.SimpleUnitCell
 
Image - Class in org.jmol.awt
methods required by Jmol that access java.awt.Image private to org.jmol.awt
Image() - Constructor for class org.jmol.awt.Image
 
image - Variable in class org.jmol.export.image.ImageSelection
The image to transfer into the clipboard.
image - Variable in class org.jmol.export.image.PngEncoder
 
image - Static variable in class org.jmol.script.Token
 
image - Variable in class org.jmol.shape.Text
 
imageChoices - Variable in class org.jmol.export.dialog.Dialog
 
imageChoices - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
imageChooser - Static variable in class org.jmol.export.dialog.Dialog
 
imageComplete(int) - Method in class org.jmol.export.image.ImageEncoder
 
ImageCreator - Class in org.jmol.export.image
 
ImageCreator() - Constructor for class org.jmol.export.image.ImageCreator
 
ImageCreator(JmolViewer) - Constructor for class org.jmol.export.image.ImageCreator
 
ImageEncoder - Class in org.jmol.export.image
 
ImageEncoder(Image, OutputStream) - Constructor for class org.jmol.export.image.ImageEncoder
 
ImageEncoder(ImageProducer, OutputStream) - Constructor for class org.jmol.export.image.ImageEncoder
 
imageExtensions - Variable in class org.jmol.export.dialog.Dialog
 
imageExtensions - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
imageFontScaling - Variable in class org.jmol.shape.EchoRenderer
 
imageFontScaling - Variable in class org.jmol.shape.FontLineShapeRenderer
 
imageFontScaling - Variable in class org.jmol.shape.MeshRenderer
 
imageFontScaling - Variable in class org.jmol.viewer.Viewer
 
ImageHeight - Variable in class org.jmol.util.Huffman
 
imageHeight - Variable in class org.jmol.util.JpegInfo
 
imageobj - Variable in class org.jmol.util.JpegInfo
 
imageOffscreen - Variable in class org.jmol.g3d.Platform3D
 
imagePixelBuffer - Variable in class org.jmol.g3d.Platform3D
 
ImageSelection - Class in org.jmol.export.image
This class is used to transfer an Image into the clipboard.
ImageSelection(Image) - Constructor for class org.jmol.export.image.ImageSelection
Constructs a ImageSelection.
ImageSelection(String) - Constructor for class org.jmol.export.image.ImageSelection
Constructs a ImageSelection.
imageSizeChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Called when the ImageSize check box is modified
imageSizeHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeRatioBox - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeRatioCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeTextHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeTextWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imagestate - Static variable in class org.jmol.script.Token
 
imageState - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
imageType - Variable in class org.jmol.export.dialog.Dialog
 
imageType - Variable in class org.jmol.viewer.StatusManager
 
imageType - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ImageWidth - Variable in class org.jmol.util.Huffman
 
imageWidth - Variable in class org.jmol.util.JpegInfo
 
imesh - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
imgHeight - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
imgWidth - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
iMo0 - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
iMolecule - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
implementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
implicitHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
 
implicitStringCommand - Static variable in class org.jmol.script.Token
 
importData(JComponent, Transferable) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
in - Static variable in class org.jmol.script.Token
 
IN_JMOL - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
inchi - Static variable in class org.jmol.script.Token
 
inchikey - Static variable in class org.jmol.script.Token
 
includeAllRelatedFrames(BitSet) - Method in class org.jmol.modelset.ModelSet
 
includes(int, int) - Static method in class org.jmol.viewer.binding.Binding
 
includeValueNaN - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
incompleteCmd - Variable in class org.jmol.console.JmolConsole
 
increment(int) - Method in class org.jmol.script.ScriptVariable
 
increment - Static variable in class org.jmol.script.Token
 
incrementLineCount(String) - Method in class org.jmol.script.ScriptCompiler
 
incrementX - Variable in class org.jmol.script.ScriptMathProcessor
 
inDefinedStateBlock - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
index - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
index - Variable in class org.jmol.bspt.Bspt
 
index - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
index - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
index - Variable in class org.jmol.minimize.MinAtom
 
index - Variable in class org.jmol.modelset.Measurement
 
index - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
index - Variable in class org.jmol.quantum.SlaterData
 
index - Variable in class org.jmol.script.ScriptVariable
 
index - Variable in class org.jmol.shape.Mesh
 
index - Variable in class org.jmol.smiles.SmilesAtom
 
index - Variable in class org.jmol.smiles.SmilesMeasure
 
index - Variable in class org.jmol.symmetry.PointGroup.Operation
 
index - Variable in class org.jmol.symmetry.SpaceGroup
 
index - Variable in class org.jmol.util.JmolEdge
 
index - Variable in class org.jmol.util.Point3fi
 
index - Variable in class org.jmol.viewer.ActionManager.MotionPoint
 
indexDown(float, int) - Static method in class org.jmol.jvxl.data.VolumeData
 
indexes - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.
indexI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
indexInModel - Variable in class org.jmol.util.JmolMolecule
 
indicatedModelIndex - Variable in class org.jmol.shapespecial.Draw
 
indices - Variable in class org.jmol.smiles.SmilesMeasure
 
iNested - Variable in class org.jmol.smiles.SmilesAtom
 
iNext - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
iNext - Variable in class org.jmol.shapebio.BioShapeRenderer
 
iNext2 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
iNext3 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
info - Variable in class org.jmol.atomdata.RadiusData
 
info - Static variable in class org.jmol.script.Token
 
info - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
info - Variable in class org.jmol.symmetry.PointGroup
 
info(String) - Method in class org.jmol.util.DefaultLogger
 
info() - Method in class org.jmol.util.LimitedLineReader
 
info(String) - Static method in class org.jmol.util.Logger
og* Writes a log at INFO level.
info(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at INFO level.
INFO_A - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_ALPHA - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_B - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_BETA - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_C - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_DIMENSIONS - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_GAMMA - Static variable in class org.jmol.util.SimpleUnitCell
 
infoLabel - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
inGreyscaleMode - Variable in class org.jmol.g3d.Graphics3D
 
INHERIT_ALL - Static variable in class org.jmol.g3d.Graphics3D
 
INHERIT_COLOR - Static variable in class org.jmol.g3d.Graphics3D
 
inInput - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
init() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
init(XmlReader, AtomSetCollection) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
init() - Method in class org.jmol.applet.AppletWrapper
 
init() - Method in class org.jmol.applet.Jmol
 
init() - Method in interface org.jmol.applet.WrappedApplet
 
initApplication() - Method in class org.jmol.applet.Jmol
 
initHuf() - Method in class org.jmol.util.Huffman
 
INITIAL_ATOMS - Static variable in class org.jmol.smiles.SmilesSearch
 
initialFile - Variable in class org.jmol.export.dialog.Dialog
 
initialize(BasisFunctionReader, String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
initialize() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initialize(ModelSet) - Method in interface org.jmol.api.JmolBioResolver
 
initialize(JmolViewer, boolean, String, boolean) - Method in interface org.jmol.api.JmolPopupInterface
 
initialize(int, Point3f[], BitSet) - Method in class org.jmol.bspt.Bspf
 
initialize(Point3f, float, boolean) - Method in class org.jmol.bspt.CubeIterator
initialize to return all points within the sphere defined by center and radius
initialize(boolean) - Method in class org.jmol.g3d.Platform3D
 
initialize() - Method in class org.jmol.jvxl.readers.Parameters
 
initialize(Bspf, BitSet, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.AtomIteratorWithinModel
############## ITERATOR SHOULD BE RELEASED #################
initialize(ModelSet) - Method in class org.jmol.modelsetbio.Resolver
 
initialize(JmolViewer, boolean, String, boolean) - Method in class org.jmol.popup.JmolPopup
 
initialize(int, int, int, Point3f[]) - Method in class org.jmol.quantum.MOCalculation
 
initialize(int, int, int, Point3f[]) - Method in class org.jmol.quantum.QuantumCalculation
 
initialize - Static variable in class org.jmol.script.Token
 
initialize(int, Point3f[], Point4f) - Method in class org.jmol.shape.Mesh
 
initialize() - Method in class org.jmol.shapebio.BioShapeCollection
 
initialize() - Method in class org.jmol.shapespecial.Dots
 
initialize(boolean) - Method in class org.jmol.viewer.Viewer
 
initialize(String, NIOSocket) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
initializeAtomBondModelCounts(int) - Method in class org.jmol.modelset.ModelLoader
 
initializeBonding() - Method in class org.jmol.modelset.ModelLoader
 
initializeBspf() - Method in class org.jmol.modelset.ModelCollection
 
initializeBspt(int) - Method in class org.jmol.modelset.ModelCollection
 
initializeCartesianToFractional() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeEigen() - Method in class org.jmol.quantum.NciCalculation
 
initializeExporter(String, Viewer, double, Graphics3D, Object) - Method in interface org.jmol.api.JmolRendererInterface
 
initializeExporter(String, Viewer, double, Graphics3D, Object) - Method in class org.jmol.export.Export3D
 
initializeExporter(String, Viewer, double, Graphics3D, Object) - Method in class org.jmol.g3d.Graphics3D
 
initializeExporter(JmolRendererInterface, String, Object) - Method in class org.jmol.viewer.Viewer
 
initializeHydrogenAddition(ModelLoader, int) - Method in interface org.jmol.api.JmolBioResolver
 
initializeHydrogenAddition(ModelLoader, int) - Method in class org.jmol.modelsetbio.Resolver
 
initializeInfo(String, Map<String, Object>) - Method in class org.jmol.modelset.ModelLoader
 
initializeIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
initializeIsosurface() - Method in class org.jmol.shapesurface.Isosurface
 
initializeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
initializeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
initializeModel(boolean) - Method in class org.jmol.viewer.Viewer
 
initializeOnePoint() - Method in class org.jmol.quantum.NciCalculation
 
initializeOnePoint() - Method in class org.jmol.quantum.QuantumCalculation
 
initializeOutput(Viewer, double, Graphics3D, Object) - Method in class org.jmol.export.___Exporter
 
initializeOutput(Viewer, double, Graphics3D, Object) - Method in class org.jmol.export._ObjExporter
 
initializeOutput(Viewer, double, Graphics3D, Object) - Method in class org.jmol.export._TachyonExporter
 
initializePointers(int) - Method in class org.jmol.viewer.AnimationManager
 
initializePolymer(BioShape) - Method in class org.jmol.shapebio.BioShapeRenderer
 
initializeProperties() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
initializeReader() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
initializeReader() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.Mol3DReader
 
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianWfnReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.OdysseyReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.JmeReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
initializeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeShape(Viewer, Graphics3D, ModelSet, int) - Method in class org.jmol.shape.Shape
 
initializeSurfaceData() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
initializeSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeUnitCellAndSymmetry() - Method in class org.jmol.modelset.ModelLoader
 
initializeVolumetricData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
initIsosurface(int) - Method in class org.jmol.script.ScriptEvaluator
 
initMatrix(int) - Method in class org.jmol.util.DCT
 
initModelSet() - Method in class org.jmol.shape.AtomShape
 
initModelSet() - Method in class org.jmol.shape.Measures
 
initModelSet() - Method in class org.jmol.shape.Object2dShape
 
initModelSet() - Method in class org.jmol.shape.Shape
 
initModelSet() - Method in class org.jmol.shapebio.BioShapeCollection
 
initModelSet() - Method in class org.jmol.shapespecial.Vectors
 
initPlanes() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
initRenderer() - Method in class org.jmol.shape.AxesRenderer
 
initRenderer() - Method in class org.jmol.shape.CageRenderer
 
initRenderer() - Method in class org.jmol.shape.ShapeRenderer
 
initRenderer() - Method in class org.jmol.shape.UccageRenderer
 
initRenderer() - Method in class org.jmol.shapespecial.DotsRenderer
 
initRenderer() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
initShape() - Method in class org.jmol.shape.Axes
 
initShape() - Method in class org.jmol.shape.Bbcage
 
initShape() - Method in class org.jmol.shape.Echo
 
initShape() - Method in class org.jmol.shape.FontShape
 
initShape() - Method in class org.jmol.shape.Frank
 
initShape() - Method in class org.jmol.shape.Hover
 
initShape() - Method in class org.jmol.shape.Labels
 
initShape() - Method in class org.jmol.shape.Measures
 
initShape() - Method in class org.jmol.shape.MeshCollection
 
initShape() - Method in class org.jmol.shape.Shape
 
initShape() - Method in class org.jmol.shape.Sticks
 
initShape() - Method in class org.jmol.shape.Uccage
 
initShape() - Method in class org.jmol.shapebio.Backbone
 
initShape() - Method in class org.jmol.shapebio.Cartoon
 
initShape() - Method in class org.jmol.shapebio.MeshRibbon
 
initShape() - Method in class org.jmol.shapebio.Rockets
 
initShape() - Method in class org.jmol.shapebio.Trace
 
initShape() - Method in class org.jmol.shapespecial.Dots
 
initShape() - Method in class org.jmol.shapespecial.Draw
 
initShape() - Method in class org.jmol.shapespecial.GeoSurface
 
initShape() - Method in class org.jmol.shapesurface.Contact
 
initShape() - Method in class org.jmol.shapesurface.Isosurface
 
initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
 
initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
 
initShape() - Method in class org.jmol.shapesurface.Plot3D
 
initShape() - Method in class org.jmol.shapesurface.Pmesh
 
initSlice() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
initState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
initState() - Method in class org.jmol.shape.Halos
 
initState() - Method in class org.jmol.shapesurface.Isosurface
 
initVariables() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
initWindows() - Method in class org.jmol.applet.Jmol
 
inline - Static variable in class org.jmol.script.Token
 
inlineNewlineChar - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
inMotion - Variable in class org.jmol.viewer.AnimationManager
 
input - Variable in class org.jmol.console.AppletConsole
 
inputCode - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
inputFileName - Variable in class org.jmol.export.dialog.Dialog
 
inputOnly - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
inputOnly - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
inputOnly - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
inputTabs - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
inRange(int, int) - Method in class org.jmol.viewer.ActionManager.Mouse
 
INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
insertion - Static variable in class org.jmol.script.Token
 
INSERTION_CODE_MASK - Static variable in class org.jmol.modelset.Group
 
insertionCode - Variable in class org.jmol.adapter.smarter.Atom
 
insertMenuSubMenu(Object, Object, int) - Method in class org.jmol.popup.JmolPopup
 
insertString(int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
insideMaskTable - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
insideOut - Variable in class org.jmol.jvxl.data.JvxlData
 
insideOut - Variable in class org.jmol.jvxl.readers.Parameters
 
insideout - Static variable in class org.jmol.script.Token
 
insideOut - Variable in class org.jmol.shape.Mesh
 
inSocket - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
installMainMenu(Object) - Method in class org.jmol.popup.JmolPopup
 
instance - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
instanceList - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
instructionDispatchLoop(boolean) - Method in class org.jmol.script.ScriptEvaluator
here we go -- everything else in this class is called by this method or one of its subsidiary methods.
Int2IntHash - Class in org.jmol.util
 
Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
 
Int2IntHash() - Constructor for class org.jmol.util.Int2IntHash
 
Int2IntHash.Entry - Class in org.jmol.util
 
Int2IntHash.Entry(int, int, Int2IntHash.Entry) - Constructor for class org.jmol.util.Int2IntHash.Entry
 
intAnimThread - Variable in class org.jmol.viewer.AnimationManager
 
intAsFloat - Variable in class org.jmol.modelset.LabelToken
 
integer - Static variable in class org.jmol.script.Token
 
integerOutOfRange(int, int) - Method in class org.jmol.script.ScriptEvaluator
 
integrateSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
integration - Variable in class org.jmol.quantum.MOCalculation
 
intenseFraction - Static variable in class org.jmol.g3d.Shade3D
 
intercept(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
interestingAminoAtomIDs - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
interestingNucleicAtomIDs - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
Interface - Class in org.jmol.api
 
Interface() - Constructor for class org.jmol.api.Interface
 
interior - Static variable in class org.jmol.script.Token
 
interlace - Variable in class org.jmol.export.image.GifEncoder
 
Interlace - Variable in class org.jmol.export.image.GifEncoder
 
intermolecular - Static variable in class org.jmol.script.Token
 
internal - Static variable in class org.jmol.script.Token
 
internalRotationAngle - Variable in class org.jmol.viewer.TransformManager
 
internalRotationAxis - Variable in class org.jmol.viewer.TransformManager
 
internalRotationCenter - Variable in class org.jmol.viewer.TransformManager
 
internalSlab - Variable in class org.jmol.viewer.TransformManager
 
internalTranslation - Variable in class org.jmol.viewer.TransformManager
 
interpolate(int, int) - Method in class org.jmol.g3d.Cylinder3D
 
interpolateFraction(Point3f, Point3f, float, float, float, float[], float[], int) - Static method in class org.jmol.util.MeshSurface
 
interpolatePoint(Point3f, Point3f, float, float, float, float, float[], float[], int) - Static method in class org.jmol.util.MeshSurface
 
interpolatePrecisely(int, int) - Method in class org.jmol.g3d.Cylinder3D
 
interpolateSphere(Point3f, Point3f, float, float, double, float, float, float[], float[], int) - Method in class org.jmol.util.MeshSurface
 
interruptExecution - Variable in class org.jmol.script.ScriptEvaluator
 
interruptQueueThreads() - Method in class org.jmol.viewer.ScriptManager
 
interruptScript - Variable in class org.jmol.viewer.Viewer
 
intersectID - Variable in class org.jmol.shapespecial.Draw
 
intersection - Variable in class org.jmol.jvxl.readers.Parameters
 
intersection - Static variable in class org.jmol.script.Token
 
intersectPlane(Point4f, float, int) - Method in class org.jmol.util.BoxInfo
returns a set of points defining the geometric object within the given plane that spans the unit cell within the given margins
intersectPlane(Point4f, List<Object>, int) - Static method in class org.jmol.util.TriangleData
a generic cell - plane intersector -- used for finding the plane through a unit cell
intlTableNumber - Variable in class org.jmol.symmetry.SpaceGroup
 
intlTableNumberExt - Variable in class org.jmol.symmetry.SpaceGroup
 
intlTableNumberFull - Variable in class org.jmol.symmetry.SpaceGroup
 
intparam - Static variable in class org.jmol.script.Token
 
intParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
intParameter(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
 
intPeek() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
intproperty - Static variable in class org.jmol.script.Token
 
intramolecular - Variable in class org.jmol.modelset.MeasurementData
 
intramolecular - Static variable in class org.jmol.script.Token
 
intramolecular - Variable in class org.jmol.shape.Measures
 
intSetting(int) - Method in class org.jmol.script.ScriptEvaluator
 
intThread - Variable in class org.jmol.viewer.AnimationManager.AnimationThread
 
intToken(int) - Static method in class org.jmol.script.Token
 
intValue - Variable in class org.jmol.script.Token
 
intVariable(int) - Static method in class org.jmol.script.ScriptVariable
 
inv() - Method in class org.jmol.util.Quaternion
 
INVALID_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
invalidatedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
invalidateMesh - Variable in class org.jmol.shapebio.BioShapeRenderer
 
invalidatePolygons() - Method in class org.jmol.util.MeshSurface
 
invalidateSheets - Variable in class org.jmol.shapebio.BioShapeRenderer
 
invalidateSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
invalidateTriangles() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
invalidateTriangles() - Method in class org.jmol.shapesurface.Isosurface
 
invalidateVertices(BitSet) - Method in class org.jmol.jvxl.data.MeshData
 
invalidControl - Variable in class org.jmol.modelsetbio.BioPolymer
 
invalidLead - Variable in class org.jmol.modelsetbio.BioPolymer
 
InvalidSmilesException - Exception in org.jmol.smiles
Exception thrown for invalid SMILES String
InvalidSmilesException() - Constructor for exception org.jmol.smiles.InvalidSmilesException
Constructs a InvalideSmilesException without any detail.
InvalidSmilesException(String) - Constructor for exception org.jmol.smiles.InvalidSmilesException
Constructs a InvalidSmilesException with a detail message.
InvalidSmilesException(Throwable) - Constructor for exception org.jmol.smiles.InvalidSmilesException
Contructs a InvalidSmilesException with the specified cause and a detail message of (cause == null ? null : cause.toString()) (which typically contains the class and detail message of cause).
InvalidSmilesException(String, Throwable) - Constructor for exception org.jmol.smiles.InvalidSmilesException
Construcst a InvalidSmilesException with the specified detail message and cause.
inverseMatrix - Variable in class org.jmol.jvxl.data.VolumeData
 
inverseNormixes - Static variable in class org.jmol.g3d.Normix3D
 
invertAtomCoord(Point3f, BitSet) - Method in class org.jmol.viewer.Viewer
 
invertAtomCoord(Point4f, BitSet) - Method in class org.jmol.viewer.Viewer
 
invertInPlace(BitSet, int) - Static method in class org.jmol.util.BitSetUtil
inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
invertNormixes() - Method in class org.jmol.shape.Mesh
 
invertSelected(Point3f, Point4f, int, BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
 
invertSelected() - Method in class org.jmol.script.ScriptEvaluator
 
invertSelected - Static variable in class org.jmol.script.Token
 
invertSelected(Point3f, Point4f, int, BitSet) - Method in class org.jmol.viewer.Viewer
 
invertSelection() - Method in class org.jmol.viewer.SelectionManager
 
invertSelection() - Method in class org.jmol.viewer.Viewer
 
invMatrix - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
iObj - Variable in class org.jmol.export._IdtfExporter
 
iObj - Variable in class org.jmol.export.UseTable
 
ionic - Static variable in class org.jmol.script.Token
 
ionicRadii - Variable in class org.jmol.modelset.AtomCollection
 
ioRead(byte[], int, int) - Method in class org.jmol.util.BinaryDocument
 
ioReadByte() - Method in class org.jmol.util.BinaryDocument
 
ioReadDouble() - Method in class org.jmol.util.BinaryDocument
 
ioReadFloat() - Method in class org.jmol.util.BinaryDocument
 
ioReadInt() - Method in class org.jmol.util.BinaryDocument
 
ioReadLong() - Method in class org.jmol.util.BinaryDocument
 
ioReadShort() - Method in class org.jmol.util.BinaryDocument
 
iox - Variable in class org.jmol.export.image.ImageEncoder
 
iPlaneRaw - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
iPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
 
iProcess - Static variable in class org.jmol.script.ScriptEvaluator
 
is(int) - Method in class org.jmol.modelset.Bond
 
is2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
is2D - Variable in class org.jmol.modelset.ModelLoader
 
IS_HETERO_FLAG - Static variable in class org.jmol.modelset.Atom
 
IS_POINTMAPPABLE - Static variable in class org.jmol.jvxl.readers.Parameters
 
IS_SILENT - Static variable in class org.jmol.jvxl.readers.Parameters
 
IS_SLABBABLE - Static variable in class org.jmol.jvxl.readers.Parameters
 
IS_SOLVENTTYPE - Static variable in class org.jmol.jvxl.readers.Parameters
 
isActive - Variable in class org.jmol.shape.AtomShape
 
isActive - Variable in class org.jmol.shapebio.BioShape
 
isActive - Variable in class org.jmol.shapebio.BioShapeCollection
 
isActiveLevel(int) - Static method in class org.jmol.util.Logger
Tells if a logging level is active.
isAdded(int) - Method in class org.jmol.modelset.Group
 
isAdjacentSp2(Atom) - Method in class org.jmol.modelset.AtomCollection
 
isAligned(Point3f, Point3f, Point3f) - Method in class org.jmol.shapespecial.Polyhedra
 
isAll - Variable in class org.jmol.modelset.MeasurementData
 
isAll - Variable in class org.jmol.shape.Object2dShape
 
isAll - Variable in class org.jmol.shapespecial.PolyhedraRenderer
 
isAlphaMonomer() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isAlternateLocationMatch(String) - Method in class org.jmol.modelset.Atom
 
isAltKeyReleased - Variable in class org.jmol.viewer.ActionManager
 
isAmide - Variable in class org.jmol.minimize.MinBond
 
isAminoMonomer() - Method in class org.jmol.modelsetbio.AminoMonomer
 
isAngstroms - Variable in class org.jmol.adapter.readers.simple.CubeReader
 
isAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
isAngstroms - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
isAnimationOn() - Method in class org.jmol.viewer.Viewer
 
isAnisotropic - Variable in class org.jmol.jvxl.readers.Parameters
 
isAnisotropic - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isAntialiased() - Method in interface org.jmol.api.JmolRendererInterface
 
isAntialiased() - Method in class org.jmol.export.Export3D
is full scene / oversampling antialiasing in effect
isAntialiased() - Method in class org.jmol.g3d.Graphics3D
is full scene / oversampling antialiasing in effect
isAntialiased - Variable in class org.jmol.shape.HalosRenderer
 
isAntialiased - Variable in class org.jmol.shape.SticksRenderer
 
isAntialiased() - Method in class org.jmol.viewer.Viewer
 
isAntiparallel - Variable in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
isAppend - Variable in class org.jmol.viewer.FileManager.FileReader
 
isAppend - Variable in class org.jmol.viewer.FileManager.FilesReader
 
isAppendSelected() - Method in class org.jmol.export.dialog.FilePreview
 
isApplet() - Method in class org.jmol.api.JmolViewer
 
isApplet - Variable in class org.jmol.popup.SimplePopup
 
isApplet - Variable in class org.jmol.viewer.Viewer
 
isApplet() - Method in class org.jmol.viewer.Viewer
 
isApprox(Vector3d, Vector3d, double) - Static method in class org.jmol.minimize.Util
 
isArc - Variable in class org.jmol.shapespecial.Draw
 
isAromatic - Variable in class org.jmol.minimize.MinBond
 
isAromatic() - Method in class org.jmol.modelset.Bond
 
isaromatic - Static variable in class org.jmol.script.Token
 
isAromatic - Variable in class org.jmol.smiles.SmilesAtom
 
isAromatic() - Method in class org.jmol.smiles.SmilesAtom
 
isArrayItem - Variable in class org.jmol.script.ScriptMathProcessor
 
isArrayParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
isArrow - Variable in class org.jmol.shapespecial.Draw
 
isAtEnd() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
isAtomAssignable(int) - Method in class org.jmol.modelset.ModelCollection
 
isAtomAssignable(int) - Method in class org.jmol.viewer.Viewer
 
isAtomHidden(int) - Method in class org.jmol.modelset.AtomCollection
 
isAtomHidden(int) - Method in class org.jmol.modelset.Group
 
isAtomHidden(int) - Method in class org.jmol.modelset.Model
 
isAtomNameMatch(Atom, String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
isAtomPDB(int) - Method in class org.jmol.modelset.ModelCollection
 
isAtomPDB(int) - Method in class org.jmol.viewer.Viewer
 
isAtomSelected(int) - Method in class org.jmol.viewer.SelectionManager
 
isAtomSelected(int) - Method in class org.jmol.viewer.Viewer
 
isBarb - Variable in class org.jmol.shapespecial.Draw
 
isBarb - Variable in class org.jmol.shapespecial.DrawMesh
 
isBbcageDefault - Variable in class org.jmol.modelset.ModelCollection
 
isBiColor - Variable in enum org.jmol.constant.EnumStereoMode
 
isBiColor() - Method in enum org.jmol.constant.EnumStereoMode
 
isBicolorMap - Variable in class org.jmol.jvxl.data.JvxlData
 
isBicolorMap - Variable in class org.jmol.jvxl.readers.Parameters
 
isBicolorMap - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
isBigEndian - Variable in class org.jmol.util.BinaryDocument
 
isBinary - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isBinary - Variable in class org.jmol.jvxl.readers.PmeshReader
 
isBioAtom - Variable in class org.jmol.smiles.SmilesAtom
 
isBioSequence - Variable in class org.jmol.smiles.SmilesParser
 
isBioShape - Variable in class org.jmol.shape.Shape
 
isBond - Variable in class org.jmol.shapespecial.Dipoles
 
isBondBitSet - Variable in class org.jmol.modelset.BondIteratorSelected
 
isBondDipole(int) - Method in class org.jmol.shapespecial.Dipoles
 
isBonded(Atom) - Method in class org.jmol.modelset.Atom
 
isBondedCorrectly(int, int, int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
isBondedCorrectly(int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
isBondSet - Variable in class org.jmol.script.ScriptEvaluator
 
isBondType() - Method in class org.jmol.shapespecial.Dipole
 
isBondType(char, boolean, boolean) - Static method in class org.jmol.smiles.SmilesBond
 
isBound(int, int) - Method in class org.jmol.viewer.ActionManager
 
isBound(int, int) - Method in class org.jmol.viewer.binding.Binding
 
isBound(int, int) - Method in class org.jmol.viewer.Viewer
 
isBreakableContext(int) - Static method in class org.jmol.script.ScriptCompiler
 
isCarbohydrate() - Method in class org.jmol.modelset.Atom
 
isCarbohydrate() - Method in class org.jmol.modelset.Group
 
isCarbohydrate() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isCarbohydrate - Variable in class org.jmol.shapebio.BioShapeRenderer
 
isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
 
isCavity - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isCavity - Variable in class org.jmol.jvxl.readers.Parameters
 
isCell - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
isCellEditable(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
isCenterParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
isCentrosymmetric - Variable in class org.jmol.symmetry.HallInfo
 
isCheckOnly - Variable in class org.jmol.script.ScriptCompiler
 
isCircle - Variable in class org.jmol.shapespecial.Draw
 
isClickable() - Method in class org.jmol.modelset.Atom
 
isClipped(int, int, int) - Method in class org.jmol.export.Export3D
 
isClipped(int, int) - Method in class org.jmol.export.Export3D
 
isClipped(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
isClipped(int, int) - Method in class org.jmol.g3d.Graphics3D
 
isClippedXY(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
isClippedXY(int, int, int) - Method in class org.jmol.export.Export3D
 
isClippedXY(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
isClippedZ(int) - Method in interface org.jmol.api.JmolRendererInterface
 
isClippedZ(int) - Method in class org.jmol.export.Export3D
 
isClippedZ(int) - Method in class org.jmol.g3d.Graphics3D
 
isClosedFace - Variable in class org.jmol.jvxl.readers.PmeshReader
 
isCmdf - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
isCmdLine_C_Option - Variable in class org.jmol.script.ScriptEvaluator
 
isCmdLine_C_Option - Variable in class org.jmol.viewer.Viewer
 
isCmdLine_c_or_C_Option - Variable in class org.jmol.script.ScriptEvaluator
 
isCmdLine_c_or_C_Option - Variable in class org.jmol.viewer.Viewer
 
isColixColorInherited(short) - Static method in class org.jmol.g3d.Graphics3D
 
isColixLastAvailable(short) - Static method in class org.jmol.g3d.Graphics3D
 
isColixTranslucent(short) - Static method in class org.jmol.g3d.Graphics3D
 
isCollapsed - Variable in class org.jmol.shapespecial.Polyhedra
 
isColorExplicit - Variable in class org.jmol.shapesurface.Isosurface
 
isColorIndex - Variable in class org.jmol.util.ColorEncoder
 
isColorParam(int) - Method in class org.jmol.script.ScriptEvaluator
 
isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
 
isColorReversed - Variable in class org.jmol.jvxl.readers.Parameters
 
isColorSolid - Variable in class org.jmol.util.MeshSurface
 
isCommaAsOrAllowed - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
isCommandDisplayable(int) - Method in class org.jmol.script.ScriptEvaluator
provides support for the script editor
isComment - Variable in class org.jmol.script.ScriptCompiler
 
isCompoundDocument - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
isCompoundDocument(InputStream) - Static method in class org.jmol.util.CompoundDocument
 
isCompoundDocument(byte[]) - Static method in class org.jmol.util.CompoundDocument
 
isConnect() - Method in class org.jmol.modelset.ModelCollection.StateScript
 
isConnected(Atom[], int) - Method in class org.jmol.modelset.Measurement
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AminoMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.Monomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isConnectedPrevious() - Method in class org.jmol.modelset.Group
 
isConnectedPrevious() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isConnectedPrevious() - Method in class org.jmol.modelsetbio.Monomer
 
isConnectStateBug - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
isContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
 
isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isContoured - Variable in class org.jmol.jvxl.data.JvxlData
 
isContoured - Variable in class org.jmol.jvxl.readers.Parameters
 
isCore - Variable in class org.jmol.quantum.SlaterData
 
isCovalent() - Method in class org.jmol.modelset.Bond
 
isCovalent() - Method in class org.jmol.smiles.SmilesBond
 
isCovalent() - Method in class org.jmol.util.JmolEdge
 
isCovalentlyBonded(Atom) - Method in class org.jmol.modelset.Atom
 
isCrossed - Variable in class org.jmol.shapespecial.Draw
 
isCrossLinked(JmolNode) - Method in class org.jmol.modelset.Atom
 
isCrossLinked(Group) - Method in class org.jmol.modelset.Group
 
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.Monomer
 
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isCrossLinked(JmolNode) - Method in class org.jmol.smiles.SmilesAtom
 
isCrossLinked(JmolNode) - Method in interface org.jmol.util.JmolNode
 
isCubeData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isCursorOnTopOf(int, int, int, Atom) - Method in class org.jmol.modelset.Atom
 
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.AtomCollection
used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.Group
 
isCurve - Variable in class org.jmol.shapespecial.Draw
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.data.JvxlData
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
 
isCutoffAbsolute - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
isCylinder - Variable in class org.jmol.shapespecial.Draw
 
isDataFlavorSupported(DataFlavor) - Method in class org.jmol.export.image.ImageSelection
 
isDataFlavorSupported(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
isDataOnly - Variable in class org.jmol.viewer.Viewer
 
isDataOnly() - Method in class org.jmol.viewer.Viewer
 
isDataOnly - Variable in class org.openscience.jmol.app.JmolApp
 
isDefaultColorRasmol - Variable in class org.jmol.viewer.ColorManager
 
isDeleted() - Method in class org.jmol.modelset.Atom
 
isDeleted() - Method in class org.jmol.smiles.SmilesAtom
 
isDeleted() - Method in interface org.jmol.util.JmolNode
 
isDiaxial(JmolNode, JmolNode, JmolNode, JmolNode, SmilesSearch.VTemp, float) - Static method in class org.jmol.smiles.SmilesSearch
 
isDirectedTowardsCamera(short) - Method in interface org.jmol.api.JmolRendererInterface
 
isDirectedTowardsCamera(short) - Method in class org.jmol.export.Export3D
 
isDirectedTowardsCamera(short) - Method in class org.jmol.g3d.Graphics3D
 
isDirectedTowardsCamera(short) - Method in class org.jmol.g3d.Normix3D
 
isDisplayAntialiased() - Method in class org.jmol.g3d.Graphics3D
is full scene / oversampling antialiasing GENERALLY in effect
isDisplayWithinNot - Variable in class org.jmol.shape.MeshCollection
 
isDna() - Method in class org.jmol.modelset.Atom
 
isDna - Variable in class org.jmol.modelset.Chain
 
isDna() - Method in class org.jmol.modelset.Chain
 
isDna() - Method in class org.jmol.modelset.Group
 
isDna() - Method in class org.jmol.modelset.Polymer
 
isDna() - Method in class org.jmol.modelsetbio.BioPolymer
 
isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isDna() - Method in class org.jmol.smiles.SmilesAtom
 
isDna() - Method in interface org.jmol.util.JmolNode
 
isDrawType(String, int, float) - Method in class org.jmol.symmetry.PointGroup
 
isDynamic - Variable in class org.jmol.modelset.Measurement
 
isDynamic() - Method in class org.jmol.modelset.Measurement
 
isE_fr_energy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
isE_wo_entrp - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
isEccentric - Variable in class org.jmol.jvxl.readers.Parameters
 
isEccentric - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isElectronDensity - Variable in class org.jmol.quantum.MOCalculation
 
isElectronDensityCalc - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
isEmbeddedExpression - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
isEmpty - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
isEmpty() - Method in class org.jmol.util.FastBitSet
 
isEnabled - Variable in class org.jmol.util.ZipUtil.GZipData
 
isEndOfCommand - Variable in class org.jmol.script.ScriptCompiler
 
isEqual(PointGroup) - Method in class org.jmol.symmetry.PointGroup
 
isError() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
isError - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
isExcluded - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
isExecuting - Variable in class org.jmol.script.ScriptEvaluator
 
isExecutionPaused() - Method in class org.jmol.script.ScriptEvaluator
 
isExecutionStepping() - Method in class org.jmol.script.ScriptEvaluator
 
isExport - Variable in class org.jmol.shape.ShapeRenderer
 
isExpressionNext() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
isFinalized - Variable in class org.jmol.symmetry.SymmetryOperation
 
isFinite(double) - Static method in class org.jmol.minimize.Util
 
isFirst - Variable in class org.jmol.smiles.SmilesAtom
 
isFixed - Variable in class org.jmol.shape.MeshCollection
 
isFixed - Variable in class org.jmol.shapespecial.DrawMesh
 
isFlatSp2Ring(JmolNode[], BitSet, BitSet, float) - Static method in class org.jmol.smiles.SmilesAromatic
3D-SEARCH aromaticity test.
isFloatParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
isFractional - Variable in class org.jmol.adapter.readers.xtal.AimsReader
 
isFreqCalc - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isFullSceneAntialiasingEnabled - Variable in class org.jmol.g3d.Graphics3D
 
isFullyLit() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isFunction - Variable in class org.jmol.script.ScriptContext
 
isFunction(String) - Method in class org.jmol.viewer.StateManager
 
isFunction(String) - Method in class org.jmol.viewer.Viewer
 
isGesture - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
isGreaterOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
isGroup3(String) - Method in class org.jmol.modelset.Atom
 
isGroup3(String) - Method in class org.jmol.modelset.Group
 
isGuanine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isGzip(byte[]) - Static method in class org.jmol.util.ZipUtil
 
isGzip(InputStream) - Static method in class org.jmol.util.ZipUtil
 
isHbonded(int, int, int, int, int[][][][]) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
isHeader - Variable in class org.jmol.util.CifDataReader
 
isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isHelix(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
 
isHelix() - Method in class org.jmol.modelsetbio.Monomer
 
isHelix(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
isHetero - Variable in class org.jmol.adapter.smarter.Atom
 
isHetero(String) - Static method in class org.jmol.api.JmolAdapter
 
isHetero() - Method in class org.jmol.modelset.Atom
 
isHetero() - Method in class org.jmol.modelset.Group
 
isHetero(String) - Static method in class org.jmol.viewer.JmolConstants
 
isHidden - Variable in class org.jmol.modelset.Measurement
 
isHidden() - Method in class org.jmol.modelset.Measurement
 
isHighRes - Variable in class org.jmol.shapebio.BioShapeRenderer
 
isHorizontal - Variable in class org.jmol.popup.SimplePopup
 
isHover - Variable in class org.jmol.shape.Object2dShape
 
isHoverEnabled() - Method in class org.jmol.viewer.Viewer
 
iShowNormals - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
iShowSolid - Variable in class org.jmol.shapespecial.DotsRenderer
 
isHydrogen() - Method in class org.jmol.modelset.Bond
 
isHydrogen(int) - Static method in class org.jmol.modelset.Bond
 
isHydrogen() - Method in class org.jmol.smiles.SmilesBond
 
isHydrogen() - Method in class org.jmol.util.JmolEdge
 
isImproper - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
isInDisplayRange(int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
isInDisplayRange(int, int) - Method in class org.jmol.export.Export3D
 
isInDisplayRange(int, int) - Method in class org.jmol.g3d.Graphics3D
 
isInFrame() - Method in class org.jmol.modelset.Atom
 
isInitialized() - Method in class org.jmol.bspt.Bspf
 
isInitialized(int) - Method in class org.jmol.bspt.Bspf
 
isInLatticeCell(int, Point3f, Point3f, boolean) - Method in class org.jmol.modelset.ModelCollection
 
isInPosition(Vector3f, float) - Method in class org.jmol.viewer.TransformManager
 
isInPosition(Vector3f, float) - Method in class org.jmol.viewer.Viewer
 
isInRange(RadiusData, float) - Method in class org.jmol.modelset.Measurement
 
isInSelectionSubset(int) - Method in class org.jmol.viewer.SelectionManager
 
isInSelectionSubset(int) - Method in class org.jmol.viewer.Viewer
 
isInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
 
isInside(float, float, boolean) - Static method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
isInsideOut() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isInSymmetryRange(Point3f) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
isInt(float) - Static method in class org.jmol.adapter.readers.xtal.CastepReader
 
isInTetrahedron(Point3f, Point3f, Point3f, Point3f, Point3f, Point4f, Vector3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
 
isIntramolecular(Atom[], int) - Method in class org.jmol.modelset.Measurement
 
isInvalid - Variable in class org.jmol.g3d.Text3D
 
isInvertible(int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
isJmolDataFrame - Variable in class org.jmol.modelset.Model
 
isJmolDataFrame(int) - Method in class org.jmol.modelset.ModelCollection
 
isJmolDataFrame(Atom) - Method in class org.jmol.modelset.ModelCollection
 
isJmolDataFrame(int) - Method in class org.jmol.viewer.Viewer
 
isJmolDataFrame() - Method in class org.jmol.viewer.Viewer
 
isJmolManifest(String) - Static method in class org.jmol.util.ZipUtil
 
isJmolVariable(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
isJmolVariable(String) - Method in class org.jmol.viewer.Viewer
 
isJPEG - Variable in class org.jmol.export.dialog.Dialog.QualityListener
 
isJvxl - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
 
iskiosk - Static variable in class org.jmol.script.Token
 
isKiosk - Variable in class org.jmol.viewer.Viewer
 
isKiosk() - Method in class org.jmol.viewer.Viewer
 
isKiosk - Variable in class org.openscience.jmol.app.JmolApp
 
isLabelOrHover - Variable in class org.jmol.shape.Object2d
 
isLabelPropertyTok(int) - Static method in class org.jmol.modelset.LabelToken
 
isLastFrame - Variable in class org.jmol.popup.SimplePopup
 
isLastModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
after reading a model, Q: Is this the last model?
isLeadAtom() - Method in class org.jmol.modelset.Atom
 
isLeadAtom(int) - Method in class org.jmol.modelset.Group
 
isLeadAtom(int) - Method in class org.jmol.modelsetbio.Monomer
 
isLeadAtom - Variable in class org.jmol.smiles.SmilesAtom
 
isLeadAtom() - Method in class org.jmol.smiles.SmilesAtom
 
isLeadAtom() - Method in interface org.jmol.util.JmolNode
 
isLine - Variable in class org.jmol.shapespecial.Draw
 
isLinear(Point3f[]) - Method in class org.jmol.symmetry.PointGroup
 
isLineContinuation(int, boolean) - Method in class org.jmol.script.ScriptCompiler
 
isLonePair - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isLongMode - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isMac - Static variable in class org.jmol.export.dialog.Dialog
 
isMatch(String, String) - Static method in class org.jmol.adapter.readers.cifpdb.CifReader
 
isMatch(String, String, boolean, boolean) - Static method in class org.jmol.util.TextFormat
 
isMathExpressionCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
isMerged - Variable in class org.jmol.util.MeshSurface
 
isMesh - Variable in class org.jmol.shapebio.Strands
 
isModelKit - Variable in class org.jmol.modelset.Model
 
isModelkit() - Method in class org.jmol.modelset.Model
 
isModelKitMode() - Method in class org.jmol.viewer.Viewer
 
isModelPDB(int) - Method in class org.jmol.viewer.Viewer
 
isMolecular - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
isMolecular - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isMolecular - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
isMolecular - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isMonomerSelected(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
isMouseDown - Variable in class org.jmol.awt.Mouse
 
isMTClient() - Method in class org.jmol.viewer.ActionManager
 
isMTServer() - Method in class org.jmol.viewer.ActionManager
 
isMultiCell - Variable in class org.jmol.symmetry.SymmetryInfo
 
isMultiConfiguration - Variable in class org.jmol.popup.SimplePopup
 
isMultiFrame - Variable in class org.jmol.popup.SimplePopup
 
isMultiModel - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
isMultiTouchClient - Variable in class org.jmol.viewer.ActionManager
 
isMultiTouchServer - Variable in class org.jmol.viewer.ActionManager
 
isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
 
isNav - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
isNavigating() - Method in class org.jmol.viewer.TransformManager
 
isNavigating() - Method in class org.jmol.viewer.Viewer
 
isNavigationMode - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
isNci - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
isNear(double, double) - Static method in class org.jmol.minimize.Util
 
isNear(double, double, double) - Static method in class org.jmol.minimize.Util
 
isNearPlane(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
 
isNearZero(double) - Static method in class org.jmol.minimize.Util
 
isNearZero(double, double) - Static method in class org.jmol.minimize.Util
 
isNegligible(double, double) - Static method in class org.jmol.minimize.Util
 
isNegligible(double, double, double) - Static method in class org.jmol.minimize.Util
 
isNewFormat - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
isNewSet - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
isNext(String) - Method in class org.jmol.util.XmlReader
 
isNot - Variable in class org.jmol.smiles.SmilesBond
 
isNot - Variable in class org.jmol.smiles.SmilesMeasure
 
isNucleic() - Method in class org.jmol.modelset.Atom
 
isNucleic() - Method in class org.jmol.modelset.Group
 
isNucleic() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isNucleic - Variable in class org.jmol.shapebio.BioShapeRenderer
 
isNucleic() - Method in class org.jmol.smiles.SmilesAtom
 
isNucleic() - Method in interface org.jmol.util.JmolNode
 
isNucleicMonomer() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
IsoFxyReader - Class in org.jmol.jvxl.readers
 
IsoFxyReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoFxyReader
 
IsoFxyzReader - Class in org.jmol.jvxl.readers
 
IsoFxyzReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoFxyzReader
 
IsoIntersectReader - Class in org.jmol.jvxl.readers
 
IsoIntersectReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoIntersectReader
 
IsoMepReader - Class in org.jmol.jvxl.readers
 
IsoMepReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoMepReader
 
isomeshes - Variable in class org.jmol.shapesurface.Isosurface
 
IsoMlpReader - Class in org.jmol.jvxl.readers
 
IsoMlpReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoMlpReader
 
IsoMOReader - Class in org.jmol.jvxl.readers
 
IsoMOReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoMOReader
 
isOn - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
isOn - Variable in class org.jmol.util.CommandHistory
 
isOneOf(String, String) - Static method in class org.jmol.util.Parser
 
isOpFunc(Token) - Static method in class org.jmol.script.ScriptMathProcessor
 
IsoPlaneReader - Class in org.jmol.jvxl.readers
 
IsoPlaneReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoPlaneReader
 
isoPointIndexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
IsoShapeReader - Class in org.jmol.jvxl.readers
 
IsoShapeReader(SurfaceGenerator, float) - Constructor for class org.jmol.jvxl.readers.IsoShapeReader
 
IsoShapeReader(SurfaceGenerator, int, int, int, float, int) - Constructor for class org.jmol.jvxl.readers.IsoShapeReader
 
IsoSolventReader - Class in org.jmol.jvxl.readers
 
IsoSolventReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader
 
IsoSolventReader.Edge - Class in org.jmol.jvxl.readers
 
IsoSolventReader.Edge(int, int) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
IsoSolventReader.Face - Class in org.jmol.jvxl.readers
 
IsoSolventReader.Face(int, int, int, IsoSolventReader.Edge, Point3f) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Face
 
isosurface(int) - Method in class org.jmol.script.ScriptEvaluator
 
isosurface - Static variable in class org.jmol.script.Token
 
Isosurface - Class in org.jmol.shapesurface
 
Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
 
isosurface - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
isosurfacekey - Static variable in class org.jmol.script.Token
 
isosurfaceKey - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
IsosurfaceMesh - Class in org.jmol.shapesurface
 
IsosurfaceMesh(String, Graphics3D, short, int) - Constructor for class org.jmol.shapesurface.IsosurfaceMesh
 
isosurfacepropertysmoothing - Static variable in class org.jmol.script.Token
 
isosurfacePropertySmoothing - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.Token
 
isosurfacePropertySmoothingPower - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
IsosurfaceRenderer - Class in org.jmol.shapesurface
 
IsosurfaceRenderer() - Constructor for class org.jmol.shapesurface.IsosurfaceRenderer
 
isOutput - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
isOutputFile - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
isPaletteVariable(byte) - Static method in enum org.jmol.constant.EnumPalette
 
isParallel(Vector3f, Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
isParallel - Variable in class org.jmol.viewer.Viewer
 
isParallel() - Method in class org.jmol.viewer.Viewer
 
isPartial() - Method in class org.jmol.modelset.Bond
 
isPass2() - Method in interface org.jmol.api.JmolRendererInterface
 
isPass2() - Method in class org.jmol.export.Export3D
 
isPass2 - Variable in class org.jmol.g3d.Graphics3D
 
isPass2() - Method in class org.jmol.g3d.Graphics3D
 
isPaused - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
isPDB - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
isPDB - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
isPDB - Variable in class org.jmol.modelset.Model
 
isPDB - Variable in class org.jmol.modelset.ModelCollection
 
isPDB - Variable in class org.jmol.modelset.ModelLoader
 
isPDB - Variable in class org.jmol.popup.SimplePopup
 
isPdbSequential() - Method in class org.jmol.viewer.Viewer
 
isPdbWithMultipleBonds - Variable in class org.jmol.modelset.Model
 
isPeriodic() - Method in interface org.jmol.api.SymmetryInterface
 
isPeriodic - Variable in class org.jmol.jvxl.data.VolumeData
 
isPeriodic - Variable in class org.jmol.jvxl.readers.Parameters
 
isPeriodic() - Method in class org.jmol.symmetry.Symmetry
 
isPeriodic() - Method in class org.jmol.symmetry.SymmetryInfo
 
isPerpendicular - Variable in class org.jmol.shapespecial.Draw
 
isPerpendicular(Vector3f, Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
isPhaseColored - Variable in class org.jmol.shapesurface.Isosurface
 
isPhonon - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
isPhosphorusMonomer() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPickable(IsosurfaceMesh, BitSet) - Method in class org.jmol.shapesurface.Isosurface
 
isPickAtomAssignCharge - Variable in class org.jmol.viewer.ActionManager
 
isPlanar(Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.shapespecial.Polyhedra
 
isPlanarMapping - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
isPlane - Variable in class org.jmol.shapespecial.Draw
 
isPocket - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isPoint3f(int) - Method in class org.jmol.script.ScriptEvaluator
 
isPolygonDisplayable(int) - Method in class org.jmol.shape.MeshRenderer
 
isPolygonDisplayable(Mesh, int) - Static method in class org.jmol.shapespecial.Draw
 
isPolygonDisplayable(int) - Method in class org.jmol.shapespecial.DrawRenderer
 
isPolymer - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isPolymer - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
isPolymer() - Method in interface org.jmol.api.SymmetryInterface
 
isPolymer - Variable in class org.jmol.shape.CageRenderer
 
isPolymer() - Method in class org.jmol.symmetry.Symmetry
 
isPolymer() - Method in class org.jmol.util.SimpleUnitCell
 
isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
 
isPossibleHBond(EnumHBondType, EnumHBondType) - Static method in enum org.jmol.constant.EnumHBondType
 
isPreliminary - Variable in class org.jmol.minimize.forcefield.Calculations
 
isPreviewOnly - Variable in class org.jmol.viewer.Viewer
 
isPreviewOnly() - Method in class org.jmol.viewer.Viewer
 
isPrimitive - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isPrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
isPrintOnly - Variable in class org.jmol.viewer.Viewer
 
isPrintOnly - Variable in class org.openscience.jmol.app.JmolApp
 
isProgressive - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isPromolecular - Variable in class org.jmol.quantum.NciCalculation
 
isProperties - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isProtein() - Method in enum org.jmol.constant.EnumStructure
 
isProtein() - Method in class org.jmol.modelset.Atom
 
isProtein - Variable in class org.jmol.modelset.Group
 
isProtein() - Method in class org.jmol.modelset.Group
 
isProtein() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isProtein() - Method in class org.jmol.smiles.SmilesAtom
 
isProtein() - Method in interface org.jmol.util.JmolNode
 
isPurine() - Method in class org.jmol.modelset.Atom
 
isPurine() - Method in class org.jmol.modelset.Group
 
isPurine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isPurine - Variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPurine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPurine() - Method in class org.jmol.smiles.SmilesAtom
 
isPurine() - Method in interface org.jmol.util.JmolNode
 
isPyrimidine() - Method in class org.jmol.modelset.Atom
 
isPyrimidine() - Method in class org.jmol.modelset.Group
 
isPyrimidine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isPyrimidine - Variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPyrimidine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPyrimidine() - Method in class org.jmol.smiles.SmilesAtom
 
isPyrimidine() - Method in interface org.jmol.util.JmolNode
 
isQuantumBasisSupported(char) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
isQuiet - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isRadical - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isRandom - Variable in class org.jmol.util.BinaryDocument
 
isRangeSelected() - Method in class org.jmol.viewer.Viewer
 
isReadableAsString(String) - Static method in class org.jmol.viewer.PropertyManager
 
isReducedDensity - Variable in class org.jmol.quantum.NciCalculation
 
isRepaintPending() - Method in class org.jmol.viewer.Viewer
 
isReset - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
isReversed - Variable in class org.jmol.shapespecial.Draw
 
isReversed - Variable in class org.jmol.util.ColorEncoder
 
isrhombohedral - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
 
isRingBond(StringBuffer, int, int) - Static method in class org.jmol.smiles.SmilesSearch
 
isRingCheck - Variable in class org.jmol.smiles.SmilesSearch
 
isRna() - Method in class org.jmol.modelset.Atom
 
isRna - Variable in class org.jmol.modelset.Chain
 
isRna() - Method in class org.jmol.modelset.Chain
 
isRna() - Method in class org.jmol.modelset.Group
 
isRna() - Method in class org.jmol.modelset.Polymer
 
isRna() - Method in class org.jmol.modelsetbio.BioPolymer
 
isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isRna() - Method in class org.jmol.smiles.SmilesAtom
 
isRna() - Method in interface org.jmol.util.JmolNode
 
isRotated45 - Variable in class org.jmol.shapespecial.Draw
 
isRubberBandSelect(int) - Method in class org.jmol.viewer.ActionManager
 
isSameAtoms(Dipole, String) - Method in class org.jmol.shapespecial.Dipoles
 
isScaled - Variable in class org.jmol.shape.Labels
 
isScaleSet - Variable in class org.jmol.util.BoxInfo
 
isScreened - Variable in class org.jmol.g3d.Graphics3D
 
isScreenedA - Variable in class org.jmol.g3d.Cylinder3D
 
isScreenedB - Variable in class org.jmol.g3d.Cylinder3D
 
isScriptEditorVisible() - Method in class org.jmol.viewer.Viewer
 
isScriptExecuting() - Method in class org.jmol.api.JmolViewer
 
isScriptExecuting() - Method in class org.jmol.script.ScriptEvaluator
 
isScriptExecuting() - Method in class org.jmol.viewer.Viewer
 
isScriptQueued - Variable in class org.jmol.viewer.Viewer
 
isSelectAction(int) - Method in class org.jmol.viewer.ActionManager
 
isSelected(BitSet) - Method in class org.jmol.modelset.Group
 
isSelected(int) - Method in class org.jmol.viewer.SelectionManager
 
isSelected(int) - Method in class org.jmol.viewer.Viewer
 
isSequential - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
isServer() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
isServer - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
isServer() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
isSetBrace - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
isSetOrDefine - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
isShapeSecondary(int) - Static method in class org.jmol.viewer.JmolConstants
 
isShapeVisible(int) - Method in class org.jmol.modelset.Atom
 
isSheet() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isSheet(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
 
isSheet() - Method in class org.jmol.modelsetbio.Monomer
 
isSheet(int) - Method in class org.jmol.shapebio.RocketsRenderer
 
isShowCommand - Variable in class org.jmol.script.ScriptCompiler
 
isShowScriptOutput - Variable in class org.jmol.script.ScriptCompiler
 
isSigned - Variable in class org.jmol.applet.AppletWrapper
 
isSigned() - Method in class org.jmol.applet.AppletWrapper
 
isSigned - Variable in class org.jmol.applet.Jmol
 
isSigned - Variable in class org.jmol.popup.SimplePopup
 
isSignedApplet - Variable in class org.jmol.viewer.Viewer
 
isSignedApplet() - Method in class org.jmol.viewer.Viewer
 
isSignedAppletLocal - Variable in class org.jmol.viewer.Viewer
 
isSilent - Variable in class org.jmol.jvxl.readers.Parameters
 
isSilent - Variable in class org.jmol.minimize.Minimizer
 
isSilent - Variable in class org.jmol.script.ScriptCompiler
 
isSilent - Variable in class org.jmol.smiles.SmilesSearch
 
isSilent - Variable in class org.jmol.viewer.Viewer
 
isSilent - Variable in class org.openscience.jmol.app.JmolApp
 
isSlab - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isSlab - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
isSlab() - Method in interface org.jmol.api.SymmetryInterface
 
isSlab - Variable in class org.jmol.shape.CageRenderer
 
isSlab() - Method in class org.jmol.symmetry.Symmetry
 
isSlab() - Method in class org.jmol.util.SimpleUnitCell
 
isSlabbable - Variable in class org.jmol.jvxl.data.JvxlData
 
isSlabEnabled - Variable in class org.jmol.export.__RayTracerExporter
 
isSmarts - Variable in class org.jmol.smiles.SmilesParser
 
isSmarts - Variable in class org.jmol.smiles.SmilesSearch
 
isSmilesFind - Variable in class org.jmol.smiles.SmilesSearch
 
isSpaceOrTab(char) - Static method in class org.jmol.script.ScriptCompiler
 
isSpartanArchive(String) - Method in class org.jmol.adapter.readers.quantum.SpartanReader
 
isSpecTerminator(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
isSpinFixed - Variable in class org.jmol.viewer.TransformManager
 
isSpinInternal - Variable in class org.jmol.viewer.TransformManager
 
isSpinSelected - Variable in class org.jmol.viewer.TransformManager
 
isSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isSquared - Variable in class org.jmol.jvxl.data.VolumeData
 
isSquared - Variable in class org.jmol.jvxl.readers.Parameters
 
isStandard - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
isStateDataRead() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isStateScript - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
isStateScript - Variable in class org.jmol.script.ScriptContext
 
isStateScript - Variable in class org.jmol.script.ScriptEvaluator
 
isStaticFunction(String) - Static method in class org.jmol.viewer.StateManager
 
isStereo() - Method in class org.jmol.modelset.Bond
 
isStereoDouble() - Method in class org.jmol.viewer.Viewer
 
isStereoSlave - Variable in class org.jmol.applet.Jmol
 
isStringArray(String) - Static method in class org.jmol.util.Escape
 
isStructureTainted() - Method in class org.jmol.modelset.Model
 
isSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
isSurface - Variable in class org.jmol.shapespecial.Dots
 
isSurfacePoint - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isSymmetry - Variable in class org.jmol.popup.SimplePopup
 
isSynced - Variable in class org.jmol.viewer.StatusManager
 
isSyntaxCheck - Variable in class org.jmol.script.ScriptContext
 
isSyntaxCheck - Variable in class org.jmol.script.ScriptEvaluator
 
isSyntaxCheck - Variable in class org.jmol.script.ScriptMathProcessor
Reverse Polish Notation Engine for IF, SET, and %{...} -- Bob Hanson 2/16/2007 Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f hansonr@stolaf.edu
isTainted(int, byte) - Method in class org.jmol.modelset.AtomCollection
 
isTainted - Variable in class org.jmol.viewer.Viewer
 
iStep - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
isToFile - Variable in class org.jmol.export.___Exporter
 
isToken(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
isTraceAlpha - Variable in class org.jmol.shapebio.BioShapeRenderer
 
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isTrajectory - Variable in class org.jmol.modelset.Measurement
 
isTrajectory() - Method in class org.jmol.modelset.Measurement
 
isTrajectory - Variable in class org.jmol.modelset.Model
 
isTrajectory(int) - Method in class org.jmol.modelset.ModelCollection
 
isTrajectory(int[]) - Method in class org.jmol.modelset.ModelCollection
 
isTrajectory - Variable in class org.jmol.modelset.ModelLoader
 
isTrajectory(int) - Method in class org.jmol.viewer.Viewer
 
isTrajectorySubFrame(int) - Method in class org.jmol.modelset.ModelCollection
 
isTranslucent() - Method in class org.jmol.modelset.Atom
 
isTranslucent() - Method in class org.jmol.modelset.Bond
 
isTranslucent - Variable in class org.jmol.shape.MeshRenderer
 
isTranslucent - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isTranslucent - Variable in class org.jmol.util.ColorEncoder
 
isTransparent - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
isTriangleSet - Variable in class org.jmol.shape.Mesh
 
istructure - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
 
isTurn(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
 
isTwoSided - Variable in class org.jmol.shape.Mesh
 
isTypeSet - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
isUnitCell - Variable in class org.jmol.popup.SimplePopup
 
isUpdating - Variable in class org.jmol.applet.Jmol
 
isUserAction(int) - Method in class org.jmol.viewer.binding.Binding
 
isUserFunction(String) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
isUserToken - Variable in class org.jmol.script.ScriptCompiler
 
isUserValue - Variable in class org.jmol.shapespecial.Dipole
 
isUserValue - Variable in class org.jmol.shapespecial.Dipoles
 
isV3000 - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
isValid - Variable in class org.jmol.bspt.Bspf
 
isValid - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
isValid - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
isValid - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
isValid() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isValid() - Method in class org.jmol.modelset.Measurement
 
isValid() - Method in class org.jmol.modelset.ModelCollection.StateScript
 
isValid - Variable in class org.jmol.shape.Mesh
 
isValid - Variable in class org.jmol.shapespecial.Dipole
 
isValid - Variable in class org.jmol.shapespecial.Draw
 
isValid - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
isValid(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
isValidElementSymbol(char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidElementSymbol(char, char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidElementSymbolNoCaseSecondChar(char, char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidElementSymbolNoCaseSecondChar(String) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidFirstSymbolChar(char) - Static method in class org.jmol.adapter.smarter.Atom
 
isVariable(String) - Method in class org.jmol.script.ScriptFunction
 
isVariableType(Object) - Static method in class org.jmol.script.ScriptVariable
 
isVdw - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
isVector - Variable in class org.jmol.shapespecial.Draw
 
isVector - Variable in class org.jmol.shapespecial.DrawMesh
 
isVersion3 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isVersion5 - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
isVertices - Variable in class org.jmol.shapespecial.Draw
 
isVibration - Variable in class org.jmol.popup.SimplePopup
 
isVibrationOn() - Method in class org.jmol.viewer.TransformManager
 
isVibrationOn() - Method in class org.jmol.viewer.Viewer
 
isVisible() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
isVisible(int) - Method in class org.jmol.modelset.Atom
determine if an atom or its PDB group is visible
isVisible - Variable in class org.jmol.modelset.Measurement
 
isVisible() - Method in class org.jmol.modelset.Measurement
 
isVisible - Variable in class org.jmol.shape.Bbcage
 
isWhiteSpace(String, int) - Static method in class org.jmol.util.Parser
 
isWild(String) - Static method in class org.jmol.util.TextFormat
 
isWindowCentered() - Method in class org.jmol.viewer.TransformManager
 
isWindowCentered() - Method in class org.jmol.viewer.Viewer
 
isWithin(int) - Method in class org.jmol.modelsetbio.ProteinStructure
 
isWithin(Point3f) - Method in class org.jmol.util.BoxInfo
 
isWithinCell(int, Point3f, int, int, int, int, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
 
isWithinFourBonds(Atom) - Method in class org.jmol.modelset.Atom
 
isWithinNot - Variable in class org.jmol.shapesurface.Isosurface
 
isWithinRadius(Point3f) - Method in class org.jmol.bspt.CubeIterator
checks one Point3f for distance
isWithinStructure(EnumStructure) - Method in class org.jmol.modelset.Atom
 
isWithinStructure(EnumStructure) - Method in class org.jmol.modelset.Group
 
isWithinStructure(EnumStructure) - Method in class org.jmol.modelsetbio.AminoMonomer
 
isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
 
isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
 
isXLowToHigh - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isXLowToHigh - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
isXmlFile - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
isXYZ - Variable in class org.jmol.modelset.ModelCollection
 
isZapped - Variable in class org.jmol.popup.SimplePopup
 
isZeroBased - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
isZipFile(String) - Static method in class org.jmol.util.ZipUtil
 
isZipFile(InputStream) - Static method in class org.jmol.util.ZipUtil
 
isZipFile(byte[]) - Static method in class org.jmol.util.ZipUtil
 
isZoomArea(int) - Method in class org.jmol.viewer.ActionManager
 
itemStateChanged(ItemEvent) - Method in class org.jmol.export.dialog.Dialog.ExportChoiceListener
 
itemStateChanged(ItemEvent) - Method in class org.jmol.popup.SimplePopup.CheckboxMenuItemListener
 
itemStateChanged(ItemEvent) - Method in class org.openscience.chimetojmol.ChimePanel
 
itemStateChanged(ItemEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
iter - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
iter - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
iterateOverAllNewAtoms(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewBonds(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewModels(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewStructures(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
Pull in all spans of helix, etc.
iToken - Variable in class org.jmol.jvxl.readers.PmeshReader
 
iToken - Variable in class org.jmol.script.ScriptContext
 
iToken - Variable in class org.jmol.script.ScriptEvaluator
 
itokenInfix - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
iVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
iValue(Token) - Static method in class org.jmol.script.ScriptVariable
 

J

jaguarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
JaguarReader - Class in org.jmol.adapter.readers.quantum
Jaguar reader tested for the two samples files in CVS.
JaguarReader() - Constructor for class org.jmol.adapter.readers.quantum.JaguarReader
 
JaguarReader - Class in org.jmol.jvxl.readers
 
JaguarReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.JaguarReader
 
javaname - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
javascript - Static variable in class org.jmol.script.Token
 
jbr - Variable in class org.jmol.modelset.ModelLoader
 
jcd - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
JmeReader - Class in org.jmol.adapter.readers.simple
 
JmeReader() - Constructor for class org.jmol.adapter.readers.simple.JmeReader
 
Jmol - Class in org.jmol.applet
 
Jmol() - Constructor for class org.jmol.applet.Jmol
 
jmol - Static variable in class org.jmol.script.Token
 
JMOL - Static variable in class org.jmol.util.ColorEncoder
 
Jmol - Class in org.openscience.jmol.app
 
Jmol(JmolApp, Splash, JFrame, Jmol, int, int, String, Point) - Constructor for class org.openscience.jmol.app.Jmol
 
jmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
jmol - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
Jmol.MyStatusListener - Class in org.jmol.applet
 
Jmol.MyStatusListener() - Constructor for class org.jmol.applet.Jmol.MyStatusListener
 
JmolAdapter - Class in org.jmol.api
The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
JmolAdapter(String) - Constructor for class org.jmol.api.JmolAdapter
 
JmolAdapter.AtomIterator - Class in org.jmol.api
AtomIterator is used to enumerate all the clientAtom objects in a specified frame.
JmolAdapter.AtomIterator() - Constructor for class org.jmol.api.JmolAdapter.AtomIterator
 
JmolAdapter.BondIterator - Class in org.jmol.api
BondIterator is used to enumerate all the bonds
JmolAdapter.BondIterator() - Constructor for class org.jmol.api.JmolAdapter.BondIterator
 
JmolAdapter.StructureIterator - Class in org.jmol.api
StructureIterator is used to enumerate Structures Helix, Sheet, Turn
JmolAdapter.StructureIterator() - Constructor for class org.jmol.api.JmolAdapter.StructureIterator
 
JmolApp - Class in org.openscience.jmol.app
 
JmolApp() - Constructor for class org.openscience.jmol.app.JmolApp
 
JmolApp(String[]) - Constructor for class org.openscience.jmol.app.JmolApp
standard Jmol application entry point
jmolApp - Variable in class org.openscience.jmol.app.JmolData
 
jmolApp - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
JmolAppConsoleInterface - Interface in org.jmol.api
 
JmolAppletInterface - Interface in org.jmol.applet
This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
JmolAppletRegistry - Class in org.jmol.applet
 
JmolAppletRegistry() - Constructor for class org.jmol.applet.JmolAppletRegistry
 
jmolAtomCount - Variable in class org.jmol.smiles.SmilesSearch
 
jmolAtoms - Variable in class org.jmol.smiles.SmilesSearch
 
jmolBinding - Variable in class org.jmol.viewer.ActionManager
 
JmolBinding - Class in org.jmol.viewer.binding
 
JmolBinding() - Constructor for class org.jmol.viewer.binding.JmolBinding
 
JmolBinding(String) - Constructor for class org.jmol.viewer.binding.JmolBinding
 
JmolBioResolver - Interface in org.jmol.api
 
JmolCallbackListener - Interface in org.jmol.api
 
jmolCallbackListener - Variable in class org.jmol.viewer.StatusManager
 
JmolConsole - Class in org.jmol.console
 
JmolConsole() - Constructor for class org.jmol.console.JmolConsole
 
jmolConsole - Variable in class org.jmol.console.ScriptEditor
 
JmolConsole.FileChecker - Class in org.jmol.console
 
JmolConsole.FileChecker(String) - Constructor for class org.jmol.console.JmolConsole.FileChecker
 
JmolConstants - Class in org.jmol.viewer
 
JmolConstants() - Constructor for class org.jmol.viewer.JmolConstants
 
jmolData - Variable in class org.jmol.modelset.Model
 
jmolData - Variable in class org.jmol.modelset.ModelLoader
 
JmolData - Class in org.openscience.jmol.app
 
JmolData(JmolApp) - Constructor for class org.openscience.jmol.app.JmolData
 
jmolDefaultProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
jmolDefaults - Static variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
jmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
JmolDialogInterface - Interface in org.jmol.api
 
JmolEdge - Class in org.jmol.util
 
JmolEdge() - Constructor for class org.jmol.util.JmolEdge
 
JmolEdge.EnumBondOrder - Enum in org.jmol.util
 
JmolEdge.EnumBondOrder(int, String, String) - Constructor for enum org.jmol.util.JmolEdge.EnumBondOrder
 
JmolFileDropper - Class in org.jmol.export
A simple Dropping class to allow files to be dragged onto a target.
JmolFileDropper(JmolStatusListener, JmolViewer) - Constructor for class org.jmol.export.JmolFileDropper
 
JmolFilesReaderInterface - Interface in org.jmol.api
 
JmolFrame - Interface in org.jmol.console
 
jmolFrameType - Variable in class org.jmol.modelset.Model
 
JmolGestureServerInterface - Interface in org.jmol.api
 
JmolImageCreatorInterface - Interface in org.jmol.api
 
jmolIndex - Variable in class org.jmol.smiles.SmilesAtom
 
JmolInstance - Class in org.openscience.jmol.app.webexport
 
JmolInstance(JmolViewer, String, int, int, int) - Constructor for class org.openscience.jmol.app.webexport.JmolInstance
 
JmolJniClientAdapter - Class in org.jmol.multitouch.jni
 
JmolJniClientAdapter() - Constructor for class org.jmol.multitouch.jni.JmolJniClientAdapter
 
JmolLineReader - Interface in org.jmol.api
 
JmolMeasurementClient - Interface in org.jmol.api
 
JmolModelKitInterface - Interface in org.jmol.api
 
JmolMolecule - Class in org.jmol.util
an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
JmolMolecule() - Constructor for class org.jmol.util.JmolMolecule
 
JmolMolecule(JmolNode[], int, int, BitSet, int, int) - Constructor for class org.jmol.util.JmolMolecule
 
JmolMovieCreatorInterface - Interface in org.jmol.api
 
JmolMultiTouchAdapter - Interface in org.jmol.multitouch
 
JmolMultiTouchClient - Interface in org.jmol.multitouch
 
JmolMultiTouchClientAdapter - Class in org.jmol.multitouch
 
JmolMultiTouchClientAdapter() - Constructor for class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
JmolNode - Interface in org.jmol.util
 
jmolPanel - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
JmolPanel - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel(JmolApp, Splash, JFrame, JmolPanel, int, int, String, Point) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel
 
JmolPanel.AboutAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.AboutAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
 
JmolPanel.ActionChangedListener - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
 
JmolPanel.AppCloser - Class in org.openscience.jmol.app.jmolpanel
To shutdown when run as an application.
JmolPanel.AppCloser() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
 
JmolPanel.AtomSetChooserAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
 
JmolPanel.CloseAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.CloseAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
 
JmolPanel.ConsoleAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ConsoleAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
 
JmolPanel.CopyImageAction - Class in org.openscience.jmol.app.jmolpanel
An Action to copy the current image into the clipboard.
JmolPanel.CopyImageAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
 
JmolPanel.CopyScriptAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.CopyScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
 
JmolPanel.ExecuteScriptAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ExecuteScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
 
JmolPanel.ExitAction - Class in org.openscience.jmol.app.jmolpanel
Really lame implementation of an exit command
JmolPanel.ExitAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
 
JmolPanel.ExportAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ExportAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
 
JmolPanel.GaussianAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.GaussianAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
 
JmolPanel.NewAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.NewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
JmolPanel.NewAction(String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
JmolPanel.NewwinAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.NewwinAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
 
JmolPanel.OpenAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
 
JmolPanel.OpenMolAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenMolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
 
JmolPanel.OpenPdbAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenPdbAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
 
JmolPanel.OpenUrlAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenUrlAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
JmolPanel.PasteClipboardAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PasteClipboardAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
 
JmolPanel.PovrayAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PovrayAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
 
JmolPanel.PrintAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PrintAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
 
JmolPanel.RecentFilesAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.RecentFilesAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
 
JmolPanel.ResizeAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ResizeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
 
JmolPanel.ScriptEditorAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ScriptEditorAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
 
JmolPanel.ScriptWindowAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ScriptWindowAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
 
JmolPanel.SurfaceToolAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.SurfaceToolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
 
JmolPanel.ToWebAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ToWebAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
 
JmolPanel.UguideAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.UguideAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
 
JmolPanel.ViewMeasurementTableAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ViewMeasurementTableAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
 
JmolPanel.WhatsNewAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.WhatsNewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
 
JmolPanel.WriteAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.WriteAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
 
JmolPdfCreatorInterface - Interface in org.jmol.api
 
JmolPopup - Class in org.jmol.popup
 
JmolPopup() - Constructor for class org.jmol.popup.JmolPopup
 
jmolpopup - Variable in class org.jmol.viewer.Viewer
 
JmolPopupInterface - Interface in org.jmol.api
 
jmolPosition - Variable in class org.openscience.jmol.app.JmolApp
 
JmolPrompt - Class in org.jmol.console
 
JmolPrompt() - Constructor for class org.jmol.console.JmolPrompt
note: THIS CLASS SHOULD ONLY BE INVOKED USING (JmolPromptInterface) Interface.getOptionInterface("awt.console.JmolPrompt")
JmolPromptInterface - Interface in org.jmol.api
 
jmolReady() - Method in class org.jmol.applet.Jmol
 
jmolReady() - Method in interface org.jmol.applet.WrappedApplet
 
jmolRenderer - Variable in class org.jmol.export.___Exporter
 
JmolRendererInterface - Interface in org.jmol.api
 
JmolResourceHandler - Class in org.openscience.jmol.app.jmolpanel
Provides access to resources (for example, strings and images).
JmolResourceHandler() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
jmolScriptCallback(EnumCallback) - Method in class org.jmol.viewer.StatusManager
 
jmolScriptCallbacks - Variable in class org.jmol.viewer.StatusManager
 
JmolScriptEditorInterface - Interface in org.jmol.api
 
JmolSelectionListener - Interface in org.jmol.api
listen to atom selections in a Jmol Viewer
JmolSimpleViewer - Class in org.jmol.api
This is the high-level API for the JmolViewer for simple access.
JmolSimpleViewer() - Constructor for class org.jmol.api.JmolSimpleViewer
 
JmolSparshClientAdapter - Class in org.jmol.multitouch.sparshui
 
JmolSparshClientAdapter() - Constructor for class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
JmolStatusListener - Interface in org.jmol.api
 
jmolStatusListener - Variable in class org.jmol.viewer.StatusManager
 
jmolTest() - Method in class org.jmol.viewer.Viewer
 
JmolTouchSimulatorInterface - Interface in org.jmol.api
 
JmolViewer - Class in org.jmol.api
This is the high-level API for the JmolViewer for simple access.
JmolViewer() - Constructor for class org.jmol.api.JmolViewer
 
jmolViewer - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
jmolViewer - Variable in class org.openscience.molecularplayground.MPJmolApp
 
join - Static variable in class org.jmol.script.Token
 
join(Object[], char, int) - Static method in class org.jmol.util.TextFormat
 
JpegEncoder - Class in org.jmol.util
 
JpegEncoder(ApiPlatform, Object, int, OutputStream, String) - Constructor for class org.jmol.util.JpegEncoder
 
JpegInfo - Class in org.jmol.util
 
JpegInfo(ApiPlatform, Object, String) - Constructor for class org.jmol.util.JpegInfo
 
jpegNaturalOrder - Static variable in class org.jmol.util.Huffman
 
JpegObj - Variable in class org.jmol.util.JpegEncoder
 
jsEval(String) - Method in class org.jmol.viewer.StatusManager
 
jsEval(String) - Method in class org.jmol.viewer.Viewer
 
JsonNioClient - Interface in org.openscience.jmol.app.jmolpanel
a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.
JsonNioService - Class in org.openscience.jmol.app.jmolpanel
 
JsonNioService() - Constructor for class org.openscience.jmol.app.jmolpanel.JsonNioService
 
JsonNioService.JsonNioServerThread - Class in org.openscience.jmol.app.jmolpanel
 
JsonNioService.JsonNioServerThread() - Constructor for class org.openscience.jmol.app.jmolpanel.JsonNioService.JsonNioServerThread
 
JsonNioService.JsonNioThread - Class in org.openscience.jmol.app.jmolpanel
 
JsonNioService.JsonNioThread() - Constructor for class org.openscience.jmol.app.jmolpanel.JsonNioService.JsonNioThread
 
JsonNioService.JSONObject - Class in org.openscience.jmol.app.jmolpanel
 
JsonNioService.JSONObject() - Constructor for class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
 
JsonNioService.JSONObject(String) - Constructor for class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
 
justifymeasurements - Static variable in class org.jmol.script.Token
 
justifyMeasurements - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
justTransferFile(File, File, InputStream) - Method in class org.openscience.chimetojmol.ChimePanel
 
Jvxl - Class in org.openscience.jvxl
 
Jvxl() - Constructor for class org.openscience.jvxl.Jvxl
 
JVXL_VERSION - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
JVXL_VERSION1 - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
JVXL_VERSION_XML - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
jvxlAppendCharacter2(float, float, float, int, int, StringBuffer, StringBuffer) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlAppendCommandState(StringBuffer, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlAppendEncodedNumber(StringBuffer, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
JvxlCoder - Class in org.jmol.jvxl.data
 
JvxlCoder() - Constructor for class org.jmol.jvxl.data.JvxlCoder
 
jvxlColorData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlColorDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlCompressString(String, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCreateColorData(JvxlData, float[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCreateHeader(VolumeData, StringBuffer) - Static method in class org.jmol.jvxl.data.JvxlCoder
Creates a two-line header for the XJVXL file.
jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData, StringBuffer) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
JvxlData - Class in org.jmol.jvxl.data
 
JvxlData() - Constructor for class org.jmol.jvxl.data.JvxlData
 
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlData - Variable in class org.jmol.shapesurface.Isosurface
 
jvxlData - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsPrecisionColor - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDecodeBitSet(String, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlDecodeBitSet(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlDecodeContourData(JvxlData, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlDecodeTriangleData(String, String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
decode triangle data found within element as created with jvxlEncodeTriangleData (see above)
jvxlDecodeVertexData(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
decode vertex data found within element as created by jvxlEncodeVertexData (see above)
jvxlEdgeData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlEdgeDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlEncodeBitSet(BitSet) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeBitSet(BitSet, int, StringBuffer) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeBitSet0(BitSet, int, StringBuffer) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeContourData(List<Object>[], StringBuffer) - Static method in class org.jmol.jvxl.data.JvxlCoder
contour data are appended to a string buffer in the form of a triangle bitset data triangle bitset data triangle bitset data ...
jvxlExcluded - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFileHeaderBuffer - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlFileMessage - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFileTitle - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFractionAsCharacter(float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionAsCharacter(float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionFromCharacter(int, int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionFromCharacter2(int, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetData(VoxelDataCreator, Parameters, VolumeData, String[], List<Point3f>, float[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
jvxlGetFile(VolumeData, JvxlData, String[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetFile(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetFileXml(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetInfo(JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetInfo(JvxlData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetNextFraction(int, int, float) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlNSurfaceInts - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlParseEncodedInt(String, int, int, int[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlPlane - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlReadData(String, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlReadData(String, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlReadDefinitionLine(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
JvxlReader - Class in org.jmol.jvxl.readers
 
JvxlReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.JvxlReader
 
jvxlReadSurfaceInfo() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSetColorRanges(float, float, float, float, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSetCompressionRatio(StringBuffer, JvxlData, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSkipDataBlock(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlSurfaceData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlUncompressString(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlUpdateInfo(String[], long) - Method in class org.jmol.jvxl.data.JvxlData
 
jvxlUpdateInfo() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlValueAsCharacter(float, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlValueFromCharacter2(int, int, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlVolumeDataXml - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlVoxelBitSet - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
JvxlWrite - Class in org.openscience.jvxl.simplewriter
 
JvxlWrite() - Constructor for class org.openscience.jvxl.simplewriter.JvxlWrite
 
JvxlXmlReader - Class in org.jmol.jvxl.readers
 
JvxlXmlReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.JvxlXmlReader
 

K

kb - Variable in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
KCAL22 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL332 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL44 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL6 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL644 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL_TO_KJ - Static variable in class org.jmol.minimize.forcefield.Calculations
 
keepChars - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
keepCharsList - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
keepRunning - Variable in class org.jmol.applet.TickerThread
 
keepRunning - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
key - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
key - Variable in class org.jmol.console.KeyJCheckBox
 
key - Variable in class org.jmol.console.KeyJCheckBoxMenuItem
 
key - Variable in class org.jmol.console.KeyJMenu
 
key - Variable in class org.jmol.console.KeyJMenuItem
 
key - Variable in class org.jmol.console.KeyJRadioButtonMenuItem
 
key - Variable in class org.jmol.modelset.LabelToken
 
key - Variable in class org.jmol.util.Int2IntHash.Entry
 
keyBuffer - Variable in class org.jmol.awt.Mouse
 
KeyJCheckBox - Class in org.jmol.console
 
KeyJCheckBox(String, String, Map<String, AbstractButton>, boolean) - Constructor for class org.jmol.console.KeyJCheckBox
 
KeyJCheckBoxMenuItem - Class in org.jmol.console
 
KeyJCheckBoxMenuItem(String, String, Map<String, AbstractButton>, boolean) - Constructor for class org.jmol.console.KeyJCheckBoxMenuItem
 
KeyJMenu - Class in org.jmol.console
 
KeyJMenu(String, String, Map<String, AbstractButton>) - Constructor for class org.jmol.console.KeyJMenu
 
KeyJMenuItem - Class in org.jmol.console
 
KeyJMenuItem(String, String, Map<String, AbstractButton>) - Constructor for class org.jmol.console.KeyJMenuItem
 
KeyJRadioButtonMenuItem - Class in org.jmol.console
 
KeyJRadioButtonMenuItem(String, String, Map<String, AbstractButton>) - Constructor for class org.jmol.console.KeyJRadioButtonMenuItem
 
keyPressed(KeyEvent) - Method in class org.jmol.awt.Mouse
 
keyPressed(int, int) - Method in class org.jmol.viewer.ActionManager
called by MouseManager.keyPressed
keyProcessing - Variable in class org.jmol.viewer.ActionManager
 
keyReleased(KeyEvent) - Method in class org.jmol.awt.Mouse
 
keyReleased(int) - Method in class org.jmol.viewer.ActionManager
 
keys - Static variable in class org.jmol.script.Token
 
keyTyped(KeyEvent) - Method in class org.jmol.awt.Mouse
 
keyword - Variable in class org.jmol.export.UseTable
 
keyword - Static variable in class org.jmol.script.Token
 
keyXy - Variable in class org.jmol.shapesurface.Isosurface
 
KfDocument - Class in org.jmol.util
 
KfDocument() - Constructor for class org.jmol.util.KfDocument
 
kind - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
KinemageReader - Class in org.jmol.jvxl.readers
 
KinemageReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.KinemageReader
 
kinEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
kioskFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
KioskFrame - Class in org.openscience.jmol.app.jmolpanel
A borderless rectangle, like the applet, that contains the application for use in kiosk-style displays, as for example projected on the wall as in http://molecularPlayground.org
KioskFrame(int, int, int, int, JPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.KioskFrame
 
kioskFrame - Variable in class org.openscience.molecularplayground.MPJmolApp
 

L

LABEL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
label(int) - Method in class org.jmol.script.ScriptEvaluator
 
label - Static variable in class org.jmol.script.Token
 
label1 - Variable in class org.jmol.console.JmolConsole
 
LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JmolConstants
 
LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JmolConstants
 
LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
labelBoxes - Variable in class org.jmol.shape.Labels
 
labelFormat - Variable in class org.jmol.shape.Hover
 
labelMode - Variable in class org.jmol.viewer.ActionManager
 
labels - Variable in class org.jmol.console.JmolConsole
 
labels - Variable in class org.jmol.jvxl.readers.MrcBinaryReader
 
labels - Variable in class org.jmol.shape.Axes
 
Labels - Class in org.jmol.shape
 
Labels() - Constructor for class org.jmol.shape.Labels
 
labels - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
 
LabelsRenderer - Class in org.jmol.shape
 
LabelsRenderer() - Constructor for class org.jmol.shape.LabelsRenderer
 
LabelToken - Class in org.jmol.modelset
 
LabelToken(String) - Constructor for class org.jmol.modelset.LabelToken
 
LabelToken(int) - Constructor for class org.jmol.modelset.LabelToken
 
labelTokenIds - Static variable in class org.jmol.modelset.LabelToken
 
labelTokenParams - Static variable in class org.jmol.modelset.LabelToken
 
ladder - Variable in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
language - Variable in class org.jmol.applet.Jmol
 
language - Variable in class org.jmol.i18n.GT
 
language - Variable in class org.jmol.i18n.GT.Language
 
language - Static variable in class org.jmol.script.Token
 
language - Variable in class org.jmol.viewer.Viewer
 
languageList - Static variable in class org.jmol.i18n.GT
 
languagetranslation - Static variable in class org.jmol.script.Token
 
last - Static variable in class org.jmol.script.Token
 
LAST_AVAILABLE_COLIX - Static variable in class org.jmol.g3d.Graphics3D
 
lastAltLoc - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
lastAltLoc - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastAtom - Variable in class org.jmol.jvxl.readers.KinemageReader
 
lastAtomData - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastAtomIndex - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastAtomIndex - Variable in class org.jmol.modelset.Group
 
lastChainAtom - Variable in class org.jmol.smiles.SmilesSearch
 
lastColix - Variable in class org.jmol.util.MeshSurface
 
lastColor - Variable in class org.jmol.util.MeshSurface
 
lastColumnIsDummy - Variable in class org.jmol.util.JpegInfo
 
lastConnections - Variable in class org.jmol.viewer.StateManager
 
lastCoordinates - Variable in class org.jmol.viewer.StateManager
 
lastDisorderAssembly - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
lastError - Static variable in exception org.jmol.smiles.InvalidSmilesException
 
lastFlowCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
lastFrameDelay - Variable in class org.jmol.viewer.AnimationManager
 
lastFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
 
lastGroup - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastIndex - Variable in class org.jmol.modelset.MeasurementPending
 
lastInfo - Static variable in class org.jmol.symmetry.SpaceGroup
 
lastInsertion - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastLogTime - Variable in class org.jmol.multitouch.ActionManagerMT
 
lastMoData - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
lastModelIndex - Variable in class org.jmol.atomdata.AtomData
 
lastModelIndex - Variable in class org.jmol.viewer.AnimationManager
 
lastModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
lastModelPainted - Variable in class org.jmol.viewer.AnimationManager
 
lastMotionEventNumber - Variable in class org.jmol.applet.Jmol
 
lastMotionEventNumber - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
lastMoveTime - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
lastOpened - Static variable in class org.jmol.console.ScriptEditor
 
lastOrientation - Variable in class org.jmol.viewer.StateManager
 
lastQPt - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
lastRawColor - Variable in class org.jmol.g3d.Graphics3D
 
lastRowIsDummy - Variable in class org.jmol.util.JpegInfo
 
lastSelected - Variable in class org.jmol.viewer.StateManager
 
lastSequenceNumber - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
lastSetH - Variable in class org.jmol.modelsetbio.Resolver
 
lastShape - Variable in class org.jmol.viewer.StateManager
 
lastSourceSerial - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastState - Variable in class org.jmol.viewer.StateManager
 
lastTargetSerial - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastToken - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
lattice - Static variable in class org.jmol.script.Token
 
lattice - Variable in class org.jmol.shape.Mesh
 
LATTICE_VECTOR - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
latticeCode - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
 
latticeCode - Variable in class org.jmol.symmetry.HallInfo
 
latticeCode - Variable in class org.jmol.symmetry.SpaceGroup
 
latticeExtension - Variable in class org.jmol.symmetry.HallInfo
 
latticeOffset - Variable in class org.jmol.shape.MeshRenderer
 
latticeParameter - Variable in class org.jmol.symmetry.SpaceGroup
 
latticeTranslationData - Static variable in class org.jmol.symmetry.Translation
 
latticeVectorPtr - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
layoutWindow() - Method in class org.jmol.console.AppletConsole
 
layoutWindow(Container) - Method in class org.jmol.console.ScriptEditor
 
layoutWindow(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
layoutWindow(Container) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
lcaoCartoon() - Method in class org.jmol.script.ScriptEvaluator
 
lcaocartoon - Static variable in class org.jmol.script.Token
 
LcaoCartoon - Class in org.jmol.shapesurface
 
LcaoCartoon() - Constructor for class org.jmol.shapesurface.LcaoCartoon
 
LcaoCartoonRenderer - Class in org.jmol.shapesurface
 
LcaoCartoonRenderer() - Constructor for class org.jmol.shapesurface.LcaoCartoonRenderer
 
lcaoColorNeg - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoColorPos - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoDir - Variable in class org.jmol.shapesurface.Isosurface
 
lcaoID - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoScale - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoType - Variable in class org.jmol.jvxl.readers.Parameters
 
leadAtomIndex - Variable in class org.jmol.modelset.Group
 
leadAtomIndices - Variable in class org.jmol.modelset.Polymer
 
leadAtomIndices - Variable in class org.jmol.shapebio.BioShape
 
leadAtomIndices - Variable in class org.jmol.shapebio.BioShapeRenderer
 
LEADER_CHAR_MAX - Static variable in class org.jmol.adapter.smarter.Resolver
 
leadMidpoints - Variable in class org.jmol.modelset.Polymer
 
leadPoints - Variable in class org.jmol.modelset.Polymer
 
leaf - Variable in class org.jmol.bspt.CubeIterator
 
Leaf - Class in org.jmol.bspt
A leaf of Point3f objects in the bsp tree
Leaf(Bspt) - Constructor for class org.jmol.bspt.Leaf
 
Leaf(Bspt, Leaf, int) - Constructor for class org.jmol.bspt.Leaf
 
leafCountMax - Static variable in class org.jmol.bspt.Bspt
 
leafIndex - Variable in class org.jmol.bspt.CubeIterator
 
left - Static variable in class org.jmol.script.Token
 
LEFT - Static variable in class org.jmol.viewer.binding.Binding
 
LEFT_MIDDLE_RIGHT - Static variable in class org.jmol.viewer.binding.Binding
 
leftAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
leftbrace - Static variable in class org.jmol.script.Token
 
leftBytes - Variable in class org.jmol.export.image.PngEncoder
 
leftDifference(Quaternion) - Method in class org.jmol.util.Quaternion
 
leftdivide - Static variable in class org.jmol.script.Token
 
leftOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
leftparen - Static variable in class org.jmol.script.Token
 
leftPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
leftsquare - Static variable in class org.jmol.script.Token
 
legacyautobonding - Static variable in class org.jmol.script.Token
 
legacyAutoBonding - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
len - Variable in class org.jmol.viewer.FileManager.ArrayDataReader
 
len - Variable in class org.jmol.viewer.FileManager.VectorDataReader
 
length - Static variable in class org.jmol.script.Token
 
length - Variable in class org.jmol.shapespecial.Draw
 
length() - Method in class org.jmol.util.FastBitSet
 
length() - Method in class org.jmol.util.OutputStringBuffer
 
length - Variable in class org.openscience.jvxl.MonitorInputStream
 
lengths - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
lengthsFreeEnum - Variable in class org.jmol.util.TempArray
 
lengthsFreePoints - Variable in class org.jmol.util.TempArray
 
lengthsFreeScreens - Variable in class org.jmol.util.TempArray
 
lengthUnitFactors - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
 
lengthUnitIds - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
 
lengthVector - Variable in class org.jmol.shapebio.RocketsRenderer
 
lenLine - Variable in class org.jmol.adapter.readers.more.MdCrdReader
 
lenStream - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
 
LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
 
LEVEL_ERROR - Static variable in class org.jmol.util.Logger
 
LEVEL_FATAL - Static variable in class org.jmol.util.Logger
 
LEVEL_INFO - Static variable in class org.jmol.util.Logger
 
LEVEL_MAX - Static variable in class org.jmol.util.Logger
 
LEVEL_WARN - Static variable in class org.jmol.util.Logger
 
lFill(StringBuffer, String, String) - Static method in class org.jmol.util.TextFormat
 
ligandModels - Variable in class org.jmol.viewer.Viewer
 
ligandModelSet - Variable in class org.jmol.viewer.Viewer
 
lighting - Variable in class org.jmol.export._TachyonExporter
 
lighting - Static variable in class org.jmol.script.Token
 
lighting - Variable in class org.jmol.shape.Mesh
 
lighting - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
lightSource - Variable in class org.jmol.export.___Exporter
 
LIME - Static variable in class org.jmol.g3d.Graphics3D
 
LimitedLineReader - Class in org.jmol.adapter.smarter
 
LimitedLineReader(BufferedReader, int) - Constructor for class org.jmol.adapter.smarter.LimitedLineReader
 
LimitedLineReader - Class in org.jmol.util
 
LimitedLineReader(BufferedReader, int) - Constructor for class org.jmol.util.LimitedLineReader
 
line - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
line - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
line - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
line - Static variable in class org.jmol.script.Token
 
line - Variable in class org.jmol.util.CifDataReader
 
line - Variable in class org.jmol.util.XmlReader
 
line3d - Variable in class org.jmol.g3d.Cylinder3D
 
line3d - Variable in class org.jmol.g3d.Graphics3D
 
Line3D - Class in org.jmol.g3d
 
Line3D(Graphics3D) - Constructor for class org.jmol.g3d.Line3D
 
line3d - Variable in class org.jmol.g3d.Triangle3D
 
linearCombination - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
linearCombination - Variable in class org.jmol.quantum.MOCalculation
 
linearOffsets - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
linearOffsets - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
linearSearch() - Method in class org.jmol.minimize.forcefield.ForceField
 
linearTolerance - Variable in class org.jmol.symmetry.PointGroup
 
lineBits - Variable in class org.jmol.g3d.Line3D
 
lineBond - Variable in class org.jmol.shape.SticksRenderer
 
lineCache - Variable in class org.jmol.g3d.Line3D
 
lineCurrent - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
linedata - Static variable in class org.jmol.script.Token
 
lineData - Variable in class org.jmol.shape.Mesh
 
lineData - Variable in class org.jmol.shapespecial.Draw
 
lineEnd - Variable in class org.jmol.script.ScriptContext
 
lineEnd - Variable in class org.jmol.script.ScriptEvaluator
 
lineHeight - Variable in class org.jmol.shape.Text
 
lineIndices - Variable in class org.jmol.script.ScriptCompiler
 
lineIndices - Variable in class org.jmol.script.ScriptContext
 
lineIndices - Variable in class org.jmol.script.ScriptEvaluator
 
lineIndices - Variable in class org.jmol.script.ScriptFunction
 
lineLength - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lineNumbers - Variable in class org.jmol.script.ScriptCompiler
 
lineNumbers - Variable in class org.jmol.script.ScriptContext
 
lineNumbers - Variable in class org.jmol.script.ScriptEvaluator
 
lineNumbers - Variable in class org.jmol.script.ScriptFunction
 
lineOptions - Static variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
linePt - Variable in class org.jmol.jvxl.readers.XplorReader
 
lines - Static variable in class org.jmol.script.Token
 
lines - Variable in class org.jmol.shape.Text
 
lineStart - Variable in class org.jmol.script.ScriptFlowContext
 
lineStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
lineTypeX - Variable in class org.jmol.g3d.Line3D
 
lineWidthMad - Variable in class org.jmol.export.___Exporter
 
link - Static variable in class org.jmol.script.Token
 
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
Follows the reference in an link.
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
Follows the reference in an link.
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
Follows the reference in an link.
linkedMesh - Variable in class org.jmol.shape.Mesh
 
linkedMesh - Variable in class org.jmol.shape.MeshCollection
 
list - Static variable in class org.jmol.script.Token
 
listCommands - Variable in class org.jmol.viewer.Viewer
 
listCommands - Variable in class org.openscience.jmol.app.JmolApp
 
listeners - Variable in class org.jmol.viewer.SelectionManager
 
listf - Static variable in class org.jmol.script.Token
 
listIsosurface(int) - Method in class org.jmol.script.ScriptEvaluator
 
listLabel - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
listSavedStates() - Method in class org.jmol.viewer.StateManager
 
listSavedStates() - Method in class org.jmol.viewer.Viewer
 
listValue(Token) - Static method in class org.jmol.script.ScriptVariable
 
lltoken - Variable in class org.jmol.script.ScriptCompiler
 
lnLength - Variable in class org.jmol.script.ScriptCompiler
 
lo - Variable in class org.jmol.util.ColorEncoder
 
load() - Method in class org.jmol.export.history.HistoryFile
Loads properties from the history file.
load() - Method in class org.jmol.script.ScriptEvaluator
 
load - Static variable in class org.jmol.script.Token
 
LOAD_ATOM_DATA_TYPES - Static variable in class org.jmol.viewer.JmolConstants
 
loadAtomDataAndReturnError(Object, int) - Method in class org.jmol.viewer.Viewer
or just apply the data to the current model set
loadatomdatatolerance - Static variable in class org.jmol.script.Token
 
loadAtomDataTolerance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
loadButton - Variable in class org.jmol.console.AppletConsole
 
loadButton - Variable in class org.jmol.console.ScriptEditor
 
loadCoordinates(String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
 
loadDefaultShapes(ModelSet) - Method in class org.jmol.viewer.ShapeManager
 
loadDOMNode(JSObject) - Method in class org.jmol.applet.Jmol
 
loadDOMNode(JSObject) - Method in interface org.jmol.applet.JmolAppletInterface
 
loadFile(String) - Method in class org.jmol.export.JmolFileDropper
 
loadFiles(List<File>) - Method in class org.jmol.export.JmolFileDropper
 
loadformat - Static variable in class org.jmol.script.Token
 
loadFormat - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
loadGeometries - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
loading - Variable in class org.jmol.applet.Jmol
 
loadInline(String) - Method in class org.jmol.api.JmolViewer
 
loadInline(String, boolean) - Method in class org.jmol.api.JmolViewer
 
loadInline(String, char) - Method in class org.jmol.api.JmolViewer
 
loadInline(String[]) - Method in class org.jmol.api.JmolViewer
 
loadInline(String[], boolean) - Method in class org.jmol.api.JmolViewer
 
loadInline(List<Object>, boolean) - Method in class org.jmol.api.JmolViewer
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
loadInline(String) - Method in class org.jmol.applet.Jmol
Deprecated.  
loadInline(String, String) - Method in class org.jmol.applet.Jmol
Deprecated.  
loadInline(String[]) - Method in class org.jmol.applet.Jmol
Deprecated.  
loadInline(String[], String) - Method in class org.jmol.applet.Jmol
Deprecated.  
loadInline(String) - Method in interface org.jmol.applet.JmolAppletInterface
Deprecated.  
loadInline(String[]) - Method in interface org.jmol.applet.JmolAppletInterface
Deprecated.  
loadInline(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
Deprecated.  
loadInline(String[], String) - Method in interface org.jmol.applet.JmolAppletInterface
Deprecated.  
loadInline(String) - Method in class org.jmol.viewer.Viewer
 
loadInline(String, char) - Method in class org.jmol.viewer.Viewer
 
loadInline(String, boolean) - Method in class org.jmol.viewer.Viewer
 
loadInline(String[]) - Method in class org.jmol.viewer.Viewer
 
loadInline(String[], boolean) - Method in class org.jmol.viewer.Viewer
 
loadInline(List<Object>, boolean) - Method in class org.jmol.viewer.Viewer
does not preserver state, intentionally!
loadInline(String, char, boolean, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
loadInlineArray(String[], String, boolean) - Method in class org.jmol.applet.Jmol
 
loadInlineArray(String[], String, boolean) - Method in interface org.jmol.applet.JmolAppletInterface
 
loadInlineSeparated(String, String) - Method in class org.jmol.applet.Jmol
 
loadInlineString(String, String, boolean) - Method in class org.jmol.applet.Jmol
 
loadInlineString(String, String, boolean) - Method in interface org.jmol.applet.JmolAppletInterface
 
loadligandformat - Static variable in class org.jmol.script.Token
 
loadLigandFormat - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
loadModelFromFile(String, String, String[], Object, boolean, Map<String, Object>, StringBuffer, int) - Method in class org.jmol.viewer.Viewer
Used by the ScriptEvaluator LOAD command to open one or more files.
loadNodeId(String) - Method in class org.jmol.applet.Jmol
 
loadNodeId(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
loadNote - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
loadScript - Variable in class org.jmol.modelset.Model
 
loadShape(int) - Method in class org.jmol.viewer.ShapeManager
 
loadShape(int) - Method in class org.jmol.viewer.Viewer
 
loadState - Variable in class org.jmol.modelset.Model
 
loadVibrations - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
lobe - Static variable in class org.jmol.script.Token
 
localAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
localAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
localArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
localArrayListType - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
localFunctions - Variable in class org.jmol.viewer.StateManager
 
localize(boolean, Properties) - Method in class org.jmol.popup.PopupResource
 
localSpaceGroupName - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
lock - Variable in class org.jmol.script.ParallelProcessor
 
log(String) - Method in interface org.jmol.atomdata.AtomDataServer
 
log(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
log() - Method in class org.jmol.script.ScriptEvaluator
 
log - Static variable in class org.jmol.script.Token
 
log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger
Method to output a log.
log(String) - Method in class org.jmol.viewer.Viewer
 
log(String) - Method in class org.openscience.chimetojmol.ChimePanel
 
log(String) - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
logArea - Variable in class org.openscience.chimetojmol.ChimePanel
 
logArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
logcommands - Static variable in class org.jmol.script.Token
 
logCommands - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
logCommands() - Method in class org.jmol.viewer.Viewer
 
logCompression - Variable in class org.jmol.jvxl.readers.Parameters
 
logCube - Variable in class org.jmol.jvxl.readers.Parameters
 
logData - Variable in class org.jmol.minimize.forcefield.Calculations
 
logDebugScript(int) - Method in class org.jmol.script.ScriptEvaluator
 
logEvent(String, Point3f) - Method in class org.jmol.multitouch.ActionManagerMT
 
logfile - Static variable in class org.jmol.script.Token
 
logFile - Variable in class org.jmol.viewer.Viewer
 
logFilePath - Variable in class org.jmol.viewer.Viewer
 
Logger - Class in org.jmol.util
Logger mechanism.
Logger() - Constructor for class org.jmol.util.Logger
 
LoggerInterface - Interface in org.jmol.util
Interface used for the logging mechanism.
loggestures - Static variable in class org.jmol.script.Token
 
logGestures - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
logging - Variable in class org.jmol.minimize.forcefield.Calculations
 
loggingEnabled - Variable in class org.jmol.minimize.forcefield.Calculations
 
loglevel - Static variable in class org.jmol.script.Token
 
logLevel() - Static method in class org.jmol.util.Logger
Indicates if the level is logged.
logLevel(boolean) - Static method in class org.jmol.util.Logger
Indicates if the level is logged.
logLoadInfo(String) - Method in class org.jmol.script.ScriptEvaluator
 
logMessages - Variable in class org.jmol.jvxl.readers.Parameters
 
logMessages - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
logMessages - Variable in class org.jmol.script.ScriptEvaluator
 
logMessages - Variable in class org.jmol.script.ScriptMathProcessor
 
LogPanel - Class in org.openscience.jmol.app.webexport
 
LogPanel() - Constructor for class org.openscience.jmol.app.webexport.LogPanel
 
logScrollPane - Variable in class org.openscience.chimetojmol.ChimePanel
 
logTime - Variable in class org.jmol.viewer.RepaintManager
 
lonepair - Static variable in class org.jmol.script.Token
 
lookingAtBitset() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtBraceSyntax() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtComment() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtDecimal() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtEndOfLine() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtEndOfStatement() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtExponential() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtImpliedString(boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
An "implied string" is a parameter that is not quoted but because of its position in a command is implied to be a string.
lookingAtInteger() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtLeadingWhitespace() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtLoadFormat() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtLookupToken(int) - Method in class org.jmol.script.ScriptCompiler
 
lookingAtMathContinuation(int) - Method in class org.jmol.script.ScriptCompiler
 
lookingAtMatrix() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtObjectID(boolean) - Method in class org.jmol.script.ScriptCompiler
 
lookingAtSeqcode() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtString(boolean) - Method in class org.jmol.script.ScriptCompiler
 
lookup(String) - Static method in class org.jmol.symmetry.Rotation
 
lookupCode - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
lookupGroupID(String) - Static method in class org.jmol.api.JmolAdapter
 
lookupGroupID(String) - Static method in class org.jmol.modelset.Group
 
lookupIdentifierValue(String) - Method in class org.jmol.script.ScriptEvaluator
 
lookupInterpolatedVoxelValue(Point3f) - Method in interface org.jmol.api.VolumeDataInterface
 
lookupInterpolatedVoxelValue(Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
lookupSpecialAtomID(String) - Static method in class org.jmol.viewer.JmolConstants
 
lookupValue(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
loop - Static variable in class org.jmol.script.Token
 
loopData - Variable in class org.jmol.util.CifDataReader
 
LoopedStreams - Class in org.openscience.jmol.app.jmolpanel
 
LoopedStreams() - Constructor for class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
LOW - Static variable in class org.jmol.util.ColorEncoder
 
lowdenCharges - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
lowerNeighborIsHelixOrSheet() - Method in class org.jmol.modelsetbio.ProteinStructure
 
lp - Static variable in class org.jmol.script.Token
 
ltoken - Variable in class org.jmol.script.ScriptCompiler
 
ltokenPostfix - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
lumo - Static variable in class org.jmol.script.Token
 
lumoEnergy - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
 

M

m - Variable in class org.jmol.export._IdtfExporter
 
MAC_COMMAND - Static variable in class org.jmol.viewer.binding.Binding
 
mad - Variable in class org.jmol.modelset.Bond
 
mad - Variable in class org.jmol.shape.Bbcage
 
mad - Variable in class org.jmol.shape.Measures
 
mad - Variable in class org.jmol.shape.ShapeRenderer
 
mad - Variable in class org.jmol.shapespecial.Dipole
 
mad - Variable in class org.jmol.viewer.StateManager.Connection
 
madAtom - Variable in class org.jmol.modelset.Atom
 
madBeg - Variable in class org.jmol.shape.ShapeRenderer
 
madDnaRna - Variable in class org.jmol.shapebio.BioShapeCollection
 
madEnd - Variable in class org.jmol.shape.ShapeRenderer
 
madHelixSheet - Variable in class org.jmol.shapebio.BioShapeCollection
 
madMid - Variable in class org.jmol.shape.ShapeRenderer
 
madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JmolConstants
 
madOn - Variable in class org.jmol.shapebio.BioShapeCollection
 
mads - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
mads - Variable in class org.jmol.shape.AtomShape
 
mads - Variable in class org.jmol.shapebio.BioShape
 
mads - Variable in class org.jmol.shapebio.BioShapeRenderer
 
madTurnRandom - Variable in class org.jmol.shapebio.BioShapeCollection
 
mag2d - Variable in class org.jmol.shape.SticksRenderer
 
MAGENTA - Static variable in class org.jmol.g3d.Graphics3D
 
magicNumbers - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
magnitudeLight - Static variable in class org.jmol.g3d.Shade3D
 
main(String[]) - Static method in class org.openscience.chimetojmol.ChimeToJmol
 
main(String[]) - Static method in class org.openscience.jmol.app.Jmol
 
main(String[]) - Static method in class org.openscience.jmol.app.JmolData
 
main(String[]) - Static method in class org.openscience.jvxl.Jvxl
 
main(String[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
main(String[]) - Static method in class org.openscience.molecularplayground.MPJmolApp
 
mainMenu - Variable in class org.jmol.popup.JmolPopup
 
MainPopupResourceBundle - Class in org.jmol.popup
 
MainPopupResourceBundle(String, Properties) - Constructor for class org.jmol.popup.MainPopupResourceBundle
 
makeColorScheme(String, int[], boolean) - Method in class org.jmol.util.ColorEncoder
 
makeConnections(float, float, int, int, BitSet, BitSet, BitSet, boolean, boolean, float) - Method in class org.jmol.modelset.ModelCollection
 
makeConnections(float, float, int, int, BitSet, BitSet, BitSet, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
 
makeConnections(float, float, int, int, BitSet, BitSet, BitSet, boolean, boolean, float) - Method in class org.jmol.viewer.Viewer
 
makePlane(float, float, float, Point4f) - Static method in class org.openscience.jmol.app.surfacetool.Slice
 
makePoints - Variable in class org.jmol.shapespecial.Draw
 
manifest - Static variable in class org.jmol.script.Token
 
map(AbstractButton, String, String, Map<String, AbstractButton>) - Static method in class org.jmol.console.KeyJMenuItem
 
map - Variable in class org.jmol.quantum.MOCalculation
 
map - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
 
mapAtomName(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mapc - Variable in class org.jmol.jvxl.readers.MapFileReader
 
MapFileReader - Class in org.jmol.jvxl.readers
 
MapFileReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.MapFileReader
 
mapJavaScriptColors - Static variable in class org.jmol.g3d.Graphics3D
 
mapMostRecentAtomName() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mapMostRecentAtomSerialNumber() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mapPartialCharge(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mappedDataMax - Variable in class org.jmol.jvxl.data.JvxlData
 
mappedDataMax - Variable in class org.jmol.jvxl.readers.Parameters
 
mappedDataMin - Variable in class org.jmol.jvxl.data.JvxlData
 
mappedDataMin - Variable in class org.jmol.jvxl.readers.Parameters
 
mappingPlane - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
mappingPlane - Variable in class org.jmol.jvxl.data.VolumeData
 
mappingPlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
 
mapProperty() - Method in class org.jmol.script.ScriptEvaluator
 
mapProperty - Static variable in class org.jmol.script.Token
 
mapr - Variable in class org.jmol.jvxl.readers.MapFileReader
 
maps - Variable in class org.jmol.jvxl.readers.MapFileReader
 
mapSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
mapT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
mapValue(String) - Method in class org.jmol.script.ScriptVariable
 
mapWidth - Variable in class org.jmol.g3d.Text3D
 
marBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
MarchingCubes - Class in org.jmol.jvxl.calc
 
MarchingCubes() - Constructor for class org.jmol.jvxl.calc.MarchingCubes
 
MarchingCubes(VertexDataServer, VolumeData, Parameters, BitSet) - Constructor for class org.jmol.jvxl.calc.MarchingCubes
 
marchingCubes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MarchingSquares - Class in org.jmol.jvxl.calc
 
MarchingSquares(VertexDataServer, VolumeData, Point4f, float[], int, int, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingSquares
 
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MarchingSquares.ContourVertex - Class in org.jmol.jvxl.calc
 
MarchingSquares.ContourVertex(Point3f) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
MarchingSquares.Triangle - Class in org.jmol.jvxl.calc
 
MarchingSquares.Triangle(int, int, int, int, int) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
margin - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
mark(long) - Method in class org.jmol.viewer.FileManager.ArrayDataReader
 
mark(long) - Method in class org.jmol.viewer.FileManager.VectorDataReader
 
mark(int) - Method in class org.openscience.jvxl.MonitorInputStream
 
markFaceVoxels(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
markLines(String, char) - Static method in class org.jmol.util.Parser
 
markPlaneVoxels(Point3f, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
markPosition - Variable in class org.openscience.jvxl.MonitorInputStream
 
markSphereVoxels(float, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
markToroidVoxels() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
MAROON - Static variable in class org.jmol.g3d.Graphics3D
 
masks - Variable in class org.jmol.export.image.GifEncoder
 
mass - Static variable in class org.jmol.script.Token
 
mat - Variable in class org.jmol.g3d.Sphere3D
 
mat - Variable in class org.jmol.shapebio.BioShapeRenderer
 
mat - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
mat - Variable in class org.jmol.util.Quaternion
 
mat4 - Variable in class org.jmol.modelset.ModelSet
 
mat4 - Variable in class org.jmol.shape.Mesh
 
mat4t - Variable in class org.jmol.modelset.ModelSet
 
match(String, JmolNode[], int, BitSet, BitSet, boolean, boolean, boolean, int) - Method in class org.jmol.smiles.SmilesMatcher
 
matchAllAtoms - Variable in class org.jmol.smiles.SmilesSearch
 
matchingAtom - Variable in class org.jmol.smiles.SmilesAtom
 
matchingBond - Variable in class org.jmol.smiles.SmilesBond
 
matEllipsoidToScreen - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
mathExpressionCommand - Static variable in class org.jmol.script.Token
 
mathfunc - Static variable in class org.jmol.script.Token
 
mathop - Static variable in class org.jmol.script.Token
 
mathproperty - Static variable in class org.jmol.script.Token
 
matInv - Variable in class org.jmol.modelset.ModelSet
 
matrix3f - Static variable in class org.jmol.script.Token
 
matrix4f - Static variable in class org.jmol.script.Token
 
matrixCartesianToFractional - Variable in class org.jmol.util.SimpleUnitCell
 
matrixCtoFAbsolute - Variable in class org.jmol.util.SimpleUnitCell
 
matrixEnd - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
matrixFractionalToCartesian - Variable in class org.jmol.util.SimpleUnitCell
 
matrixFtoCAbsolute - Variable in class org.jmol.util.SimpleUnitCell
 
matrixRotate - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
matrixRotate - Variable in class org.jmol.viewer.TransformManager
 
matrixStart - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
matrixStartInv - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
matrixStep - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
matrixStereo - Variable in class org.jmol.viewer.TransformManager
 
matrixT - Variable in class org.jmol.shape.MeasuresRenderer
 
matrixTemp - Variable in class org.jmol.viewer.TransformManager
 
matrixTemp3 - Variable in class org.jmol.viewer.TransformManager
 
matrixTemp4 - Variable in class org.jmol.viewer.TransformManager
 
matrixTest - Variable in class org.jmol.viewer.TransformManager
 
matrixTransform - Variable in class org.jmol.viewer.TransformManager
 
matrixTransformInv - Variable in class org.jmol.viewer.TransformManager
 
matScreenToCartesian - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
matScreenToEllipsoid - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
matTemp - Variable in class org.jmol.modelset.ModelSet
 
matUnitCellOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
max - Static variable in class org.jmol.script.Token
 
max - Variable in class org.jmol.smiles.SmilesMeasure
 
MAX_ACTION_UNDO - Static variable in class org.jmol.viewer.Viewer
 
MAX_ADJACENT_PHOSPHORUS_DISTANCE - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
MAX_BOND_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shape.Sticks
 
MAX_BONDS_LENGTH_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
 
MAX_DOUBLE_CLICK_MILLIS - Static variable in class org.jmol.viewer.ActionManager
 
MAX_FILES - Static variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
MAX_ITEMS - Static variable in class org.jmol.popup.JmolPopup
 
MAX_LEVEL - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
MAX_LEVEL - Static variable in class org.jmol.shapespecial.Dots
 
MAX_NUM_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
 
MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapespecial.Draw
 
MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapesurface.Isosurface
 
max_squarable_double - Static variable in class org.jmol.minimize.Util
 
MAX_TREE_DEPTH - Static variable in class org.jmol.bspt.Bspt
 
MAX_VERTICES - Static variable in class org.jmol.shapespecial.Polyhedra
 
maxAxis - Static variable in class org.jmol.symmetry.PointGroup
 
maxbits - Variable in class org.jmol.export.image.GifEncoder
 
maxBondingRadius - Variable in class org.jmol.modelset.AtomCollection
 
maxcode - Variable in class org.jmol.export.image.GifEncoder
 
MAXCODE(int) - Method in class org.jmol.export.image.GifEncoder
 
maxColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
 
maxData - Variable in class org.jmol.shapesurface.Contact
 
maxDistance - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
maxElement - Variable in class org.jmol.symmetry.PointGroup
 
maxGrid - Variable in class org.jmol.jvxl.data.VolumeData
 
maxGrid - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
maxHbondAlphaDistance - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
maxHbondAlphaDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
MaxHsampFactor - Variable in class org.jmol.util.JpegInfo
 
MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JmolConstants
 
MAXIMUM_CLICK_TIME - Static variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
MAXIMUM_QUEUE_LENGTH - Static variable in class org.jmol.viewer.StatusManager
 
MAXIMUM_ZOOM_PERCENTAGE - Static variable in class org.jmol.viewer.TransformManager
 
MAXIMUM_ZOOM_PERSPECTIVE_DEPTH - Static variable in class org.jmol.viewer.TransformManager
 
maximumSize - Variable in class org.jmol.viewer.Viewer
 
maxLeft - Variable in class org.jmol.bspt.Node
 
maxLevel - Static variable in class org.jmol.geodesic.Geodesic
 
maxmaxcode - Variable in class org.jmol.export.image.GifEncoder
 
maxMemoryForNewerJvm() - Method in class org.jmol.popup.JmolPopup
 
maxOddSizeSphere - Static variable in class org.jmol.g3d.Sphere3D
 
maxPos - Variable in class org.jmol.export.image.PngEncoder
 
maxRadius - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
maxRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
maxRight - Variable in class org.jmol.bspt.Node
 
maxSerial - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
maxSerial - Variable in class org.jmol.modelsetbio.Resolver
 
maxSet - Variable in class org.jmol.jvxl.readers.Parameters
 
maxset - Static variable in class org.jmol.script.Token
 
maxSize - Variable in class org.jmol.util.CommandHistory
 
maxSphereCache - Static variable in class org.jmol.g3d.Sphere3D
 
maxSphereDiameter - Static variable in class org.jmol.g3d.Sphere3D
 
maxSphereDiameter2 - Static variable in class org.jmol.g3d.Sphere3D
 
MAXUNDO - Static variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
maxVanderwaalsRadius - Variable in class org.jmol.modelset.AtomCollection
 
maxVectorLength - Variable in class org.jmol.jvxl.data.VolumeData
 
MaxVsampFactor - Variable in class org.jmol.util.JpegInfo
 
maxX - Variable in class org.jmol.g3d.Sphere3D
 
maxXYZ - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
maxXYZ0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
maxY - Variable in class org.jmol.g3d.Sphere3D
 
maxZ - Variable in class org.jmol.g3d.Sphere3D
 
maybeGetBaseRing5Points(Point3f[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
mayScript - Variable in class org.jmol.applet.Jmol
 
MdCrdReader - Class in org.jmol.adapter.readers.more
Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
MdCrdReader() - Constructor for class org.jmol.adapter.readers.more.MdCrdReader
 
mDeriv - Variable in class org.jmol.g3d.Sphere3D
 
mDeriv - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
mdlLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
mDsimulation - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
mdTopLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MdTopReader - Class in org.jmol.adapter.readers.more
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
MdTopReader() - Constructor for class org.jmol.adapter.readers.more.MdTopReader
 
measure() - Method in class org.jmol.script.ScriptEvaluator
 
measure - Static variable in class org.jmol.script.Token
 
Measure - Class in org.jmol.util
 
Measure() - Constructor for class org.jmol.util.Measure
 
MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
measureallmodels - Static variable in class org.jmol.script.Token
 
measureAllModels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
measureDistanceUnits - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Measurement - Class in org.jmol.modelset
 
Measurement(ModelSet, Measurement, float, short, String, int) - Constructor for class org.jmol.modelset.Measurement
 
Measurement(ModelSet, int[], Point3fi[], TickInfo) - Constructor for class org.jmol.modelset.Measurement
 
measurement - Variable in class org.jmol.shape.MeasuresRenderer
 
measurementCount - Variable in class org.jmol.shape.Measures
 
MeasurementData - Class in org.jmol.modelset
 
MeasurementData(List<Object>, int, RadiusData, String, String, TickInfo, boolean, boolean, Boolean, boolean) - Constructor for class org.jmol.modelset.MeasurementData
 
measurementHeaders - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
measurementlabels - Static variable in class org.jmol.script.Token
 
measurementLabels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
measurementnumbers - Static variable in class org.jmol.script.Token
 
MeasurementPending - Class in org.jmol.modelset
 
MeasurementPending(ModelSet) - Constructor for class org.jmol.modelset.MeasurementPending
 
measurementPending - Variable in class org.jmol.shape.Measures
 
measurementPending - Variable in class org.jmol.viewer.ActionManager
 
measurementQueued - Variable in class org.jmol.viewer.ActionManager
 
measurements - Static variable in class org.jmol.script.Token
 
measurements - Variable in class org.jmol.shape.Measures
 
measurementsAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
measurementStrings - Variable in class org.jmol.modelset.MeasurementData
 
measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
MeasurementTable - Class in org.openscience.jmol.app.jmolpanel
 
MeasurementTable(JmolViewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable
Constructor
measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
MeasurementTable.MeasurementListWindowListener - Class in org.openscience.jmol.app.jmolpanel
 
MeasurementTable.MeasurementListWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementListWindowListener
 
MeasurementTable.MeasurementTableModel - Class in org.openscience.jmol.app.jmolpanel
 
MeasurementTable.MeasurementTableModel() - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
measurementTableModel - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
measurementunits - Static variable in class org.jmol.script.Token
 
Measures - Class in org.jmol.shape
 
Measures() - Constructor for class org.jmol.shape.Measures
 
measures - Variable in class org.jmol.smiles.SmilesSearch
 
measuresEnabled - Variable in class org.jmol.viewer.ActionManager
 
MeasuresRenderer - Class in org.jmol.shape
 
MeasuresRenderer() - Constructor for class org.jmol.shape.MeasuresRenderer
 
mediaTracker - Variable in class org.jmol.applet.AppletWrapper
 
mem - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
memBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
MEMORY_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
menu - Static variable in class org.jmol.script.Token
 
menubar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
menuContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
menuContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
 
menuEnabled() - Method in class org.jmol.viewer.Viewer
 
menuFile - Variable in class org.openscience.jmol.app.JmolApp
 
MENUITEM_HEIGHT - Static variable in class org.jmol.popup.JmolPopup
 
menuItems - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
menuListener - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
menuMap - Variable in class org.jmol.console.JmolConsole
 
menuStructure - Variable in class org.jmol.api.JmolViewer
 
menuText - Variable in class org.jmol.popup.SimplePopup
 
mep - Static variable in class org.jmol.script.Token
 
mep_calcType - Variable in class org.jmol.jvxl.readers.Parameters
 
mep_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
mep_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
MEP_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
mep_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
mepCalc - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
MepCalculation - Class in org.jmol.quantum
 
MepCalculation() - Constructor for class org.jmol.quantum.MepCalculation
 
MepCalculationInterface - Interface in org.jmol.api
 
mepType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
merge(Shape) - Method in class org.jmol.shape.MeshCollection
called by ParallelProcessor at completion
merge(Shape) - Method in class org.jmol.shape.Shape
 
merge(Shape) - Method in class org.jmol.shapesurface.Isosurface
 
merge(MeshData) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
merge(Shape) - Method in class org.jmol.shapesurface.LcaoCartoon
 
merge(Shape) - Method in class org.jmol.shapesurface.MolecularOrbital
 
mergeAssociatedNormalCount - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
mergeAtomArrays(AtomCollection) - Method in class org.jmol.modelset.AtomCollection
 
mergeBufferPixel(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
 
mergeGroups - Variable in class org.jmol.modelset.ModelLoader
 
mergeGroups() - Method in class org.jmol.modelset.ModelLoader
 
mergeLimits(Point3i, Point3i, Point3i, Point3i) - Static method in class org.jmol.jvxl.readers.IsoSolventReader
 
mergeMesh(MeshData) - Method in class org.jmol.shapesurface.Contact
 
mergeModelArrays(ModelSet) - Method in class org.jmol.modelset.ModelCollection
initial transfer of model data from old to new model set.
mergeModels(ModelSet) - Method in class org.jmol.modelset.ModelCollection
 
mergeModelSet - Variable in class org.jmol.modelset.ModelLoader
 
mergeOpaqueAndTranslucentBuffers() - Method in class org.jmol.g3d.Graphics3D
 
mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
 
mergePolygons(MeshSurface, int, int, int[][]) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
mergeResults(List<ShapeManager>) - Method in class org.jmol.script.ParallelProcessor
 
mergeSets(int, int) - Method in class org.jmol.jvxl.data.MeshData
 
mergeShapes(Shape[]) - Method in class org.jmol.viewer.ShapeManager
 
mergeShapes(Shape[]) - Method in class org.jmol.viewer.Viewer
 
mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
 
merging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
merging - Variable in class org.jmol.modelset.ModelLoader
 
mesh - Static variable in class org.jmol.script.Token
 
Mesh - Class in org.jmol.shape
 
Mesh(String, JmolRendererInterface, short, int) - Constructor for class org.jmol.shape.Mesh
 
mesh - Variable in class org.jmol.shape.MeshRenderer
 
meshColix - Variable in class org.jmol.shape.Mesh
 
meshColix - Variable in class org.jmol.shapesurface.Isosurface
 
MeshCollection - Class in org.jmol.shape
 
MeshCollection() - Constructor for class org.jmol.shape.MeshCollection
 
meshColor - Variable in class org.jmol.jvxl.data.JvxlData
 
meshColor - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
meshCount - Variable in class org.jmol.shape.MeshCollection
 
MeshData - Class in org.jmol.export
Class to generate mesh data (faces, vertices, and normals) for several kinds of generic meshes.
MeshData() - Constructor for class org.jmol.export.MeshData
 
MeshData - Class in org.jmol.jvxl.data
 
MeshData() - Constructor for class org.jmol.jvxl.data.MeshData
 
meshData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
meshData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MeshData.Data - Class in org.jmol.export
This internal class is a container for the return values of the getXxxData methods.
MeshData.Data() - Constructor for class org.jmol.export.MeshData.Data
 
MeshData.SortSet - Class in org.jmol.jvxl.data
 
MeshData.SortSet() - Constructor for class org.jmol.jvxl.data.MeshData.SortSet
 
MeshData.SSet - Class in org.jmol.jvxl.data
 
MeshData.SSet(BitSet) - Constructor for class org.jmol.jvxl.data.MeshData.SSet
 
MeshDataServer - Interface in org.jmol.jvxl.api
 
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
meshes - Variable in class org.jmol.shape.MeshCollection
 
meshes - Variable in class org.jmol.shapebio.BioShape
 
meshes - Variable in class org.jmol.shapebio.BioShapeRenderer
 
meshOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
meshReady - Variable in class org.jmol.shapebio.BioShape
 
meshReady - Variable in class org.jmol.shapebio.BioShapeRenderer
 
MeshRenderer - Class in org.jmol.shape
 
MeshRenderer() - Constructor for class org.jmol.shape.MeshRenderer
 
meshRibbon - Static variable in class org.jmol.script.Token
 
MeshRibbon - Class in org.jmol.shapebio
 
MeshRibbon() - Constructor for class org.jmol.shapebio.MeshRibbon
 
MeshRibbonRenderer - Class in org.jmol.shapebio
 
MeshRibbonRenderer() - Constructor for class org.jmol.shapebio.MeshRibbonRenderer
 
MeshSurface - Class in org.jmol.util
 
MeshSurface() - Constructor for class org.jmol.util.MeshSurface
 
MeshSurface(int[][], Tuple3f[], int, Tuple3f[], int) - Constructor for class org.jmol.util.MeshSurface
 
MeshSurface(Point3f[], float[], int, int[][], int, int) - Constructor for class org.jmol.util.MeshSurface
 
meshTranslucency - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
meshType - Variable in class org.jmol.util.MeshSurface
 
message() - Method in class org.jmol.script.ScriptEvaluator
 
message - Variable in exception org.jmol.script.ScriptEvaluator.ScriptException
 
message - Static variable in class org.jmol.script.Token
 
messageQueue - Variable in class org.jmol.viewer.StatusManager
 
messagestylechime - Static variable in class org.jmol.script.Token
 
messageStyleChime - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
META_MASK - Static variable in class org.jmol.api.Event
 
meth - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
methBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
METHOD_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mf - Variable in class org.jmol.util.JmolMolecule
 
middle - Static variable in class org.jmol.script.Token
 
MIDDLE - Static variable in class org.jmol.viewer.binding.Binding
 
middle - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
mil - Variable in class org.jmol.popup.SimplePopup
 
min - Static variable in class org.jmol.script.Token
 
min - Variable in class org.jmol.smiles.SmilesMeasure
 
MIN_AXIS_LEN - Static variable in class org.jmol.shape.Axes
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
MIN_CONE_HEIGHT - Static variable in class org.jmol.shapebio.RocketsRenderer
 
MIN_MESH_RENDER_SIZE - Static variable in class org.jmol.shapebio.BioShapeRenderer
 
min_squarable_double - Static variable in class org.jmol.minimize.Util
 
MinAtom - Class in org.jmol.minimize
 
MinAtom(int, Atom, double[], String) - Constructor for class org.jmol.minimize.MinAtom
 
minAtoms - Variable in class org.jmol.minimize.Minimizer
 
MinBond - Class in org.jmol.minimize
 
MinBond(int[], boolean, boolean) - Constructor for class org.jmol.minimize.MinBond
 
minbonddistance - Static variable in class org.jmol.script.Token
 
minBondDistance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minBondDistance - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
minBonds - Variable in class org.jmol.minimize.Minimizer
 
minBytesStandardStream - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
minColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
 
minData - Variable in class org.jmol.shapesurface.Contact
 
minDist(Point3f, Point3f[]) - Static method in class org.jmol.util.MeshSurface
 
minDistanceForPlanarity - Static variable in class org.jmol.shapespecial.Polyhedra
 
minGrid - Variable in class org.jmol.jvxl.data.VolumeData
 
miniLogArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
MINIMIZATION_ATOM_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
minimizationcriterion - Static variable in class org.jmol.script.Token
 
minimizationCriterion - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minimizationOn - Variable in class org.jmol.minimize.Minimizer
 
minimizationrefresh - Static variable in class org.jmol.script.Token
 
minimizationRefresh - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minimizationsilent - Static variable in class org.jmol.script.Token
 
minimizationSilent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minimizationsteps - Static variable in class org.jmol.script.Token
 
minimizationSteps - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minimizationThread - Variable in class org.jmol.minimize.Minimizer
 
minimize(int, double, BitSet, BitSet, boolean, boolean) - Method in interface org.jmol.api.MinimizerInterface
 
minimize(int, double, BitSet, BitSet, boolean, boolean) - Method in class org.jmol.minimize.Minimizer
 
minimize() - Method in class org.jmol.script.ScriptEvaluator
 
minimize - Static variable in class org.jmol.script.Token
 
minimize(boolean) - Method in class org.jmol.viewer.ActionManager
 
minimize(int, float, BitSet, BitSet, float, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JmolConstants
 
minimizer - Variable in class org.jmol.minimize.forcefield.ForceField
 
Minimizer - Class in org.jmol.minimize
 
Minimizer() - Constructor for class org.jmol.minimize.Minimizer
 
minimizer - Variable in class org.jmol.viewer.Viewer
 
Minimizer.MinimizationThread - Class in org.jmol.minimize
 
Minimizer.MinimizationThread() - Constructor for class org.jmol.minimize.Minimizer.MinimizationThread
 
MinimizerInterface - Interface in org.jmol.api
 
minimizeWithoutThread() - Method in class org.jmol.minimize.Minimizer
 
MINIMUM_ELAPSED_SECONDS - Static variable in class org.jmol.applet.AppletWrapper
 
minimumHbondDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
MININUM_GESTURE_DELAY_MILLISECONDS - Static variable in class org.jmol.viewer.ActionManager
 
minLeft - Variable in class org.jmol.bspt.Node
 
minMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
minMax - Variable in class org.jmol.viewer.ShapeManager
 
minmaxmask - Static variable in class org.jmol.script.Token
 
minpixelselradius - Static variable in class org.jmol.script.Token
 
minPixelSelRadius - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minRight - Variable in class org.jmol.bspt.Node
 
minScreenDimension - Variable in class org.jmol.export.__RayTracerExporter
 
minSet - Variable in class org.jmol.jvxl.readers.Parameters
 
minset - Static variable in class org.jmol.script.Token
 
minSyncRepeatMs - Variable in class org.jmol.viewer.StatusManager
 
minToPlaneDistance - Variable in class org.jmol.jvxl.data.VolumeData
 
minus - Static variable in class org.jmol.script.Token
 
minusMinus - Static variable in class org.jmol.script.Token
 
minX - Variable in class org.jmol.g3d.Sphere3D
 
minXYZ - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
minXYZ0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
minY - Variable in class org.jmol.g3d.Sphere3D
 
minZ - Variable in class org.jmol.g3d.Sphere3D
 
minZ - Variable in class org.jmol.shape.LabelsRenderer
 
misc - Static variable in class org.jmol.script.Token
 
missingHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
 
mlp - Static variable in class org.jmol.script.Token
 
MlpCalculation - Class in org.jmol.quantum
 
MlpCalculation() - Constructor for class org.jmol.quantum.MlpCalculation
 
mo(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
mo - Static variable in class org.jmol.script.Token
 
MO_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
mo_occ - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
MOCalculation - Class in org.jmol.quantum
 
MOCalculation() - Constructor for class org.jmol.quantum.MOCalculation
 
moCoeff - Variable in class org.jmol.quantum.MOCalculation
 
moCoefficients - Variable in class org.jmol.quantum.MOCalculation
 
moColorNeg - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moColorPos - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moCount - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
 
moCount - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
moCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
moCutoff - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moData - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
moData - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
moData - Variable in class org.jmol.jvxl.readers.Parameters
 
mode - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
mode - Variable in class org.jmol.jvxl.readers.MapFileReader
 
mode - Static variable in class org.jmol.script.Token
 
mode - Variable in class org.jmol.viewer.TransformManager
 
mode - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
MODE_ARRAY - Static variable in class org.jmol.smiles.SmilesMatcher
 
MODE_BITSET - Static variable in class org.jmol.smiles.SmilesMatcher
 
MODE_BITSET - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
MODE_CUBE - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_CUBE - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
MODE_FILL_COORDS - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_MOLECULES - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_MULTIMODEL - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_RADII - Static variable in class org.jmol.atomdata.AtomData
 
MODE_GET_ATTACHED_HYDROGENS - Static variable in class org.jmol.atomdata.AtomData
 
MODE_GET_COLOR_INDEXES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_GET_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_GETXYZ - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
MODE_JVXL - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_MAP - Static variable in class org.jmol.smiles.SmilesMatcher
 
MODE_NAVIGATION - Static variable in class org.jmol.viewer.TransformManager
 
MODE_PERSPECTIVE_CENTER - Static variable in class org.jmol.viewer.TransformManager
 
MODE_PLANES - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_PUT_SETS - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_PUT_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_STANDARD - Static variable in class org.jmol.viewer.TransformManager
 
moDebug - Variable in class org.jmol.shapesurface.MolecularOrbital
 
model(int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
model - Variable in class org.jmol.modelset.Chain
 
Model - Class in org.jmol.modelset
 
Model(ModelSet, int, int, String, Properties, Map<String, Object>) - Constructor for class org.jmol.modelset.Model
 
model - Variable in class org.jmol.modelset.Polymer
 
model - Static variable in class org.jmol.script.Token
 
MODEL_NO - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
modelAdapter - Variable in class org.jmol.viewer.Viewer
 
modelAdapter - Variable in class org.openscience.jmol.app.JmolApp
 
modelAdapter - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
modelbased - Static variable in class org.jmol.script.Token
 
modelCenterOffset - Variable in class org.jmol.viewer.TransformManager
 
ModelCollection - Class in org.jmol.modelset
 
ModelCollection() - Constructor for class org.jmol.modelset.ModelCollection
 
ModelCollection.StateScript - Class in org.jmol.modelset
 
ModelCollection.StateScript(int, String, BitSet, BitSet, BitSet, String, boolean) - Constructor for class org.jmol.modelset.ModelCollection.StateScript
 
modelCount - Variable in class org.jmol.modelset.ModelCollection
 
modelCount - Variable in class org.jmol.popup.SimplePopup
 
modelFilename - Variable in class org.openscience.jmol.app.JmolApp
 
modelFileNumberFromFloat(float) - Static method in class org.jmol.modelset.ModelCollection
 
modelFileNumbers - Variable in class org.jmol.modelset.ModelCollection
 
modelFlags - Variable in class org.jmol.shapespecial.DrawMesh
 
modelHasVibrationVectors(int) - Method in class org.jmol.api.JmolViewer
 
modelHasVibrationVectors(int) - Method in class org.jmol.modelset.ModelCollection
 
modelHasVibrationVectors(int) - Method in class org.jmol.viewer.Viewer
 
modelIndex - Variable in class org.jmol.adapter.smarter.Structure
 
modelIndex - Variable in class org.jmol.atomdata.AtomData
 
modelIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
modelIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
modelIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
modelIndex - Variable in class org.jmol.modelset.Model
 
modelIndex - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
modelIndex - Variable in class org.jmol.popup.SimplePopup
 
modelindex - Static variable in class org.jmol.script.Token
 
modelIndex - Variable in class org.jmol.shape.Mesh
 
modelIndex - Variable in class org.jmol.shape.MeshCollection
 
modelIndex - Variable in class org.jmol.shape.Object2d
 
modelIndex - Variable in class org.jmol.shapebio.BioShape
 
modelIndex - Variable in class org.jmol.shapespecial.Dipole
 
modelIndex - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
modelIndex - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
modelIndex - Variable in class org.jmol.util.JmolMolecule
 
modelIndex - Variable in class org.jmol.util.Point3fi
 
modelInfo - Variable in class org.jmol.popup.SimplePopup
 
modelInfo - Variable in class org.jmol.shapespecial.Draw
 
ModelKit - Class in org.jmol.modelkit
 
ModelKit() - Constructor for class org.jmol.modelkit.ModelKit
 
ModelKit(JmolViewer, JFrame) - Constructor for class org.jmol.modelkit.ModelKit
 
modelkit - Variable in class org.jmol.viewer.Viewer
 
MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JmolConstants
 
MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JmolConstants
 
modelkitMenu - Variable in class org.jmol.modelkit.ModelKit
 
modelkitmode - Static variable in class org.jmol.script.Token
 
modelKitMode - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ModelKitPopup - Class in org.jmol.modelkit
 
ModelKitPopup(JmolViewer, String, PopupResource) - Constructor for class org.jmol.modelkit.ModelKitPopup
 
ModelKitPopupResourceBundle - Class in org.jmol.modelkit
 
ModelKitPopupResourceBundle() - Constructor for class org.jmol.modelkit.ModelKitPopupResourceBundle
 
ModelLoader - Class in org.jmol.modelset
 
ModelLoader(Viewer, String) - Constructor for class org.jmol.modelset.ModelLoader
 
ModelLoader(Viewer, StringBuffer, Object, ModelSet, String, BitSet) - Constructor for class org.jmol.modelset.ModelLoader
 
modelLoader - Variable in class org.jmol.modelsetbio.Resolver
 
ModelManager - Class in org.jmol.viewer
 
ModelManager(Viewer) - Constructor for class org.jmol.viewer.ModelManager
 
modelManager - Variable in class org.jmol.viewer.Viewer
 
modelName - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
modelName - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
modelName - Variable in class org.jmol.atomdata.AtomData
 
modelNames - Variable in class org.jmol.modelset.ModelCollection
 
modelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
modelNumberParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
modelNumbers - Variable in class org.jmol.modelset.ModelCollection
 
modelNumbersForAtomLabel - Variable in class org.jmol.modelset.ModelCollection
 
modelRadius - Variable in class org.jmol.viewer.TransformManager
 
modelRadiusPixels - Variable in class org.jmol.viewer.TransformManager
 
modelRead - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
models - Variable in class org.jmol.export._IdtfExporter
 
models - Variable in class org.jmol.modelset.ModelCollection
 
modelSet - Variable in class org.jmol.modelset.Chain
 
modelSet - Variable in class org.jmol.modelset.Measurement
 
modelSet - Variable in class org.jmol.modelset.Model
 
modelSet - Variable in class org.jmol.modelset.ModelLoader
 
ModelSet - Class in org.jmol.modelset
 
ModelSet(Viewer, String) - Constructor for class org.jmol.modelset.ModelSet
 
modelSet - Variable in class org.jmol.modelsetbio.Resolver
 
modelSet - Variable in class org.jmol.shape.Shape
 
modelSet - Variable in class org.jmol.shape.ShapeRenderer
 
modelSet - Variable in class org.jmol.viewer.ModelManager
 
modelSet - Variable in class org.jmol.viewer.ShapeManager
 
modelSet - Variable in class org.jmol.viewer.Viewer
 
modelSetAuxiliaryInfo - Variable in class org.jmol.modelset.ModelCollection
 
modelSetFileName - Variable in class org.jmol.popup.SimplePopup
 
modelSetHasVibrationVectors() - Method in class org.jmol.modelset.AtomCollection
 
modelSetHasVibrationVectors() - Method in class org.jmol.viewer.Viewer
 
modelSetInfo - Variable in class org.jmol.popup.SimplePopup
 
modelSetName - Variable in class org.jmol.modelset.ModelCollection
 
modelSetName - Variable in class org.jmol.popup.SimplePopup
 
modelSetProperties - Variable in class org.jmol.modelset.ModelCollection
 
modelSetRoot - Variable in class org.jmol.popup.SimplePopup
 
modelSetTypeName - Variable in class org.jmol.modelset.ModelSet
 
modelsOf(BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
 
modelVisibilityFlags - Variable in class org.jmol.shapebio.BioShape
 
modelZeroBased - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
modeMultipleBond - Variable in class org.jmol.shape.SticksRenderer
 
modeMultipleBond - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
modifiers - Variable in class org.jmol.export._IdtfExporter
 
modifiers - Variable in class org.jmol.viewer.ActionManager.Mouse
 
modifiersWhenPressed10 - Variable in class org.jmol.awt.Mouse
 
modify - Static variable in class org.jmol.script.Token
 
modifyorcreate - Static variable in class org.jmol.script.Token
 
moDots - Variable in class org.jmol.shapesurface.MolecularOrbital
 
MODULE - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
moduleNestingLevel - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
moFactor - Variable in class org.jmol.quantum.MOCalculation
 
moFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
moFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
moFill - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moFrontOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moInfo - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
moIsPositiveOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
 
Mol2Reader - Class in org.jmol.adapter.readers.more
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
Mol2Reader() - Constructor for class org.jmol.adapter.readers.more.Mol2Reader
 
mol2Records - Static variable in class org.jmol.adapter.smarter.Resolver
 
Mol3DReader - Class in org.jmol.adapter.readers.molxyz
3D only
Mol3DReader() - Constructor for class org.jmol.adapter.readers.molxyz.Mol3DReader
 
moldenFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MoldenReader - Class in org.jmol.adapter.readers.quantum
A molecular structure and orbital reader for MolDen files.
MoldenReader() - Constructor for class org.jmol.adapter.readers.quantum.MoldenReader
 
MolecdeleteButton - Variable in class org.openscience.jmol.app.webexport.Molecules
 
MolecList - Variable in class org.openscience.jmol.app.webexport.Molecules
 
MolecopenButton - Variable in class org.openscience.jmol.app.webexport.Molecules
 
molectohtml(int, int, File, JList, String) - Method in class org.openscience.jmol.app.webexport.Molecules
 
molecular - Static variable in class org.jmol.script.Token
 
MolecularOrbital - Class in org.jmol.shapesurface
 
MolecularOrbital() - Constructor for class org.jmol.shapesurface.MolecularOrbital
 
MolecularOrbitalRenderer - Class in org.jmol.shapesurface
 
MolecularOrbitalRenderer() - Constructor for class org.jmol.shapesurface.MolecularOrbitalRenderer
 
molecularType - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
MOLECULE - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
molecule - Static variable in class org.jmol.script.Token
 
MOLECULE_ATOM - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_ARRAY - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_BUILTIN - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_SCALAR - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_ARRAY - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_BUILTIN - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_FORMULA - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
moleculeCount - Variable in class org.jmol.modelset.BondCollection
 
moleculeCount - Variable in class org.jmol.modelset.Model
 
moleculeIndex - Variable in class org.jmol.util.JmolMolecule
 
moleculeNesting - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
molecules - Variable in class org.jmol.modelset.BondCollection
 
Molecules - Class in org.openscience.jmol.app.webexport
 
Molecules() - Constructor for class org.openscience.jmol.app.webexport.Molecules
 
moleculeXml - Variable in class org.jmol.jvxl.data.JvxlData
 
moLinearCombination - Variable in class org.jmol.shapesurface.Isosurface
 
moLinearCombination - Variable in class org.jmol.shapesurface.MolecularOrbital
 
molProImplementedAttributes - Static variable in class org.jmol.adapter.readers.xml.XmlMolproReader
 
MolReader - Class in org.jmol.adapter.readers.molxyz
A reader for MDLI mol and sdf files.
MolReader() - Constructor for class org.jmol.adapter.readers.molxyz.MolReader
 
moMesh - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moMonteCarloCount - Variable in class org.jmol.shapesurface.MolecularOrbital
 
monitorenergy - Static variable in class org.jmol.script.Token
 
monitorEnergy - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
MonitorInputStream - Class in org.openscience.jvxl
 
MonitorInputStream(InputStream, int) - Constructor for class org.openscience.jvxl.MonitorInputStream
 
Monomer - Class in org.jmol.modelsetbio
 
Monomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.Monomer
 
monomer - Static variable in class org.jmol.script.Token
 
monomerCount - Variable in class org.jmol.modelset.Polymer
 
monomerCount - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomerCount - Variable in class org.jmol.shapebio.BioShape
 
monomerCount - Variable in class org.jmol.shapebio.BioShapeRenderer
 
monomerIndex - Variable in class org.jmol.modelsetbio.Monomer
 
monomerIndexFirst - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomerIndexLast - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomers - Variable in class org.jmol.modelsetbio.BioPolymer
 
monomers - Variable in class org.jmol.shapebio.BioShape
 
monomers - Variable in class org.jmol.shapebio.BioShapeRenderer
 
monteCarloCount - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
monteCarloDone - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
moNumber - Variable in class org.jmol.shapesurface.Isosurface
 
moNumber - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moOffset(int) - Method in class org.jmol.script.ScriptEvaluator
 
mopacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MopacGraphfReader - Class in org.jmol.adapter.readers.quantum
Reads Mopac 2007 GRAPHF output files
MopacGraphfReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
MopacReader - Class in org.jmol.adapter.readers.simple
Reads Mopac 93, 6, 7, 2002, or 2009 output files
MopacReader() - Constructor for class org.jmol.adapter.readers.simple.MopacReader
 
MopacSlaterReader - Class in org.jmol.adapter.readers.quantum
 
MopacSlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
mopacVersion - Variable in class org.jmol.adapter.readers.simple.MopacReader
 
moPlane - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moRandomSeed - Variable in class org.jmol.shapesurface.MolecularOrbital
 
MOReader - Class in org.jmol.adapter.readers.quantum
General methods for reading molecular orbital data, including embedded output from the NBO program.
MOReader() - Constructor for class org.jmol.adapter.readers.quantum.MOReader
 
moResolution - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moreTokens() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
mos - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
mos - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
mosaicPreviewChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Called when the MosaicPreview check box is modified
mosaicPreviewCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
mosaicPreviewComboEnd - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
mosaicPreviewComboStart - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
mosaicPreviewEnd - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
mosaicPreviewStart - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
moScale - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moSlab - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moSlabValue - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moSymmetry - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
motion - Variable in class org.jmol.viewer.TransformManager
 
motionEventNumber - Variable in class org.jmol.viewer.Viewer
 
moTitleFormat - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moTranslucency - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moTranslucentLevel - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moType - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
moTypes - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
Mouse - Class in org.jmol.awt
formerly org.jmol.viewer.MouseManager14 methods required by Jmol that access java.awt.event private to org.jmol.awt
Mouse(Viewer, ActionManager) - Constructor for class org.jmol.awt.Mouse
 
mouse - Variable in class org.jmol.awt.Platform
 
MOUSE_NONE - Static variable in class org.jmol.viewer.JmolConstants
 
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.multitouch.ActionManagerMT
 
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.viewer.ActionManager
 
mouseClicked(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseClicked(long, int, int, int, int) - Method in class org.jmol.awt.Mouse
 
mouseDown - Variable in class org.jmol.multitouch.ActionManagerMT
 
mousedragfactor - Static variable in class org.jmol.script.Token
 
mouseDragFactor - Variable in class org.jmol.viewer.ActionManager
 
mouseDragged(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mouseDragged(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseDragged(long, int, int, int) - Method in class org.jmol.awt.Mouse
 
mouseEnabled - Variable in class org.jmol.viewer.Viewer
 
mouseEntered(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseEntered(long, int, int) - Method in class org.jmol.awt.Mouse
 
mouseEntered(long, int, int) - Method in class org.jmol.viewer.ActionManager
 
mouseExited(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseExited(long, int, int) - Method in class org.jmol.awt.Mouse
 
mouseExited(long, int, int) - Method in class org.jmol.viewer.ActionManager
 
mouseMoved(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseMoved(long, int, int, int) - Method in class org.jmol.awt.Mouse
 
mouseMoved(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
mouseMoved(int, int) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
mousePressed(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mousePressed(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mousePressed(long, int, int, int, boolean) - Method in class org.jmol.awt.Mouse
 
mouseReleased(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mouseReleased(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseReleased(long, int, int, int) - Method in class org.jmol.awt.Mouse
 
mouseWheel(long, int, int) - Method in class org.jmol.awt.Mouse
 
mousewheelfactor - Static variable in class org.jmol.script.Token
 
mouseWheelFactor - Variable in class org.jmol.viewer.ActionManager
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awt.Mouse
 
movableX - Variable in class org.jmol.shape.Object2d
 
movableXPercent - Variable in class org.jmol.shape.Object2d
 
movableY - Variable in class org.jmol.shape.Object2d
 
movableYPercent - Variable in class org.jmol.shape.Object2d
 
movableZ - Variable in class org.jmol.shape.Object2d
 
movableZPercent - Variable in class org.jmol.shape.Object2d
 
MOVE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
move() - Method in class org.jmol.script.ScriptEvaluator
 
move - Static variable in class org.jmol.script.Token
 
move(Vector3f, float, Vector3f, float, float, int) - Method in class org.jmol.viewer.TransformManager
 
move(Vector3f, float, Vector3f, float, float, int) - Method in class org.jmol.viewer.Viewer
 
move2D(int, int, int) - Method in class org.jmol.shape.Labels
 
move2D(DrawMesh, int[], int, int, int, boolean) - Method in class org.jmol.shapespecial.Draw
 
moveAtoms(Matrix3f, Matrix3f, Vector3f, BitSet, Point3f, boolean) - Method in class org.jmol.modelset.ModelSet
 
moveAtoms(Matrix3f, Matrix3f, Vector3f, Point3f, boolean, BitSet) - Method in class org.jmol.viewer.Viewer
 
moveAtomWithHydrogens(int, int, int, int, BitSet) - Method in class org.jmol.viewer.Viewer
 
moved - Variable in class org.jmol.viewer.ActionManager
 
MOVED - Static variable in class org.jmol.viewer.binding.Binding
 
movepict(String) - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
moveRotationCenter(Point3f, boolean) - Method in class org.jmol.viewer.TransformManager
 
moveSelected(int, int, int, int, int, BitSet, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
moveto() - Method in class org.jmol.script.ScriptEvaluator
 
moveto - Static variable in class org.jmol.script.Token
 
moveTo(float, Point3f, Tuple3f, float, Matrix3f, float, float, float, float, Point3f, float, float, float) - Method in class org.jmol.viewer.TransformManager
 
moveTo(float, Point3f, Vector3f, float, Matrix3f, float, float, float, float, Point3f, float, float, float) - Method in class org.jmol.viewer.Viewer
 
moveToText - Variable in class org.jmol.viewer.StateManager.Orientation
 
movetoTime - Variable in class org.openscience.jmol.app.webexport.Test
 
moveUpdate(float) - Method in class org.jmol.viewer.Viewer
 
movingSelected - Variable in class org.jmol.viewer.Viewer
 
MPJmolApp - Class in org.openscience.molecularplayground
 
MPJmolApp(int) - Constructor for class org.openscience.molecularplayground.MPJmolApp
 
MPJmolApp.KioskPanel - Class in org.openscience.molecularplayground
 
MPJmolApp.KioskPanel() - Constructor for class org.openscience.molecularplayground.MPJmolApp.KioskPanel
 
mrc - Static variable in class org.jmol.script.Token
 
MrcBinaryReader - Class in org.jmol.jvxl.readers
 
MrcBinaryReader(SurfaceGenerator, String) - Constructor for class org.jmol.jvxl.readers.MrcBinaryReader
 
ms - Variable in class org.jmol.viewer.ActionManager.TimeoutThread
 
MSAT0 - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
msms - Static variable in class org.jmol.script.Token
 
MsmsReader - Class in org.jmol.jvxl.readers
 
MsmsReader(SurfaceGenerator, String, BufferedReader) - Constructor for class org.jmol.jvxl.readers.MsmsReader
 
mTemp - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
mtlbw - Variable in class org.jmol.export._ObjExporter
BufferedWriter for the .mtl file.
mtlFile - Variable in class org.jmol.export._ObjExporter
File for the .mtl file.
mtlos - Variable in class org.jmol.export._ObjExporter
FileOutputStream for the .mtl file.
mu - Variable in class org.jmol.modelset.Group
 
mul - Static variable in class org.jmol.script.Token
 
mul(float) - Method in class org.jmol.util.Quaternion
 
mul(Quaternion) - Method in class org.jmol.util.Quaternion
 
mult - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
MULTI_POINT_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JmolConstants
 
MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JmolConstants
 
MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JmolConstants
 
MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JmolConstants
 
multiModel - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
multiplebondradiusfactor - Static variable in class org.jmol.script.Token
 
multipleBondRadiusFactor - Variable in class org.jmol.shape.SticksRenderer
 
multipleBondRadiusFactor - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
multiplebondspacing - Static variable in class org.jmol.script.Token
 
multipleBondSpacing - Variable in class org.jmol.shape.SticksRenderer
 
multipleBondSpacing - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
multiplier - Variable in class org.jmol.viewer.TransformManager11
 
multiprocessor - Static variable in class org.jmol.script.Token
 
multiProcessor - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
multiTouch - Variable in class org.jmol.viewer.Viewer
 
multSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mustBeConnected - Variable in class org.jmol.modelset.MeasurementData
 
mustBeConnected - Variable in class org.jmol.shape.Measures
 
mustNotBeConnected - Variable in class org.jmol.modelset.MeasurementData
 
mustNotBeConnected - Variable in class org.jmol.shape.Measures
 
mustRender - Variable in class org.jmol.viewer.Viewer
 
mustRenderFlag() - Method in class org.jmol.viewer.Viewer
 
myAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
myAtoms - Variable in class org.jmol.util.ContactPair
 
myBsA - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
myBsB - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
myColorPt - Variable in class org.jmol.shapesurface.LcaoCartoon
 
myColorPt - Variable in class org.jmol.shapesurface.MolecularOrbital
 
myDir - Variable in class org.openscience.chimetojmol.ChimePanel
 
myDistanceFactor - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
myFaceCenterOffset - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
myIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
myMask - Variable in class org.jmol.shape.Sticks
 
myName - Variable in class org.jmol.script.ScriptVariable
 
myName - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
myStatusListener - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
myType - Variable in class org.jmol.shape.FontShape
 
myType - Variable in class org.jmol.shape.MeshCollection
 
myVisibilityFlag - Static variable in class org.jmol.modelset.Bond
 
myVisibilityFlag - Variable in class org.jmol.shape.Shape
 
myVisibilityFlag - Variable in class org.jmol.shape.ShapeRenderer
 
myX - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
myX2 - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
myY - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
myY2 - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
myZ - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
myZ2 - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 

N

n - Variable in class org.jmol.jvxl.data.MeshData.SSet
 
N - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
N - Static variable in class org.jmol.util.DCT
DCT Block Size - default 8
n - Variable in class org.jmol.util.Eigen
Row and column dimension (square matrix).
N1 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N3 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N7 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N9 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
n_bits - Variable in class org.jmol.export.image.GifEncoder
 
na - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nada - Static variable in class org.jmol.script.Token
 
nAdditionalMATsectors - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
nAltLocs - Variable in class org.jmol.modelset.Model
 
name - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
name - Variable in enum org.jmol.constant.EnumAnimationMode
 
name - Variable in enum org.jmol.constant.EnumCallback
 
name - Variable in enum org.jmol.constant.EnumPalette
 
name - Variable in enum org.jmol.constant.EnumStereoMode
 
name - Variable in enum org.jmol.constant.EnumStructure
 
name - Variable in class org.jmol.export._MayaExporter
 
name - Variable in class org.jmol.script.ScriptFunction
 
name - Static variable in class org.jmol.script.Token
 
name - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
 
name - Variable in class org.jmol.symmetry.PointGroup
 
name - Variable in enum org.jmol.util.JmolEdge.EnumBondOrder
 
name - Variable in class org.jmol.viewer.ActionManager.TimeoutThread
 
name - Variable in class org.jmol.viewer.binding.Binding
 
name - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
name - Variable in class org.openscience.jmol.app.webexport.Widgets.Widget
 
name0 - Variable in class org.jmol.script.ContextToken
 
NAME_HALL - Static variable in class org.jmol.symmetry.SpaceGroup
 
NAME_HM - Static variable in class org.jmol.symmetry.SpaceGroup
 
nameAsGiven - Variable in class org.jmol.viewer.FileManager
 
nameAsGivenIn - Variable in class org.jmol.viewer.FileManager.FileReader
 
nameList - Static variable in enum org.jmol.constant.EnumCallback
 
nameOf(int) - Static method in class org.jmol.script.Token
note: nameOf is a very inefficient mechanism for getting the name of a token.
names - Variable in class org.jmol.script.ScriptFunction
 
namesAsGivenIn - Variable in class org.jmol.viewer.FileManager.FilesReader
 
naNoH - Static variable in class org.jmol.viewer.JmolConstants
 
nativeLanguage - Variable in class org.jmol.i18n.GT.Language
 
nAtoms - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
nAtoms - Variable in class org.jmol.adapter.readers.more.MdTopReader
 
nAtoms - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
nAtoms - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nAtoms - Variable in class org.jmol.symmetry.PointGroup
 
nAtomsOr - Variable in class org.jmol.smiles.SmilesAtom
 
naturalIsotopeMasses - Static variable in class org.jmol.util.Elements
 
naturalIsotopes - Static variable in class org.jmol.util.Elements
 
NAV_MODE_IGNORE - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_NEWXY - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_NEWXYZ - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_NEWZ - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_NONE - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_RESET - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_ZOOMED - Static variable in class org.jmol.viewer.TransformManager11
 
navCenter - Variable in class org.jmol.viewer.StateManager.Orientation
 
navCenter - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
navDepth - Variable in class org.jmol.viewer.StateManager.Orientation
 
navDepth - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
navDepthDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
navDepthStart - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
navfps - Static variable in class org.jmol.script.Token
 
navFps - Variable in class org.jmol.viewer.TransformManager
 
navigate() - Method in class org.jmol.script.ScriptEvaluator
 
navigate - Static variable in class org.jmol.script.Token
 
navigate(int) - Method in class org.jmol.shapesurface.Isosurface
 
navigate(int, int) - Method in class org.jmol.viewer.TransformManager
entry point for keyboard-based navigation
navigate(float, Point3f) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navigate(float, Vector3f, float) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navigate(float, Point3f[], float[], int, int) - Method in class org.jmol.viewer.TransformManager
scripted navigation
navigate(float, Point3f[][]) - Method in class org.jmol.viewer.TransformManager
follows a path guided by orientation and offset vectors (as Point3fs)
navigate(int, int) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Point3f) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Vector3f, float) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Point3f[][]) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Point3f[], float[], int, int) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Point3f[][], Point3f[], float[], int, int) - Method in class org.jmol.viewer.TransformManager11
 
navigate(int, int) - Method in class org.jmol.viewer.Viewer
 
navigate(float, Point3f[], float[], int, int) - Method in class org.jmol.viewer.Viewer
 
navigate(float, Point3f) - Method in class org.jmol.viewer.Viewer
 
navigate(float, Point3f[][]) - Method in class org.jmol.viewer.Viewer
 
navigate(float, Vector3f, float) - Method in class org.jmol.viewer.Viewer
 
navigatesurface - Static variable in class org.jmol.script.Token
 
navigateSurface - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
navigateSurface - Variable in class org.jmol.viewer.StateManager.Orientation
 
navigateSurface(float, String) - Method in class org.jmol.viewer.TransformManager
 
navigateSurface(int) - Method in class org.jmol.viewer.TransformManager11
 
navigateSurface(float, String) - Method in class org.jmol.viewer.TransformManager11
 
navigateSurface(float, String) - Method in class org.jmol.viewer.Viewer
 
navigateTo(float, Vector3f, float, Point3f, float, float, float) - Method in class org.jmol.viewer.TransformManager11
 
navigating - Variable in class org.jmol.viewer.TransformManager
 
navigationCenter - Variable in class org.jmol.viewer.TransformManager
 
navigationdepth - Static variable in class org.jmol.script.Token
 
navigationDepth - Variable in class org.jmol.viewer.TransformManager11
 
navigationmode - Static variable in class org.jmol.script.Token
 
navigationMode - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
navigationMode - Variable in class org.jmol.viewer.StateManager.Orientation
 
navigationOffset - Variable in class org.jmol.viewer.TransformManager
 
navigationperiodic - Static variable in class org.jmol.script.Token
 
navigationPeriodic - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
navigationShiftXY - Variable in class org.jmol.viewer.TransformManager
 
navigationslab - Static variable in class org.jmol.script.Token
 
navigationSlabOffset - Variable in class org.jmol.viewer.TransformManager11
 
navigationspeed - Static variable in class org.jmol.script.Token
 
navigationSpeed - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
navMode - Variable in class org.jmol.viewer.TransformManager11
 
navOn - Variable in class org.jmol.viewer.TransformManager
 
navTranslate(float, Point3f) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navTranslate(float, Point3f) - Method in class org.jmol.viewer.TransformManager11
 
navTranslate(float, Point3f) - Method in class org.jmol.viewer.Viewer
 
navTranslatePercent(float, float, float) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navTranslatePercent(float, float, float) - Method in class org.jmol.viewer.TransformManager11
 
navTranslatePercent(float, float, float) - Method in class org.jmol.viewer.Viewer
 
navx - Static variable in class org.jmol.script.Token
 
navX - Variable in class org.jmol.viewer.TransformManager
 
NAVY - Static variable in class org.jmol.g3d.Graphics3D
 
navy - Static variable in class org.jmol.script.Token
 
navY - Variable in class org.jmol.viewer.TransformManager
 
navz - Static variable in class org.jmol.script.Token
 
navZ - Variable in class org.jmol.viewer.TransformManager
 
nAxes - Variable in class org.jmol.symmetry.PointGroup
 
nb - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nBackbonesDisplayed - Variable in class org.jmol.modelset.Atom
 
nBalls - Variable in class org.jmol.export._MayaExporter
 
nBasis - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
nBasisFunctions - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
nBF - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
nBits - Variable in class org.jmol.g3d.Line3D
 
nbitsets - Variable in class org.jmol.shapespecial.Draw
 
nBlock - Variable in class org.jmol.jvxl.readers.XplorReader
 
nBonds - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nBonds - Variable in class org.jmol.minimize.MinAtom
 
nBondsDisplayed - Variable in class org.jmol.modelset.Atom
 
nBondsOr - Variable in class org.jmol.smiles.SmilesBond
 
nBrickX - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
nBrickY - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
nBytes - Variable in class org.jmol.export.___Exporter
 
nBytes - Variable in class org.jmol.jvxl.data.JvxlData
 
nBytes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nBytes - Variable in class org.jmol.util.BinaryDocument
 
nBytes - Variable in class org.jmol.util.OutputStringBuffer
 
nBytes - Variable in class org.jmol.util.ZipUtil.GZipData
 
nBytesUnicodeName - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
nc - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nCached - Variable in class org.jmol.g3d.Line3D
 
nCharNewLine(int) - Method in class org.jmol.script.ScriptCompiler
 
nci - Static variable in class org.jmol.script.Token
 
NciCalculation - Class in org.jmol.quantum
 
NciCalculation() - Constructor for class org.jmol.quantum.NciCalculation
 
nCoefficients - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
nContourMax - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
nContourMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
nContours - Variable in class org.jmol.jvxl.data.JvxlData
 
nContours - Variable in class org.jmol.jvxl.readers.Parameters
 
nContourSegments - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
nCyl - Variable in class org.jmol.export._MayaExporter
 
nData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nDataPoints - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nDegrees - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
nDir - Variable in class org.openscience.chimetojmol.ChimePanel
 
nDirEntriesperSector - Variable in class org.jmol.util.CompoundDocument
 
nDots - Variable in class org.jmol.jvxl.readers.KinemageReader
 
ne - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
nearbyAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
nEdges - Variable in class org.jmol.jvxl.data.JvxlData
 
needAromatic - Variable in class org.jmol.smiles.SmilesSearch
 
needEllipsoids - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
needRightParen - Variable in class org.jmol.script.ScriptCompiler
 
needRingData - Variable in class org.jmol.smiles.SmilesSearch
 
needRingMemberships - Variable in class org.jmol.smiles.SmilesSearch
 
needToCompleteInitialization - Variable in class org.jmol.applet.AppletWrapper
 
needToFill - Variable in class org.jmol.g3d.Hermite3D
 
negate() - Method in class org.jmol.util.Quaternion
 
negativeAtomCount - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
negCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
neighborCenters - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborIndices - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborPlusProbeRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborVertexesArrays - Static variable in class org.jmol.g3d.Normix3D
 
neighborVertexesArrays - Static variable in class org.jmol.geodesic.Geodesic
 
neighborVertexesIcosahedron - Static variable in class org.jmol.geodesic.Geodesic
 
nElements - Variable in class org.jmol.util.JmolMolecule
 
nError - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
nestedBond - Variable in class org.jmol.smiles.SmilesSearch
 
newAction(int, String, String) - Static method in class org.jmol.viewer.ActionManager
 
newAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
newAntialiasing - Variable in class org.jmol.g3d.Graphics3D
 
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
newAtomSet(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
newAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newAtomSet(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
newBitSet(int, int) - Static method in class org.jmol.util.BitSetUtil
 
newBufferedImage(Object, int, int) - Method in interface org.jmol.api.ApiPlatform
 
newBufferedImage(Object, int, int) - Static method in class org.jmol.awt.Image
 
newBufferedImage(int, int) - Static method in class org.jmol.awt.Image
 
newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
 
newBufferedRgbImage(int, int) - Method in interface org.jmol.api.ApiPlatform
 
newBufferedRgbImage(int, int) - Method in class org.jmol.awt.Platform
 
newCloneAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newFont(String, boolean, boolean, float) - Method in interface org.jmol.api.ApiPlatform
 
newFont(String, boolean, boolean, float) - Static method in class org.jmol.awt.Font
 
newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
 
newJButton(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJCheckBox(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJCheckBoxMenuItem(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJRadioButtonMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newline - Static variable in class org.openscience.jmol.app.webexport.Orbitals
 
newMean(Quaternion[], Quaternion) - Static method in class org.jmol.util.Quaternion
 
newMenu(String, String) - Method in class org.jmol.popup.SimplePopup
 
newNavigationCenter() - Method in class org.jmol.viewer.TransformManager11
We do not want the fixed navigation offset to change, but we need a new model-based equivalent position.
newPoint(int, Point3f, Point3f, int, int, int) - Method in class org.jmol.symmetry.SpaceGroup
 
newPoint(Point3f, Point3f, int, int, int) - Method in class org.jmol.symmetry.SymmetryOperation
 
newRockets - Variable in class org.jmol.shapebio.CartoonRenderer
 
newScale - Variable in class org.jmol.shapespecial.Draw
 
newSet() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
newSg() - Method in class org.jmol.shapesurface.Isosurface
 
newSpaceGroupPoint(int, Point3f, Point3f, int, int, int) - Method in interface org.jmol.api.SymmetryInterface
 
newSpaceGroupPoint(int, Point3f, Point3f, int, int, int) - Method in class org.jmol.symmetry.Symmetry
 
newSurface(int, ContactPair, BitSet, BitSet, RadiusData, float[], Object, boolean, VolumeData) - Method in class org.jmol.shapesurface.Contact
 
newVertex(Point3f, Vector3f, float) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
newVoxelDataCube() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
newwinAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
newWindowHeight - Variable in class org.jmol.g3d.Graphics3D
 
newWindowWidth - Variable in class org.jmol.g3d.Graphics3D
 
next - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
next() - Method in interface org.jmol.api.AtomIndexIterator
 
next - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
next() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
next() - Method in interface org.jmol.modelset.BondIterator
 
next() - Method in class org.jmol.modelset.BondIteratorSelected
 
next - Static variable in class org.jmol.script.Token
 
next - Variable in class org.jmol.util.Int2IntHash.Entry
 
NEXT - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
nextChar() - Method in class org.jmol.script.ScriptCompiler
 
nextCommand - Variable in class org.jmol.util.CommandHistory
Position of the next command.
nextElement() - Method in class org.jmol.bspt.CubeIterator
normal iterator method
nextFileName(String, int) - Method in class org.jmol.console.JmolConsole
 
nextIndex() - Method in interface org.jmol.modelset.BondIterator
 
nextIndex() - Method in class org.jmol.modelset.BondIteratorSelected
 
nextMeasure(int, int, Measurement, int) - Method in class org.jmol.modelset.MeasurementData
iterator for measurements
nextRandom8Bit() - Static method in class org.jmol.g3d.Shade3D
Implements RANDU algorithm for random noise in lighting/shading.
nextSetBit(int) - Method in class org.jmol.util.FastBitSet
 
nextToken() - Method in class org.jmol.jvxl.readers.PmeshReader
 
nextToken() - Method in class org.jmol.util.CifDataReader
assume that hasMoreTokens() has been called and that ich is pointing at a non-white character.
nextVoxel() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.XplorReader
 
nf - Variable in class org.jmol.shape.UccageRenderer
 
nf - Variable in class org.jmol.shapesurface.MolecularOrbitalRenderer
 
nFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
nfformat(float) - Method in class org.jmol.shape.UccageRenderer
 
nFilePoints - Variable in class org.jmol.jvxl.readers.CastepDensityReader
 
nFiles - Variable in class org.openscience.chimetojmol.ChimePanel
 
nFiltered - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
nFound - Variable in class org.jmol.g3d.Line3D
 
nFrankList - Variable in class org.jmol.popup.JmolPopup
 
nFree - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
nGaussians - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nGaussians - Variable in class org.jmol.quantum.MOCalculation
 
nhChecked - Variable in class org.jmol.modelsetbio.AminoMonomer
 
nHits - Variable in class org.jmol.viewer.TransformManager11
 
nidentifiers - Variable in class org.jmol.shapespecial.Draw
 
nihResolverFormat - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
nImage - Variable in class org.jmol.export.___Exporter
 
nIn - Static variable in class org.jmol.g3d.Sphere3D
 
nInsertions - Variable in class org.jmol.modelset.Model
 
nIntPerSector - Variable in class org.jmol.util.CompoundDocument
 
nInvalid - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
nioClosed(JsonNioService) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
nioClosed(JsonNioService) - Method in interface org.openscience.jmol.app.jmolpanel.JsonNioClient
 
nioClosed(JsonNioService) - Method in class org.openscience.molecularplayground.MPJmolApp
 
nitrogenHydrogenPoint - Variable in class org.jmol.modelsetbio.AlphaMonomer
 
nLatticeTypes - Static variable in class org.jmol.symmetry.Translation
 
nLatticeVectors - Variable in class org.jmol.adapter.readers.xtal.AimsReader
 
nLCAO - Variable in class org.jmol.shapesurface.Isosurface
 
nMatrixElements - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
nModels - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
nModules - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
nMolecular - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
nMolecules - Variable in class org.jmol.quantum.NciCalculation
 
nMtlBytes - Variable in class org.jmol.export._ObjExporter
Bytes written to the .mtl file.
NN - Static variable in class org.jmol.util.DCT
 
nNested - Variable in class org.jmol.smiles.SmilesSearch
 
nNormals - Variable in class org.jmol.export.MeshData.Data
 
NO_ALPHA - Static variable in class org.jmol.export.image.PngEncoder
Constant specifying that alpha channel should not be encoded.
NO_ANISOTROPY - Static variable in class org.jmol.jvxl.readers.Parameters
 
NO_VALUE - Static variable in class org.jmol.quantum.NciCalculation
 
noArgs - Static variable in class org.jmol.script.Token
 
noAromatic - Variable in class org.jmol.smiles.SmilesSearch
 
noAtoms - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
 
noAutoBond - Variable in class org.jmol.modelset.ModelLoader
 
NOBASIS_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
nocontourlines - Static variable in class org.jmol.script.Token
 
nocross - Static variable in class org.jmol.script.Token
 
noCross - Variable in class org.jmol.shapespecial.Dipole
 
Node - Class in org.jmol.bspt
Nodes of the bspt.
Node(Bspt, int, Leaf) - Constructor for class org.jmol.bspt.Node
 
nodebug - Static variable in class org.jmol.script.Token
 
nodes - Variable in class org.jmol.util.JmolMolecule
 
nodes - Variable in class org.jmol.viewer.ActionManager.Gesture
 
nodots - Static variable in class org.jmol.script.Token
 
noedges - Static variable in class org.jmol.script.Token
 
noFaceSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
nofill - Static variable in class org.jmol.script.Token
 
nohead - Static variable in class org.jmol.script.Token
 
noHead - Variable in class org.jmol.shapespecial.Draw
 
noHead - Variable in class org.jmol.shapespecial.DrawMesh
 
NOHISTORYATALL_FLAG - Static variable in class org.jmol.util.CommandHistory
 
NOHISTORYLINE_FLAG - Static variable in class org.jmol.util.CommandHistory
 
noload - Static variable in class org.jmol.script.Token
 
nomesh - Static variable in class org.jmol.script.Token
 
NONE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
none - Static variable in class org.jmol.script.Token
 
noneSelected - Variable in class org.jmol.viewer.Viewer
 
nonhydrogenDegree - Variable in class org.jmol.smiles.SmilesAtom
 
NONPOLY_COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
NONPOLY_ENTITY_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
NONPOLY_NAME - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
nonpolyFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
noplane - Static variable in class org.jmol.script.Token
 
nOps - Variable in class org.jmol.symmetry.PointGroup
 
nOrbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
nOrbitals0 - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
norm - Variable in class org.jmol.shapebio.BioShapeRenderer
 
normal - Static variable in class org.jmol.script.Token
 
normalCount - Variable in class org.jmol.util.MeshSurface
 
normalizeShell(int) - Method in class org.jmol.quantum.MOCalculation
 
normalizeTranslation(Matrix4f) - Static method in class org.jmol.symmetry.SymmetryOperation
 
normalizeTwelfths(float, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
normalizeUV - Variable in class org.jmol.export._ObjExporter
Whether to normalize UV texture coordinates.
normalMode - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
normalOrAxis - Variable in class org.jmol.symmetry.PointGroup.Operation
 
normals - Variable in class org.jmol.export.MeshData.Data
 
normals - Variable in class org.jmol.util.MeshSurface
 
normAnglePanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
normix3d - Variable in class org.jmol.g3d.Graphics3D
 
Normix3D - Class in org.jmol.g3d
Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
Normix3D() - Constructor for class org.jmol.g3d.Normix3D
 
NORMIX_GEODESIC_LEVEL - Static variable in class org.jmol.g3d.Normix3D
 
NORMIX_NULL - Static variable in class org.jmol.g3d.Graphics3D
 
NORMIX_NULL - Static variable in class org.jmol.g3d.Normix3D
 
normixCount - Static variable in class org.jmol.g3d.Normix3D
 
normixCount - Variable in class org.jmol.shape.Mesh
 
normixes - Variable in class org.jmol.shape.Mesh
 
normixes - Variable in class org.jmol.shape.MeshRenderer
 
normixes - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
normixesT - Variable in class org.jmol.shapespecial.Polyhedra
 
not - Variable in class org.jmol.smiles.SmilesAtom
 
notBondedIndex - Variable in class org.jmol.smiles.SmilesAtom
 
notCrossLinked - Variable in class org.jmol.smiles.SmilesAtom
 
notfrontonly - Static variable in class org.jmol.script.Token
 
notifyAtomPicked(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyBackgroundChange(int) - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
notifyBufferReady() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
notifyCallback(EnumCallback, Object[]) - Method in interface org.jmol.api.JmolCallbackListener
 
notifyCallback(EnumCallback, Object[]) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
notifyCallback(EnumCallback, Object[]) - Method in class org.jmol.console.JmolConsole
 
notifyCallback(EnumCallback, Object[]) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyContext(ScriptContext, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
notifyContext(ScriptContext, Object[]) - Method in class org.jmol.console.ScriptEditor
 
notifyEnabled(EnumCallback) - Method in interface org.jmol.api.JmolCallbackListener
 
notifyEnabled(EnumCallback) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
notifyEnabled(EnumCallback) - Method in class org.jmol.console.JmolConsole
 
notifyEnabled(EnumCallback) - Method in class org.jmol.viewer.StatusManager
 
notifyEnabled(EnumCallback) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyEndOfRendering() - Method in class org.jmol.g3d.Platform3D
 
notifyError(String, String, String) - Method in class org.jmol.viewer.StatusManager
 
notifyError(String, String, String) - Method in class org.jmol.viewer.Viewer
 
notifyFileLoaded(String, String, String, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyFileOpen(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
notifyFileOpen(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
notifyMinimizationStatus(String, Integer, Float, Float) - Method in class org.jmol.viewer.StatusManager
 
notifyMinimizationStatus() - Method in class org.jmol.viewer.Viewer
 
notifyMouseClicked(int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
notifyScriptStart() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
notifyScriptStart() - Method in class org.jmol.console.ScriptEditor
 
notifyScriptTermination() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
notifyScriptTermination() - Method in class org.jmol.applet.Jmol.MyStatusListener
 
notifyScriptTermination() - Method in class org.jmol.console.ScriptEditor
 
notifySurfaceGenerationCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
notifySurfaceGenerationCompleted() - Method in class org.jmol.shapesurface.Isosurface
 
notifySurfaceMappingCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
notifySurfaceMappingCompleted() - Method in class org.jmol.shapesurface.Isosurface
 
notifySync(String, String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
notifyViewerRepaintDone() - Method in class org.jmol.api.JmolViewer
 
notifyViewerRepaintDone() - Method in class org.jmol.viewer.Viewer
 
notionalUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
notionalUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
notionalUnitcell - Variable in class org.jmol.util.SimpleUnitCell
 
notionalUnitcellTags - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
NotPDB - Variable in class org.jmol.popup.SimplePopup
 
notriangles - Static variable in class org.jmol.script.Token
 
nOut - Static variable in class org.jmol.g3d.Sphere3D
 
noValuesAtAll - Variable in class org.jmol.quantum.NciCalculation
 
now - Static variable in class org.jmol.script.Token
 
NP - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
nPairs - Variable in class org.jmol.smiles.SmilesGenerator
 
nParameters - Variable in class org.jmol.script.ScriptFunction
 
nPoints - Variable in class org.jmol.jvxl.data.VolumeData
 
nPoints - Variable in class org.jmol.shapespecial.Draw
 
nPoints - Variable in class org.jmol.smiles.SmilesMeasure
 
nPointsX - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsX - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nPointsY - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsY - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nPointsZ - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsZ - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nPolygons - Variable in class org.jmol.jvxl.readers.PmeshReader
 
npqd - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
nPrimitives - Variable in class org.jmol.smiles.SmilesAtom
 
nPrimitives - Variable in class org.jmol.smiles.SmilesBond
 
nProcessors - Static variable in class org.jmol.viewer.Viewer
 
nRead - Variable in class org.jmol.jvxl.readers.XplorReader
 
nRes - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
nRotations - Variable in class org.jmol.symmetry.HallInfo
 
nSATsectors - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
nSemiSkip - Variable in class org.jmol.script.ScriptCompiler
 
nSets - Variable in class org.jmol.util.MeshSurface
 
nSFO - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
nShortSectorsPerStandardSector - Variable in class org.jmol.util.CompoundDocument
 
nSkip - Variable in class org.jmol.jvxl.readers.CastepDensityReader
 
nSkipX - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nSkipY - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nSkipZ - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nSlaters - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nSSATsectors - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
nSurfaceAtoms - Variable in class org.jmol.modelset.AtomCollection
 
nSurfaceInts - Variable in class org.jmol.jvxl.data.JvxlData
 
nSurfaces - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nTab - Variable in class org.jmol.console.JmolConsole
 
nTest - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
nText - Variable in class org.jmol.export.___Exporter
 
nTokens - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
nTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
nTriangles - Variable in class org.jmol.jvxl.readers.PolygonFileReader
 
nTries - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
nuclearCharges - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
nucleic - Static variable in class org.jmol.script.Token
 
NucleicMonomer - Class in org.jmol.modelsetbio
 
NucleicMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.NucleicMonomer
 
NucleicPolymer - Class in org.jmol.modelsetbio
 
NucleicPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.NucleicPolymer
 
nullGroup - Variable in class org.jmol.modelset.ModelLoader
 
nullModelSetName - Variable in class org.jmol.popup.SimplePopup
 
nullNeighbor - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
nullShadeIndex - Static variable in class org.jmol.g3d.Normix3D
 
nullToken - Static variable in class org.jmol.shape.Labels
 
number - Variable in enum org.jmol.util.JmolEdge.EnumBondOrder
 
NumberOfComponents - Variable in class org.jmol.util.JpegInfo
 
numberOfLeadingZeros(int) - Static method in class org.jmol.util.FastBitSet
 
numberOutOfRange(float, float) - Method in class org.jmol.script.ScriptEvaluator
 
numCached - Variable in class org.jmol.modelset.BondCollection
 
NumOfACTables - Variable in class org.jmol.util.Huffman
 
NumOfDCTables - Variable in class org.jmol.util.Huffman
 
numSet - Variable in class org.jmol.modelset.MeasurementPending
 
numWindows - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
nUnique - Static variable in class org.jmol.symmetry.PointGroup
 
nUNK - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
nUnnamed - Variable in class org.jmol.shape.MeshCollection
 
nValue(Token) - Static method in class org.jmol.script.ScriptVariable
 
nVertexColors - Variable in class org.jmol.jvxl.data.JvxlData
 
nVertices - Variable in class org.jmol.export.MeshData.Data
 
nVertices - Variable in class org.jmol.jvxl.readers.PolygonFileReader
 
nVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
nVibrations - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nwchemContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
nwChemMode - Variable in class org.jmol.quantum.MOCalculation
 
NWChemReader - Class in org.jmol.adapter.readers.quantum
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
NWChemReader() - Constructor for class org.jmol.adapter.readers.quantum.NWChemReader
 
nWidgets - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
nx - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nX - Variable in class org.jmol.quantum.QuantumCalculation
 
nXX - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
nxyzStart - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nY - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
ny - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nY - Variable in class org.jmol.quantum.QuantumCalculation
 
nY - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
nZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
nz - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nZ - Variable in class org.jmol.quantum.QuantumCalculation
 
nZ - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 

O

O - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
O1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O3Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O5Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
obj - Static variable in class org.jmol.script.Token
 
OBJ_AXIS1 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_AXIS2 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_AXIS3 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_BACKGROUND - Static variable in class org.jmol.viewer.StateManager
 
OBJ_BOUNDBOX - Static variable in class org.jmol.viewer.StateManager
 
OBJ_FRANK - Static variable in class org.jmol.viewer.StateManager
 
OBJ_MAX - Static variable in class org.jmol.viewer.StateManager
 
OBJ_UNITCELL - Static variable in class org.jmol.viewer.StateManager
 
objCls1 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
objCls2 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
objColors - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
object - Static variable in class org.jmol.script.Token
 
Object2d - Class in org.jmol.shape
 
Object2d() - Constructor for class org.jmol.shape.Object2d
 
Object2d(Viewer, Graphics3D, String, short, int, int, float) - Constructor for class org.jmol.shape.Object2d
 
Object2dShape - Class in org.jmol.shape
 
Object2dShape() - Constructor for class org.jmol.shape.Object2dShape
 
objectNameList - Static variable in class org.jmol.viewer.StateManager
 
objectNameParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
objectOf(DefaultListModel, Object) - Static method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
objects - Variable in class org.jmol.shape.Object2dShape
 
objectsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
objFileRootName - Variable in class org.jmol.export._ObjExporter
Path of the OBJ file without the extension.
objID1 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
objID2 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
objMad - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ObjReader - Class in org.jmol.jvxl.readers
 
ObjReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.ObjReader
 
objStateOn - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
obtainBufferForClient() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
obtainScreenBuffer() - Method in class org.jmol.g3d.Platform3D
 
occupancies - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
occupancies - Variable in class org.jmol.modelset.AtomCollection
 
OCCUPANCY - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
occupancy - Variable in class org.jmol.adapter.smarter.Atom
 
occupancy - Variable in class org.jmol.quantum.MOCalculation
 
occupancy - Static variable in class org.jmol.script.Token
 
octantPoints - Variable in class org.jmol.g3d.Sphere3D
 
octants - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
odysseyImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
OdysseyReader - Class in org.jmol.adapter.readers.quantum
 
OdysseyReader() - Constructor for class org.jmol.adapter.readers.quantum.OdysseyReader
 
off - Static variable in class org.jmol.script.Token
 
officialRelease - Static variable in class org.jmol.viewer.JmolConstants
 
offset - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
offset - Static variable in class org.jmol.script.Token
 
offset - Variable in class org.jmol.shape.UccageRenderer
 
offset - Variable in class org.jmol.shapespecial.DipolesRenderer
 
offset - Variable in class org.jmol.shapespecial.Draw
 
offset(Vector3f) - Method in class org.jmol.shapespecial.DrawMesh
 
offset - Variable in class org.jmol.shapesurface.Isosurface
 
offset - Variable in class org.jmol.util.MeshSurface
 
offsetAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
offsetAngstroms - Variable in class org.jmol.shapespecial.Dipole
 
offsetCenter(Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
offsetPbufBeginLine - Variable in class org.jmol.g3d.Sphere3D
 
offsetPercent - Variable in class org.jmol.shapespecial.Dipole
 
offsets - Variable in class org.jmol.modelsetbio.Monomer
 
offsets - Variable in class org.jmol.shape.Labels
 
offsetside - Static variable in class org.jmol.script.Token
 
offsetSide - Variable in class org.jmol.shapespecial.Dipole
 
offsetT - Variable in class org.jmol.shape.UccageRenderer
 
offsetX - Variable in class org.jmol.shape.Object2d
 
offsetY - Variable in class org.jmol.shape.Object2d
 
OK - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
OK - Static variable in class org.jmol.script.ScriptCompiler
 
ok() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
OK2 - Static variable in class org.jmol.script.ScriptCompiler
 
okButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
okButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
 
oldDir - Variable in class org.openscience.chimetojmol.ChimePanel
 
oldType - Variable in class org.jmol.util.ContactPair
 
OLIVE - Static variable in class org.jmol.g3d.Graphics3D
 
omega - Variable in class org.jmol.modelset.Group
 
omega - Static variable in class org.jmol.script.Token
 
on - Static variable in class org.jmol.script.Token
 
once - Static variable in class org.jmol.script.Token
 
ONE_OVER_D - Static variable in class org.jmol.quantum.MepCalculation
 
ONE_OVER_ONE_PLUS_D - Static variable in class org.jmol.quantum.MepCalculation
 
oneFifth - Static variable in class org.jmol.geodesic.Geodesic
 
onePerLine - Variable in class org.jmol.jvxl.readers.PmeshReader
 
oneTenth - Static variable in class org.jmol.geodesic.Geodesic
 
only - Static variable in class org.jmol.script.Token
 
onlySelectedDots - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
oopCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
opacityFractionalFromArgb(int) - Static method in class org.jmol.export.___Exporter
 
opacityFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
 
opAnd - Static variable in class org.jmol.script.Token
 
opAND - Static variable in class org.jmol.script.Token
 
opaque - Static variable in class org.jmol.script.Token
 
OPAQUE_MASK - Static variable in class org.jmol.g3d.Graphics3D
 
openAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
openBufferedReader(String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader(String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
 
openButton - Variable in class org.jmol.console.ScriptEditor
 
openChooser - Static variable in class org.jmol.export.dialog.Dialog
 
openDocument(StringBuffer) - Static method in class org.jmol.util.XmlUtil
 
openDOM(Object) - Method in class org.jmol.api.JmolSimpleViewer
 
openDOM(Object) - Method in class org.jmol.viewer.Viewer
applet DOM method -- does not preserve state
openFile(String) - Method in class org.jmol.api.JmolSimpleViewer
 
openFile(String) - Method in class org.jmol.viewer.Viewer
for JmolSimpleViewer -- external applications only
openFileAsynchronously(String) - Method in class org.jmol.api.JmolViewer
 
openFileAsynchronously(String) - Method in class org.jmol.viewer.Viewer
opens a file as a model, a script, or a surface via the creation of a script that is queued \t at the beginning disallows script option - used by JmolFileDropper and JmolPanel file-open actions - sets up a script to load the file
openFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
openFiles(String[]) - Method in class org.jmol.api.JmolSimpleViewer
 
openFiles(String[]) - Method in class org.jmol.viewer.Viewer
for JmolSimpleViewer -- external applications only
openmolAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
openpdbAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
openPreview - Variable in class org.jmol.export.dialog.Dialog
 
openReader(String, String, Reader) - Method in class org.jmol.api.JmolViewer
Opens the file and creates the model set, given the reader.
openReader(String, String, Reader) - Method in class org.jmol.viewer.Viewer
Opens the file, given an already-created reader.
openStringInline(String) - Method in class org.jmol.api.JmolSimpleViewer
 
openStringInline(String) - Method in class org.jmol.viewer.Viewer
 
openStringInline(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
 
openStringsInline(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
 
openTag(StringBuffer, String) - Static method in class org.jmol.util.XmlUtil
 
openTag(StringBuffer, String, Object[]) - Static method in class org.jmol.util.XmlUtil
 
openurlAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
opEQ - Static variable in class org.jmol.script.Token
 
operate() - Method in class org.jmol.script.ScriptMathProcessor
 
OPERATION_IMPROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_INVERSION_CENTER - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_PLANE - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_PROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
 
operationCount - Variable in class org.jmol.symmetry.SpaceGroup
 
operations - Variable in class org.jmol.symmetry.SpaceGroup
 
opGE - Static variable in class org.jmol.script.Token
 
opGT - Static variable in class org.jmol.script.Token
 
opId - Variable in class org.jmol.symmetry.SymmetryOperation
 
opIf - Static variable in class org.jmol.script.Token
 
opLE - Static variable in class org.jmol.script.Token
 
opLT - Static variable in class org.jmol.script.Token
 
opNE - Static variable in class org.jmol.script.Token
 
opNot - Static variable in class org.jmol.script.Token
 
opOr - Static variable in class org.jmol.script.Token
 
oPt - Variable in class org.jmol.script.ScriptMathProcessor
 
opToggle - Static variable in class org.jmol.script.Token
 
optOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
optParameterAsString(int) - Method in class org.jmol.script.ScriptEvaluator
 
optsField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
opXor - Static variable in class org.jmol.script.Token
 
or(FastBitSet) - Method in class org.jmol.util.FastBitSet
 
ORANGE - Static variable in class org.jmol.g3d.Graphics3D
 
OrbdeleteButton - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
orbital - Static variable in class org.jmol.script.Token
 
orbitalData - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
orbitalInfo - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
orbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
orbitals - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
Orbitals - Class in org.openscience.jmol.app.webexport
 
Orbitals() - Constructor for class org.openscience.jmol.app.webexport.Orbitals
 
orbitalsRead - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
orbitalType - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
OrbList - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
OrbopenButton - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
orbtohtml(int, int, File, String, JList, String) - Method in class org.openscience.jmol.app.webexport.Orbitals
 
order - Variable in class org.jmol.adapter.smarter.Bond
 
order - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
order - Variable in class org.jmol.symmetry.PointGroup.Operation
 
order - Variable in class org.jmol.util.JmolEdge
 
order - Variable in class org.jmol.viewer.StateManager.Connection
 
ORDER_AROMATIC - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_AROMATIC_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_AROMATIC_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_TRIPLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_HBOND - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL01 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL12 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL23 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL32 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_FAR - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_NEAR - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_UNSPECIFIED - Static variable in class org.jmol.api.JmolAdapter
 
org.jmol.adapter.readers.cifpdb - package org.jmol.adapter.readers.cifpdb
 
org.jmol.adapter.readers.molxyz - package org.jmol.adapter.readers.molxyz
 
org.jmol.adapter.readers.more - package org.jmol.adapter.readers.more
 
org.jmol.adapter.readers.quantum - package org.jmol.adapter.readers.quantum
 
org.jmol.adapter.readers.simple - package org.jmol.adapter.readers.simple
 
org.jmol.adapter.readers.xml - package org.jmol.adapter.readers.xml
 
org.jmol.adapter.readers.xtal - package org.jmol.adapter.readers.xtal
 
org.jmol.adapter.smarter - package org.jmol.adapter.smarter
 
org.jmol.api - package org.jmol.api
 
org.jmol.applet - package org.jmol.applet
 
org.jmol.atomdata - package org.jmol.atomdata
 
org.jmol.awt - package org.jmol.awt
 
org.jmol.bspt - package org.jmol.bspt
Provides Binary Space Partitioning Functionality to spacially separate data structures in n-dimensions
org.jmol.console - package org.jmol.console
 
org.jmol.constant - package org.jmol.constant
 
org.jmol.export - package org.jmol.export
 
org.jmol.export.dialog - package org.jmol.export.dialog
 
org.jmol.export.history - package org.jmol.export.history
 
org.jmol.export.image - package org.jmol.export.image
 
org.jmol.g3d - package org.jmol.g3d
Provides a software implementation of complete 3D graphics engine for rendering molecules and associated shapes.
org.jmol.geodesic - package org.jmol.geodesic
 
org.jmol.i18n - package org.jmol.i18n
 
org.jmol.jvxl.api - package org.jmol.jvxl.api
 
org.jmol.jvxl.calc - package org.jmol.jvxl.calc
 
org.jmol.jvxl.data - package org.jmol.jvxl.data
 
org.jmol.jvxl.readers - package org.jmol.jvxl.readers
 
org.jmol.minimize - package org.jmol.minimize
 
org.jmol.minimize.forcefield - package org.jmol.minimize.forcefield
 
org.jmol.modelkit - package org.jmol.modelkit
 
org.jmol.modelset - package org.jmol.modelset
 
org.jmol.modelsetbio - package org.jmol.modelsetbio
 
org.jmol.multitouch - package org.jmol.multitouch
 
org.jmol.multitouch.jni - package org.jmol.multitouch.jni
 
org.jmol.multitouch.sparshui - package org.jmol.multitouch.sparshui
 
org.jmol.popup - package org.jmol.popup
 
org.jmol.quantum - package org.jmol.quantum
 
org.jmol.script - package org.jmol.script
 
org.jmol.shape - package org.jmol.shape
 
org.jmol.shapebio - package org.jmol.shapebio
 
org.jmol.shapespecial - package org.jmol.shapespecial
 
org.jmol.shapesurface - package org.jmol.shapesurface
 
org.jmol.smiles - package org.jmol.smiles
org.jmol.symmetry - package org.jmol.symmetry
 
org.jmol.util - package org.jmol.util
 
org.jmol.viewer - package org.jmol.viewer
 
org.jmol.viewer.binding - package org.jmol.viewer.binding
 
org.openscience.chimetojmol - package org.openscience.chimetojmol
 
org.openscience.jmol.app - package org.openscience.jmol.app
 
org.openscience.jmol.app.jmolpanel - package org.openscience.jmol.app.jmolpanel
 
org.openscience.jmol.app.surfacetool - package org.openscience.jmol.app.surfacetool
 
org.openscience.jmol.app.webexport - package org.openscience.jmol.app.webexport
 
org.openscience.jvxl - package org.openscience.jvxl
 
org.openscience.jvxl.simplewriter - package org.openscience.jvxl.simplewriter
 
org.openscience.molecularplayground - package org.openscience.molecularplayground
 
orientation - Variable in class org.jmol.modelset.Model
 
orientation - Static variable in class org.jmol.script.Token
 
origin - Variable in class org.jmol.jvxl.data.VolumeData
 
origin - Variable in class org.jmol.jvxl.readers.MapFileReader
 
origin - Variable in class org.jmol.jvxl.readers.Parameters
 
origin - Static variable in class org.jmol.script.Token
 
origin - Variable in class org.jmol.shapespecial.Dipole
 
originalSystemProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
originBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
originPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
originPoint - Variable in class org.jmol.shape.Axes
 
originScreen - Variable in class org.jmol.shape.AxesRenderer
 
os - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
os - Variable in class org.jmol.export.___Exporter
 
os - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
os - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
os - Variable in class org.jmol.util.BinaryDocument
 
oStack - Variable in class org.jmol.script.ScriptMathProcessor
 
OT - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
otherAtoms - Variable in class org.jmol.shapespecial.Polyhedra
 
out - Variable in class org.jmol.export.image.ImageEncoder
 
out - Static variable in class org.jmol.script.Token
 
output(String) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
output(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
output - Variable in class org.jmol.console.AppletConsole
 
output(String) - Method in class org.jmol.console.AppletConsole
 
output(String, AttributeSet) - Method in class org.jmol.console.AppletConsole
 
output(String) - Method in class org.jmol.console.ScriptEditor
 
output - Variable in class org.jmol.export.___Exporter
 
output(String) - Method in class org.jmol.export.___Exporter
 
output(Tuple3f) - Method in class org.jmol.export.___Exporter
 
output(Tuple3f) - Method in class org.jmol.export._IdtfExporter
 
output(Tuple3f, StringBuffer, boolean) - Method in class org.jmol.export._IdtfExporter
 
output(Tuple3f) - Method in class org.jmol.export._MayaExporter
 
output(Tuple3f) - Method in class org.jmol.export._ObjExporter
 
output(Tuple3f) - Method in class org.jmol.export._PovrayExporter
 
output(Tuple3f) - Method in class org.jmol.export._TachyonExporter
 
output(Tuple3f) - Method in class org.jmol.export._VrmlExporter
 
output(int, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
outputAlphaCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputAppearance(short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputAppearance(short, boolean) - Method in class org.jmol.export._X3dExporter
 
outputBeforePrompt(String, SimpleAttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
outputBuffer - Variable in class org.jmol.applet.Jmol
 
outputBuffer - Variable in class org.jmol.script.ScriptContext
 
outputBuffer - Variable in class org.jmol.script.ScriptEvaluator
 
outputCircle(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
outputCircle(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputCircle(Point3f, Point3f, short, float) - Method in class org.jmol.export._IdtfExporter
 
outputCircle(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._MayaExporter
 
outputCircle(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._ObjExporter
 
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCircle(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputCircle(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._X3dExporter
 
outputCircle1(Point3f, Point3f, short, float) - Method in class org.jmol.export._ObjExporter
Local implementation of outputCircle.
outputColorIndices(int[][], int, BitSet, int, Map<Short, Integer>, short[], short[]) - Method in class org.jmol.export._VrmlExporter
 
outputColors(List<Short>) - Method in class org.jmol.export._VrmlExporter
 
outputComment(String) - Method in class org.jmol.export.___Exporter
 
outputCone(Point3f, Point3f, float, short) - Method in class org.jmol.export.__CartesianExporter
 
outputCone(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
outputCone(Point3f, Point3f, float, short) - Method in class org.jmol.export._IdtfExporter
 
outputCone(Point3f, Point3f, float, short) - Method in class org.jmol.export._MayaExporter
 
outputCone(Point3f, Point3f, float, short) - Method in class org.jmol.export._ObjExporter
 
outputCone(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCone(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCone(Point3f, Point3f, float, short) - Method in class org.jmol.export._VrmlExporter
 
outputCone(Point3f, Point3f, float, short) - Method in class org.jmol.export._X3dExporter
 
outputCone1(Point3f, Point3f, float, short) - Method in class org.jmol.export._ObjExporter
Local implementation of outputCone.
outputCylinder(Point3f, Point3f, Point3f, short, byte, float, Point3f, Point3f, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputCylinder(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
outputCylinder(Point3f, Point3f, Point3f, short, byte, float, Point3f, Point3f, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputCylinder(Point3f, Point3f, Point3f, short, byte, float, Point3f, Point3f, boolean) - Method in class org.jmol.export._MayaExporter
 
outputCylinder(Point3f, Point3f, Point3f, short, byte, float, Point3f, Point3f, boolean) - Method in class org.jmol.export._ObjExporter
 
outputCylinder(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCylinder(Point3f, Point3f, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCylinder(Point3f, Point3f, Point3f, short, byte, float, Point3f, Point3f, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputCylinder(Point3f, Point3f, Point3f, short, byte, float, Point3f, Point3f, boolean) - Method in class org.jmol.export._X3dExporter
 
outputCylinder1(Point3f, Point3f, Point3f, short, byte, float, Point3f, Point3f) - Method in class org.jmol.export._ObjExporter
Local implementation of outputCylinder.
outputCylinderChild(Point3f, Point3f, short, byte, float) - Method in class org.jmol.export._VrmlExporter
 
outputCylinderChild(Point3f, Point3f, short, byte, float) - Method in class org.jmol.export._X3dExporter
 
outputCylinderConical(Point3f, Point3f, float, float, short) - Method in class org.jmol.export.__RayTracerExporter
 
outputCylinderConical(Point3f, Point3f, float, float, short) - Method in class org.jmol.export._PovrayExporter
 
outputCylinderConical(Point3f, Point3f, float, float, short) - Method in class org.jmol.export._TachyonExporter
 
outputDocument - Variable in class org.jmol.console.AppletConsole
 
outputEcho(String) - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
outputEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
outputEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
outputEllipse(Point3f, Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._IdtfExporter
 
outputEllipse1(Point3f, Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._ObjExporter
Local implementation of outputEllipse.
outputEllipsoid(Point3f, Point3f[], short) - Method in class org.jmol.export.__CartesianExporter
 
outputEllipsoid(Point3f, float, double[], short) - Method in class org.jmol.export.__RayTracerExporter
 
outputEllipsoid(Point3f, Point3f[], short) - Method in class org.jmol.export._IdtfExporter
 
outputEllipsoid(Point3f, Matrix4f, short) - Method in class org.jmol.export._IdtfExporter
 
outputEllipsoid(Point3f, Point3f[], short) - Method in class org.jmol.export._MayaExporter
 
outputEllipsoid(Point3f, Point3f[], short) - Method in class org.jmol.export._ObjExporter
 
outputEllipsoid(Point3f, float, double[], short) - Method in class org.jmol.export._PovrayExporter
 
outputEllipsoid(Point3f, float, double[], short) - Method in class org.jmol.export._TachyonExporter
 
outputEllipsoid(Point3f, Point3f[], short) - Method in class org.jmol.export._VrmlExporter
 
outputEllipsoid(Point3f, Point3f[], short) - Method in class org.jmol.export._X3dExporter
 
outputEllipsoid1(Point3f, float, float, float, AxisAngle4f, short) - Method in class org.jmol.export._ObjExporter
Local implementation of outputEllipsoid.
outputError(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
outputError(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
outputErrorForeground(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
outputErrorForeground(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
outputExtension - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputFace(int[], int[], int) - Method in class org.jmol.export.__CartesianExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._IdtfExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._MayaExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._ObjExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._VrmlExporter
 
outputFace1(int[], int[], int[]) - Method in class org.jmol.export._ObjExporter
Local implementation of outputFace used for no texture coordinates.
outputFace2(int[], int, int[], int[]) - Method in class org.jmol.export._ObjExporter
Local implementation of outputFace used with texture coordinates.
outputFileName - Variable in class org.jmol.export.dialog.Dialog
 
outputFileType - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputFooter() - Method in class org.jmol.export.___Exporter
 
outputFooter() - Method in class org.jmol.export._IdtfExporter
 
outputFooter() - Method in class org.jmol.export._TachyonExporter
 
outputFooter() - Method in class org.jmol.export._VrmlExporter
 
outputFooter() - Method in class org.jmol.export._X3dExporter
 
outputFormatChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Called when the OutputFormat check box is modified
outputFormatCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputFormatCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputHeader() - Method in class org.jmol.export.___Exporter
 
outputHeader() - Method in class org.jmol.export.__RayTracerExporter
 
outputHeader() - Method in class org.jmol.export._IdtfExporter
 
outputHeader() - Method in class org.jmol.export._MayaExporter
 
outputHeader() - Method in class org.jmol.export._ObjExporter
 
outputHeader() - Method in class org.jmol.export._PovrayExporter
 
outputHeader() - Method in class org.jmol.export._TachyonExporter
 
outputHeader() - Method in class org.jmol.export._VrmlExporter
 
outputHeader() - Method in class org.jmol.export._X3dExporter
 
outputHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputIndices(int[][], int[], int, BitSet, int) - Method in class org.jmol.export.__CartesianExporter
 
outputJmolPerspective() - Method in class org.jmol.export.___Exporter
 
outputList(Tuple3f[], int, Matrix4f, String, BitSet) - Method in class org.jmol.export._ObjExporter
create the v or vn list
outputMtl(String) - Method in class org.jmol.export._ObjExporter
Write to the .mtl file and keep track of the bytes written.
outputNodes() - Method in class org.jmol.export._IdtfExporter
 
outputNormals(List<String>) - Method in class org.jmol.export._VrmlExporter
 
outputQuaternionFrame(Point3f, Point3f, Point3f, Point3f, float, String, String) - Method in class org.jmol.export._VrmlExporter
 
outputRing(int, int, int, Vector3f, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputSphere(Point3f, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputSphere(float, float, float, float, short) - Method in class org.jmol.export.__RayTracerExporter
 
outputSphere(Point3f, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputSphere(Point3f, float, short, boolean) - Method in class org.jmol.export._MayaExporter
 
outputSphere(Point3f, float, short, boolean) - Method in class org.jmol.export._ObjExporter
 
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._PovrayExporter
 
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._TachyonExporter
 
outputSphere(Point3f, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputSphereChild(Point3f, float, short) - Method in class org.jmol.export._VrmlExporter
 
outputSphereChild(Point3f, float, short) - Method in class org.jmol.export._X3dExporter
 
outputStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
outputStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
OutputStringBuffer - Class in org.jmol.util
 
OutputStringBuffer(BufferedOutputStream) - Constructor for class org.jmol.util.OutputStringBuffer
 
outputSurface(Point3f[], Vector3f[], short[], int[][], short[], int, int, int, BitSet, int, short, List<Short>, Map<Short, Integer>, Point3f) - Method in class org.jmol.export.___Exporter
 
outputSurface(Point3f[], Vector3f[], short[], int[][], short[], int, int, int, BitSet, int, short, List<Short>, Map<Short, Integer>, Point3f) - Method in class org.jmol.export._IdtfExporter
 
outputSurface(Point3f[], Vector3f[], short[], int[][], short[], int, int, int, BitSet, int, short, List<Short>, Map<Short, Integer>, Point3f) - Method in class org.jmol.export._MayaExporter
 
outputSurface(Point3f[], Vector3f[], short[], int[][], short[], int, int, int, BitSet, int, short, List<Short>, Map<Short, Integer>, Point3f) - Method in class org.jmol.export._PovrayExporter
 
outputSurface(Point3f[], Vector3f[], short[], int[][], short[], int, int, int, BitSet, int, short, List<Short>, Map<Short, Integer>, Point3f) - Method in class org.jmol.export._TachyonExporter
 
outputSurface(Point3f[], Vector3f[], short[], int[][], short[], int, int, int, BitSet, int, short, List<Short>, Map<Short, Integer>, Point3f) - Method in class org.jmol.export._VrmlExporter
 
outputSurface(Point3f[], Vector3f[], short[], int[][], short[], int, int, int, BitSet, int, short, List<Short>, Map<Short, Integer>, Point3f) - Method in class org.jmol.export._X3dExporter
 
outputTextPixel(Point3f, int) - Method in class org.jmol.export.__CartesianExporter
 
outputTextPixel(int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
 
outputTextPixel(Point3f, int) - Method in class org.jmol.export._IdtfExporter
 
outputTextPixel(Point3f, int) - Method in class org.jmol.export._MayaExporter
 
outputTextPixel(Point3f, int) - Method in class org.jmol.export._ObjExporter
 
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._PovrayExporter
 
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._TachyonExporter
 
outputTextPixel(Point3f, int) - Method in class org.jmol.export._VrmlExporter
 
outputTextPixel(Point3f, int) - Method in class org.jmol.export._X3dExporter
 
outputTexture(short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputTexture(int, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputTexture2(String, String, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputTextureCode() - Method in class org.jmol.export._TachyonExporter
 
outputTransRot(Point3f, Point3f, int, int, int) - Method in class org.jmol.export._VrmlExporter
 
outputTransRot(Point3f, Point3f, int, int, int, String, String) - Method in class org.jmol.export._VrmlExporter
 
outputTransRot(Point3f, Point3f, int, int, int) - Method in class org.jmol.export._X3dExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export.__CartesianExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export.__RayTracerExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._IdtfExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._MayaExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._ObjExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._PovrayExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._TachyonExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._VrmlExporter
 
outputTriangle(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._X3dExporter
 
outputTriangle1(Point3f, Point3f, Point3f, short) - Method in class org.jmol.export._ObjExporter
Local implementation of outputCylinder.
outputVertex(Point3f, Point3f) - Method in class org.jmol.export.___Exporter
 
outputVertex(Point3f, Point3f) - Method in class org.jmol.export.__RayTracerExporter
 
outputVertices(Point3f[], int, Point3f) - Method in class org.jmol.export.___Exporter
 
outputWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outSocket - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
outStream - Variable in class org.jmol.util.JpegEncoder
 
oValue(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
 

P

p - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
P - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
p0 - Variable in class org.jmol.quantum.NciCalculation
 
p1 - Variable in class org.jmol.quantum.NciCalculation
 
p1 - Variable in class org.jmol.shape.SticksRenderer
 
p2 - Variable in class org.jmol.quantum.NciCalculation
 
p2 - Variable in class org.jmol.shape.SticksRenderer
 
p2nLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
P2nReader - Class in org.jmol.adapter.readers.more
P2N file reader.
P2nReader() - Constructor for class org.jmol.adapter.readers.more.P2nReader
 
P_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
P_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
packageJSON(String, StringBuilder) - Static method in class org.jmol.util.Escape
 
packageJSON(String, String) - Static method in class org.jmol.util.Escape
 
packageReadable(String, String, StringBuilder) - Static method in class org.jmol.util.Escape
 
packageReadable(String, String, String) - Static method in class org.jmol.util.Escape
 
packed - Static variable in class org.jmol.script.Token
 
pageAuthorName - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
pageAuthorName - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
pages - Variable in class org.openscience.chimetojmol.ChimePanel
 
paint(Graphics) - Method in class org.jmol.applet.AppletWrapper
 
paint(Graphics) - Method in class org.jmol.applet.Jmol
 
paint(Graphics) - Method in interface org.jmol.applet.WrappedApplet
 
paint(Graphics) - Method in class org.jmol.export.dialog.FilePreview.FPPanel
 
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
paint(Graphics) - Method in class org.openscience.molecularplayground.MPJmolApp.KioskPanel
 
paintCounter - Variable in class org.jmol.applet.Jmol
 
pairSearch(List<Object[]>, CalculationsUFF.PairCalc) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
PALETTE_ALTLOC - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_AMINO - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_CHAIN - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_CPK - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_ENERGY - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_FIXEDTEMP - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_FORMAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_GROUP - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_INSERTION - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_JMOL - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_MOLECULE - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_MONOMER - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_NONE - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_PARTIAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_POLYMER - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_PROPERTY - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_RASMOL - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_SHAPELY - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_STRAIGHTNESS - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_STRUCTURE - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_SURFACE - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_TEMP - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_TYPE - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_VARIABLE - Static variable in class org.jmol.constant.StaticConstants
 
PALETTE_VOLATILE - Static variable in class org.jmol.constant.StaticConstants
 
paletteBW - Variable in class org.jmol.util.ColorEncoder
 
paletteID - Variable in class org.jmol.modelset.Atom
 
paletteID - Variable in class org.jmol.modelset.HBond
 
paletteIDs - Variable in class org.jmol.shape.AtomShape
 
paletteIDs - Variable in class org.jmol.shapebio.BioShape
 
paletteWB - Variable in class org.jmol.util.ColorEncoder
 
palindrome - Static variable in class org.jmol.script.Token
 
panel() - Method in class org.openscience.jmol.app.webexport.Test
 
panelIndex - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
panelName - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
PAR_D - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_HARD - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_R - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_RADIUS - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_THETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_U - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_V - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_X - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_XI - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_Z - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_ZETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
parA - Variable in class org.jmol.minimize.forcefield.Calculation
 
parallel - Static variable in class org.jmol.script.Token
 
ParallelProcessor - Class in org.jmol.script
 
ParallelProcessor(String, int) - Constructor for class org.jmol.script.ParallelProcessor
 
parallelProcessor - Variable in class org.jmol.script.ScriptContext
 
parallelProcessor - Variable in class org.jmol.script.ScriptEvaluator
 
ParallelProcessor.Process - Class in org.jmol.script
the idea here is that the process { ...
ParallelProcessor.Process(String, ScriptContext) - Constructor for class org.jmol.script.ParallelProcessor.Process
 
ParallelProcessor.RunProcess - Class in org.jmol.script
 
ParallelProcessor.RunProcess(ParallelProcessor.Process, Object, ShapeManager) - Constructor for class org.jmol.script.ParallelProcessor.RunProcess
 
parameterAsString(int) - Method in class org.jmol.script.ScriptEvaluator
 
parameterExpression(int, int, String, boolean, boolean, int, boolean, Map, String) - Method in class org.jmol.script.ScriptEvaluator
This is the primary driver of the RPN (reverse Polish notation) expression processor.
parameterExpressionBoolean(int, int) - Method in class org.jmol.script.ScriptEvaluator
 
parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
parameterExpressionString(int, int) - Method in class org.jmol.script.ScriptEvaluator
 
parameterExpressionToken(int) - Method in class org.jmol.script.ScriptEvaluator
 
parameterIndex(String) - Static method in class org.jmol.adapter.readers.xtal.GulpReader
 
Parameters - Class in org.jmol.jvxl.readers
 
Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
 
parameters - Variable in class org.jmol.jvxl.readers.Parameters
 
parameters - Static variable in class org.jmol.script.Token
 
params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
params - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
paramTypes - Static variable in class org.jmol.script.Token
 
parB - Variable in class org.jmol.minimize.forcefield.Calculation
 
parC - Variable in class org.jmol.minimize.forcefield.Calculation
 
parenCount - Variable in class org.jmol.script.ScriptCompiler
 
parenCount - Variable in class org.jmol.script.ScriptMathProcessor
 
parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
parent - Variable in class org.jmol.script.ScriptFlowContext
 
parent - Variable in class org.jmol.smiles.SmilesAtom
 
parent - Variable in class org.jmol.smiles.SmilesSearch
 
parentContext - Variable in class org.jmol.script.ScriptContext
 
parse(String) - Method in class org.jmol.smiles.SmilesParser
Parses a SMILES String
parseAtom(SmilesSearch, SmilesAtom, String, SmilesAtom, SmilesBond, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
Parses an atom definition
parseBond(SmilesSearch, SmilesBond, String, SmilesBond, SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
 
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
parseCommandLine(String[]) - Method in class org.openscience.jmol.app.JmolApp
 
parseCommandParameter(String) - Method in class org.jmol.script.ScriptCompiler
 
parsedContext - Variable in class org.jmol.console.ScriptEditor
 
parsedData - Variable in class org.jmol.console.ScriptEditor
 
parseFloat(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
parseFloat() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloat(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloat(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloat() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseFloat(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseFloat(String) - Static method in class org.jmol.util.Parser
 
parseFloat(String, int[]) - Static method in class org.jmol.util.Parser
 
parseFloat(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseFloatArray(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseFloatArray() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseFloatArray(String) - Static method in class org.jmol.util.Parser
 
parseFloatArray(String, int[]) - Static method in class org.jmol.util.Parser
 
parseFloatArray(String[], BitSet, float[]) - Static method in class org.jmol.util.Parser
 
parseFloatArray(String[], float[]) - Static method in class org.jmol.util.Parser
parses a string array for floats.
parseFloatArray(String[], float[], int) - Static method in class org.jmol.util.Parser
parses a string array for floats.
parseFloatArray2d(String) - Static method in class org.jmol.util.Parser
 
parseFloatArray3d(String) - Static method in class org.jmol.util.Parser
 
parseFloatArrayFromMatchAndField(String, BitSet, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
the major lifter here.
parseFloatChecked(String, int, int[], boolean) - Static method in class org.jmol.util.Parser
 
parseFloatStrict(String) - Static method in class org.jmol.util.Parser
 
parseInt(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
parseInt() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseInt(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseInt(String) - Static method in class org.jmol.util.Parser
 
parseInt(String, int[]) - Static method in class org.jmol.util.Parser
 
parseInt(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseIntChecked(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseIntNext(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseKnownToken(String) - Method in class org.jmol.script.ScriptCompiler
 
parseLattRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseLineParameters(String[], byte[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
sets up arrays and variables for tokenizer.getData()
parseMeasure(SmilesSearch, String, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
 
parseNested(SmilesSearch, String) - Method in class org.jmol.smiles.SmilesParser
 
Parser - Class in org.jmol.util
 
Parser() - Constructor for class org.jmol.util.Parser
 
parseReaderXML(XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
parseRing(SmilesSearch, int, SmilesAtom, SmilesBond) - Method in class org.jmol.smiles.SmilesParser
Parses a ring definition
parseScript(String) - Method in class org.jmol.console.ScriptEditor
 
parseScript(boolean) - Method in class org.jmol.script.ScriptCompiler
 
parseSfacCoefficients(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseSfacElementSymbols(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseSfacRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseSmiles(SmilesSearch, String, SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesParser
Parses a part of a SMILES String
parseStringInfestedFloatArray(String, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseStringInfestedFloatArray(String, BitSet, float[]) - Static method in class org.jmol.util.Parser
parses a "dirty" string for floats.
parseSymmRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseToken() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseToken(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseToken(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseToken(String) - Static method in class org.jmol.util.Parser
 
parseToken(String, int[]) - Static method in class org.jmol.util.Parser
 
parseToken(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseTokenChecked(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseTokenNext(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTrimmed(String, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTrimmed(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTrimmed(String) - Static method in class org.jmol.util.Parser
 
parseTrimmed(String, int) - Static method in class org.jmol.util.Parser
 
parseTrimmed(String, int, int) - Static method in class org.jmol.util.Parser
 
parseTrimmedChecked(String, int, int) - Static method in class org.jmol.util.Parser
 
parseVariableLength(String) - Method in class org.jmol.smiles.SmilesParser
 
parseVariables(String) - Method in class org.jmol.smiles.SmilesParser
 
PARTIAL_CHARGE_COLIX_BLUE - Static variable in class org.jmol.viewer.JmolConstants
 
PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JmolConstants
 
PARTIAL_CHARGE_COLIX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
 
PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JmolConstants
 
partialCharge - Variable in class org.jmol.adapter.smarter.Atom
 
partialcharge - Static variable in class org.jmol.script.Token
 
partialCharges - Variable in class org.jmol.adapter.readers.simple.AmpacReader
 
partialCharges - Variable in class org.jmol.minimize.forcefield.Calculations
 
partialCharges - Variable in class org.jmol.minimize.Minimizer
 
partialCharges - Variable in class org.jmol.modelset.AtomCollection
 
partialdots - Static variable in class org.jmol.script.Token
 
partialDots - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Pass - Variable in class org.jmol.export.image.GifEncoder
 
pasteClipboardAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
path() - Method in class org.jmol.script.ScriptFlowContext
 
path - Static variable in class org.jmol.script.Token
 
PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
AtomSetCollectionReader.readData() will close any BufferedReader
PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
PathButton - Variable in class org.openscience.jmol.app.webexport.Test
 
pattern - Variable in class org.jmol.smiles.SmilesSearch
 
patternAtoms - Variable in class org.jmol.smiles.SmilesSearch
 
pause() - Method in class org.jmol.script.ScriptEvaluator
 
pause - Static variable in class org.jmol.script.Token
 
PAUSE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
pauseAnimation() - Method in class org.jmol.viewer.AnimationManager
 
pauseButton - Variable in class org.jmol.console.ScriptEditor
 
pauseExecution(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
pauseScript(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
pauseScriptExecution() - Method in class org.jmol.viewer.Viewer
 
pBotLeft - Variable in class org.jmol.g3d.Hermite3D
 
pBotRight - Variable in class org.jmol.g3d.Hermite3D
 
pbuf - Variable in class org.jmol.g3d.Graphics3D
 
pBuffer - Variable in class org.jmol.g3d.Platform3D
 
pBufferT - Variable in class org.jmol.g3d.Platform3D
 
pbufT - Variable in class org.jmol.g3d.Graphics3D
 
pButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
pc - Variable in class org.jmol.script.ScriptContext
 
pc - Variable in class org.jmol.script.ScriptEvaluator
 
pcEnd - Variable in class org.jmol.script.ScriptContext
 
pcEnd - Variable in class org.jmol.script.ScriptEvaluator
 
pchrg - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
pcl - Variable in class org.jmol.export.JmolFileDropper
 
pcs - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
pdb - Static variable in class org.jmol.script.Token
 
pdbaddhydrogens - Static variable in class org.jmol.script.Token
 
pdbAddHydrogens - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pdbBondInfo - Static variable in class org.jmol.viewer.JmolConstants
 
pdbgetheader - Static variable in class org.jmol.script.Token
 
pdbGetHeader - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pdbHeader - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
pdbheader - Static variable in class org.jmol.script.Token
 
pdbHydrogenCount - Static variable in class org.jmol.viewer.JmolConstants
 
pdbLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
PDBOnly - Variable in class org.jmol.popup.SimplePopup
 
PdbReader - Class in org.jmol.adapter.readers.cifpdb
PDB file reader.
PdbReader() - Constructor for class org.jmol.adapter.readers.cifpdb.PdbReader
 
pdbRecords - Static variable in class org.jmol.modelset.ModelCollection
 
pdbsequential - Static variable in class org.jmol.script.Token
 
pdbSequential - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
PdfCreator - Class in org.openscience.jmol.app.jmolpanel
 
PdfCreator() - Constructor for class org.openscience.jmol.app.jmolpanel.PdfCreator
 
peekToken() - Method in class org.jmol.util.CifDataReader
just look at the next token.
pending(MeasurementPending) - Method in class org.jmol.shape.Measures
 
per - Static variable in class org.jmol.script.Token
 
percent - Static variable in class org.jmol.script.Token
 
percentToPixels(char, float) - Method in class org.jmol.viewer.TransformManager
 
percentvdwatom - Static variable in class org.jmol.script.Token
 
percentVdwAtom - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
percentVdwAtom - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
period - Static variable in class org.jmol.script.Token
 
PERIOD_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for the vibration period in seconds.
PERIOD_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Precision of the vibration period slider in seconds.
PERIOD_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Initial value for the vibration period in seconds.
periodicOriginXyz - Variable in class org.jmol.symmetry.SymmetryInfo
 
periodSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
perpendicular - Static variable in class org.jmol.script.Token
 
perspectiveAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
perspectivedepth - Static variable in class org.jmol.script.Token
 
perspectiveDepth - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
perspectiveDepth - Variable in class org.jmol.viewer.TransformManager
 
perspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
perspectiveFactor - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
perspectivemodel - Static variable in class org.jmol.script.Token
 
perspectiveModel - Variable in class org.jmol.viewer.TransformManager
 
perspectiveOffset - Variable in class org.jmol.viewer.TransformManager
 
perspectiveShiftXY - Variable in class org.jmol.viewer.TransformManager
 
pfaatBinding - Variable in class org.jmol.viewer.ActionManager
 
PfaatBinding - Class in org.jmol.viewer.binding
 
PfaatBinding() - Constructor for class org.jmol.viewer.binding.PfaatBinding
 
pfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
pFF - Variable in class org.jmol.minimize.Minimizer
 
phase - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
phase - Static variable in class org.jmol.script.Token
 
phi - Variable in class org.jmol.modelset.Group
 
phi - Static variable in class org.jmol.script.Token
 
phong - Variable in class org.jmol.export._TachyonExporter
 
phongExponent - Static variable in class org.jmol.g3d.Shade3D
 
phongexponent - Static variable in class org.jmol.script.Token
 
phongExponent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
PhosphorusMonomer - Class in org.jmol.modelsetbio
 
PhosphorusMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.PhosphorusMonomer
 
phosphorusOffsets - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
PhosphorusPolymer - Class in org.jmol.modelsetbio
 
PhosphorusPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.PhosphorusPolymer
 
PI_OVER_2 - Static variable in class org.jmol.minimize.forcefield.Calculations
 
pickAtomAssignType - Variable in class org.jmol.viewer.ActionManager
 
pickBondAssignType - Variable in class org.jmol.viewer.ActionManager
 
pickedAtom - Variable in class org.jmol.shape.Labels
 
pickedMesh - Variable in class org.jmol.shape.MeshCollection
 
pickedModel - Variable in class org.jmol.shape.MeshCollection
 
pickedOffset - Variable in class org.jmol.shape.Labels
 
pickedVertex - Variable in class org.jmol.shape.MeshCollection
 
pickedX - Variable in class org.jmol.shape.Labels
 
pickedY - Variable in class org.jmol.shape.Labels
 
picking - Static variable in class org.jmol.script.Token
 
PICKING_ASSIGN_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_ASSIGN_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_CENTER - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_CONNECT - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DELETE_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DELETE_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MINIMIZE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MINIMIZE_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_SELECTED - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAW - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_IDENTIFY - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_IDENTIFY_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_INVERT_STEREO - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_LABEL - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_SEQUENCE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_NAVIGATE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_OFF - Static variable in class org.jmol.viewer.ActionManager
picking modes set picking....
PICKING_ROTATE_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_MODEL - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_POLYMER - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_STRUCTURE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SPIN - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_STRUTS - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SYMMETRY - Static variable in class org.jmol.viewer.ActionManager
 
pickingModeNames - Static variable in class org.jmol.viewer.ActionManager
 
pickingspinrate - Static variable in class org.jmol.script.Token
 
pickingSpinRate - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pickingstyle - Static variable in class org.jmol.script.Token
 
pickingStyle - Variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.ActionManager
picking styles
PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.ActionManager
 
pickingStyleMeasure - Variable in class org.jmol.viewer.ActionManager
 
pickingStyleNames - Static variable in class org.jmol.viewer.ActionManager
 
pickingStyleSelect - Variable in class org.jmol.viewer.ActionManager
 
picklabel - Static variable in class org.jmol.script.Token
 
pickLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pictFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
pictIsScratchFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
pidOf(Object) - Static method in enum org.jmol.constant.EnumPalette
 
PINK - Static variable in class org.jmol.g3d.Graphics3D
 
pipedIS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
pipedOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
pixel - Variable in class org.jmol.g3d.Graphics3D
 
pixelScaleDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
pixelSize - Variable in class org.jmol.export._ObjExporter
The size of a pixel based on some assumptions about screen size
plane - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
plane - Variable in class org.jmol.modelsetbio.Resolver
 
plane - Static variable in class org.jmol.script.Token
 
plane - Variable in class org.jmol.shapespecial.Draw
 
plane_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
plane_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
planeCenter - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
planeExpected() - Method in class org.jmol.script.ScriptEvaluator
 
planeParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
planeRadius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
planes - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
planeShade - Variable in class org.jmol.g3d.Sphere3D
 
planeShades - Variable in class org.jmol.g3d.Sphere3D
 
planesT - Variable in class org.jmol.shapespecial.Polyhedra
 
planeU - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
planeV - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
planeValue(Token) - Method in class org.jmol.script.ScriptMathProcessor
 
Platform - Class in org.jmol.awt
 
Platform() - Constructor for class org.jmol.awt.Platform
 
platform - Variable in class org.jmol.g3d.Graphics3D
 
Platform3D - Class in org.jmol.g3d
Specifies the API to an underlying int[] buffer of ARGB values that can be converted into an Image object and a short[] for z-buffer depth.
Platform3D() - Constructor for class org.jmol.g3d.Platform3D
 
Platform3D.ClearingThread - Class in org.jmol.g3d
 
Platform3D.ClearingThread() - Constructor for class org.jmol.g3d.Platform3D.ClearingThread
 
play - Static variable in class org.jmol.script.Token
 
PLAY - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
playrev - Static variable in class org.jmol.script.Token
 
pLeft - Variable in class org.jmol.g3d.Hermite3D
 
plot(int, int, int, int, String, Font3D, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.Text3D
 
plot(Token[]) - Method in class org.jmol.script.ScriptEvaluator
 
plot - Static variable in class org.jmol.script.Token
 
plot3d - Static variable in class org.jmol.script.Token
 
Plot3D - Class in org.jmol.shapesurface
 
Plot3D() - Constructor for class org.jmol.shapesurface.Plot3D
 
Plot3DRenderer - Class in org.jmol.shapesurface
 
Plot3DRenderer() - Constructor for class org.jmol.shapesurface.Plot3DRenderer
 
plot8CircleCenteredClipped(int, int) - Method in class org.jmol.g3d.Circle3D
 
plot8CircleCenteredUnclipped(int, int) - Method in class org.jmol.g3d.Circle3D
 
plot8FilledCircleCenteredClipped(int, int) - Method in class org.jmol.g3d.Circle3D
 
plot8FilledCircleCenteredUnclipped(int, int) - Method in class org.jmol.g3d.Circle3D
 
plotByCharacter(int, int, int, int, String, Font3D, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.Text3D
 
plotCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.Circle3D
 
plotCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.Circle3D
 
plotClipped(int, int, int, int, Graphics3D, JmolRendererInterface, int, int, int[]) - Static method in class org.jmol.g3d.Text3D
 
plotDashedLine(int, boolean, int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotFilledCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.Circle3D
 
plotFilledCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.Circle3D
 
plotImage(int, int, int, Image, short, int, int) - Method in class org.jmol.export.___Exporter
 
plotImage(int, int, int, Image, short, int, int) - Method in class org.jmol.export.__CartesianExporter
 
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotImage(int, int, int, Object, Graphics3D, JmolRendererInterface, boolean, int, int, int) - Static method in class org.jmol.g3d.Text3D
 
plotImageClipped(int, int, int, Graphics3D, JmolRendererInterface, int, int, int[], int) - Static method in class org.jmol.g3d.Text3D
 
plotImageUnClipped(int, int, int, Graphics3D, int, int, int[], int) - Static method in class org.jmol.g3d.Text3D
 
plotLine(int, boolean, int, boolean, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotLineClipped(int, boolean, int, boolean, int, int, int, int, int, int, boolean, int, int) - Method in class org.jmol.g3d.Line3D
 
plotLineClipped(int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean, int, int) - Method in class org.jmol.g3d.Line3D
 
plotLineClippedBits(int[], boolean, int[], boolean, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Line3D
 
plotLineDelta(int, boolean, int, boolean, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotLineDelta(int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotLineDeltaBits(int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotPixelClipped(Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
plotPixelClipped(int, int, int) - Method in class org.jmol.export.Export3D
 
plotPixelClipped(Point3i) - Method in class org.jmol.export.Export3D
 
plotPixelClipped(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClipped(Point3i) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClipped(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClipped(int, boolean, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClippedNoSlab(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
plotPixelClippedNoSlab(int, int, int, int) - Method in class org.jmol.export.Export3D
 
plotPixelClippedNoSlab(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsClipped(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsClipped(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsUnclipped(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsUnclipped(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelUnclipped(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelUnclipped(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPoints(int, int[], int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotRaster(int) - Method in class org.jmol.g3d.Cylinder3D
 
plotRasterBits(int) - Method in class org.jmol.g3d.Cylinder3D
 
plotRasterCone(int, boolean, boolean) - Method in class org.jmol.g3d.Cylinder3D
 
plotText(int, int, int, short, String, Font3D) - Method in class org.jmol.export.___Exporter
 
plotText(int, int, int, short, String, Font3D) - Method in class org.jmol.export.__CartesianExporter
 
plotText(int, int, int, short, String, Font3D) - Method in class org.jmol.export._VrmlExporter
 
plotText(int, int, int, short, String, Font3D) - Method in class org.jmol.export._X3dExporter
 
plotText(int, int, int, int, String, Font3D, JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
 
plotUnclipped(int, int, int, int, Graphics3D, int, int, int[]) - Static method in class org.jmol.g3d.Text3D
 
PltFormattedReader - Class in org.jmol.jvxl.readers
 
PltFormattedReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.PltFormattedReader
 
plus - Static variable in class org.jmol.script.Token
 
plusPlus - Static variable in class org.jmol.script.Token
 
pmesh - Static variable in class org.jmol.script.Token
 
Pmesh - Class in org.jmol.shapesurface
 
Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
 
PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.jvxl.readers.PmeshReader
 
PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.util.SurfaceFileTyper
 
pmeshError - Variable in class org.jmol.jvxl.readers.PmeshReader
 
PmeshReader - Class in org.jmol.jvxl.readers
 
PmeshReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.PmeshReader
 
PmeshReader(SurfaceGenerator, String, BufferedReader) - Constructor for class org.jmol.jvxl.readers.PmeshReader
 
PmeshRenderer - Class in org.jmol.shapesurface
 
PmeshRenderer() - Constructor for class org.jmol.shapesurface.PmeshRenderer
 
pngBytes - Variable in class org.jmol.export.image.PngEncoder
 
pngEncode(boolean) - Method in class org.jmol.export.image.PngEncoder
Creates an array of bytes that is the PNG equivalent of the current image, specifying whether to encode alpha or not.
pngEncode() - Method in class org.jmol.export.image.PngEncoder
Creates an array of bytes that is the PNG equivalent of the current image.
PngEncoder - Class in org.jmol.export.image
PngEncoder takes a Java Image object and creates a byte string which can be saved as a PNG file.
PngEncoder() - Constructor for class org.jmol.export.image.PngEncoder
Class constructor
PngEncoder(Image) - Constructor for class org.jmol.export.image.PngEncoder
Class constructor specifying Image to encode, with no alpha channel encoding.
PngEncoder(Image, boolean) - Constructor for class org.jmol.export.image.PngEncoder
Class constructor specifying Image to encode, and whether to encode alpha.
PngEncoder(Image, boolean, int) - Constructor for class org.jmol.export.image.PngEncoder
Class constructor specifying Image to encode, whether to encode alpha, and filter to use.
PngEncoder(Image, boolean, int, int) - Constructor for class org.jmol.export.image.PngEncoder
Class constructor specifying Image source to encode, whether to encode alpha, filter to use, and compression level.
pocket - Variable in class org.jmol.jvxl.readers.Parameters
 
pocket - Static variable in class org.jmol.script.Token
 
point - Variable in class org.jmol.jvxl.readers.Parameters
 
point - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
point - Static variable in class org.jmol.script.Token
 
point3f - Static variable in class org.jmol.script.Token
 
Point3fi - Class in org.jmol.util
the Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points)
Point3fi() - Constructor for class org.jmol.util.Point3fi
 
Point3fi(Point3f) - Constructor for class org.jmol.util.Point3fi
 
Point3fi(float, float, float) - Constructor for class org.jmol.util.Point3fi
 
point3fScreenTemp - Variable in class org.jmol.viewer.TransformManager
 
point3fVibrationTemp - Variable in class org.jmol.viewer.TransformManager
 
point3iScreenTemp - Variable in class org.jmol.viewer.TransformManager
 
point4f - Static variable in class org.jmol.script.Token
 
pointA - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
pointA - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pointArc - Variable in class org.jmol.modelset.Measurement
 
pointArrowHead - Variable in class org.jmol.shapespecial.VectorsRenderer
 
pointB - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pointCorner - Variable in class org.jmol.shapebio.RocketsRenderer
 
pointer - Variable in class org.jmol.shape.Object2d
 
POINTER_BACKGROUND - Static variable in class org.jmol.shape.Object2d
 
POINTER_FLAGS - Static variable in class org.jmol.shape.Labels
 
POINTER_NONE - Static variable in class org.jmol.shape.Object2d
 
POINTER_ON - Static variable in class org.jmol.shape.Object2d
 
pointGroup - Variable in class org.jmol.modelset.ModelSet
 
pointGroup() - Method in class org.jmol.script.ScriptEvaluator
 
pointgroup - Static variable in class org.jmol.script.Token
 
PointGroup - Class in org.jmol.symmetry
 
PointGroup() - Constructor for class org.jmol.symmetry.PointGroup
 
pointGroup - Variable in class org.jmol.symmetry.Symmetry
 
PointGroup.Operation - Class in org.jmol.symmetry
 
PointGroup.Operation() - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
PointGroup.Operation(Vector3f, int) - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
PointGroup.Operation(Vector3f) - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
pointgroupdistancetolerance - Static variable in class org.jmol.script.Token
 
pointGroupDistanceTolerance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pointgrouplineartolerance - Static variable in class org.jmol.script.Token
 
pointGroupLinearTolerance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pointPlaneAngleRadians(Vector3d, Vector3d, Vector3d, Vector3d, Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
points - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
points - Variable in class org.jmol.jvxl.readers.Parameters
 
points - Variable in class org.jmol.modelset.MeasurementData
 
points - Variable in class org.jmol.quantum.QuantumCalculation
 
points - Variable in class org.jmol.shapespecial.DipolesRenderer
 
points - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
points - Variable in class org.jmol.smiles.SmilesMeasure
 
points - Variable in class org.jmol.symmetry.PointGroup
 
POINTS_ALL - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
POINTS_HETS - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
POINTS_MCMC - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
POINTS_MCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
POINTS_SCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
 
pointsperangstrom - Static variable in class org.jmol.script.Token
 
pointT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
pointT - Variable in class org.jmol.shape.FontLineShapeRenderer
 
pointT - Variable in class org.jmol.shapebio.BioShapeRenderer
 
pointT2 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
pointT2 - Variable in class org.jmol.viewer.TransformManager
 
pointT3 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
pointTipOffset - Variable in class org.jmol.shapebio.RocketsRenderer
 
pointTsp - Variable in class org.jmol.viewer.TransformManager
 
pointType - Variable in class org.jmol.jvxl.readers.KinemageReader
 
pointVectorEnd - Variable in class org.jmol.shapespecial.VectorsRenderer
 
polygon - Static variable in class org.jmol.script.Token
 
polygon - Variable in class org.jmol.shapespecial.Draw
 
polygonColixes - Variable in class org.jmol.util.MeshSurface
 
polygonColorData - Variable in class org.jmol.jvxl.data.MeshData
 
polygonCount - Variable in class org.jmol.util.MeshSurface
 
polygonCount0 - Variable in class org.jmol.util.MeshSurface
 
PolygonFileReader - Class in org.jmol.jvxl.readers
 
PolygonFileReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.PolygonFileReader
 
polygonIndexes - Variable in class org.jmol.util.MeshSurface
 
polyhedra() - Method in class org.jmol.script.ScriptEvaluator
 
polyhedra - Static variable in class org.jmol.script.Token
 
Polyhedra - Class in org.jmol.shapespecial
 
Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
 
Polyhedra.Polyhedron - Class in org.jmol.shapespecial
 
Polyhedra.Polyhedron(Atom, int, int, int, Point3f[], short[], byte[]) - Constructor for class org.jmol.shapespecial.Polyhedra.Polyhedron
 
PolyhedraRenderer - Class in org.jmol.shapespecial
 
PolyhedraRenderer() - Constructor for class org.jmol.shapespecial.PolyhedraRenderer
 
polyhedronCount - Variable in class org.jmol.shapespecial.Polyhedra
 
polyhedrons - Variable in class org.jmol.shapespecial.Polyhedra
 
Polymer - Class in org.jmol.modelset
 
Polymer() - Constructor for class org.jmol.modelset.Polymer
 
polymer - Static variable in class org.jmol.script.Token
 
polymerlength - Static variable in class org.jmol.script.Token
 
pop - Static variable in class org.jmol.script.Token
 
popContext(boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
popHoldRepaint() - Method in class org.jmol.api.JmolViewer
 
popHoldRepaint(boolean) - Method in class org.jmol.viewer.RepaintManager
 
popHoldRepaint() - Method in class org.jmol.viewer.Viewer
 
popHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
 
popInHeight - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
PopInJmol - Class in org.openscience.jmol.app.webexport
 
PopInJmol(JmolViewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.PopInJmol
 
popInWidth - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
popupMenu(int, int, char) - Method in class org.jmol.viewer.Viewer
 
PopupResource - Class in org.jmol.popup
 
PopupResource(String, Properties) - Constructor for class org.jmol.popup.PopupResource
 
port - Variable in class org.openscience.jmol.app.JmolApp
The data model.
port - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
posCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
position - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
position - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
position - Variable in class org.openscience.jvxl.MonitorInputStream
 
positionAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
positionBeforePrompt - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
positionMin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
positionSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
positionThicknessPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
postByteArray(String, byte[]) - Static method in class org.jmol.viewer.FileManager
not implemented
postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
potentials - Variable in class org.jmol.quantum.MepCalculation
 
povrayAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
povrayActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PovrayDialog - Class in org.openscience.jmol.app.jmolpanel
A dialog for controling the creation of a povray input file from a Chemframe and a display.
PovrayDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog
Creates a dialog for getting info related to output frames in povray format.
PovrayDialog.PovrayWindowListener - Class in org.openscience.jmol.app.jmolpanel
Listener for responding to dialog window events.
PovrayDialog.PovrayWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
 
povrayPathButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
povrayPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
power4 - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
PpmEncoder - Class in org.jmol.export.image
 
PpmEncoder(Image, OutputStream) - Constructor for class org.jmol.export.image.PpmEncoder
 
PpmEncoder(ImageProducer, OutputStream) - Constructor for class org.jmol.export.image.PpmEncoder
 
pqrLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
PqrReader - Class in org.jmol.adapter.readers.more
PQR file reader.
PqrReader() - Constructor for class org.jmol.adapter.readers.more.PqrReader
 
precalculateVoxelData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
precision - Variable in class org.jmol.modelset.LabelToken
 
Precision - Variable in class org.jmol.util.JpegInfo
 
predefinedArgbs - Static variable in class org.jmol.g3d.Colix3D
 
predefinedGroup1Names - Static variable in class org.jmol.viewer.JmolConstants
 
predefinedGroup3Names - Static variable in class org.jmol.viewer.JmolConstants
 
predefinedset - Static variable in class org.jmol.script.Token
 
predefinedStatic - Static variable in class org.jmol.viewer.JmolConstants
 
predefinedVariable - Static variable in class org.jmol.viewer.JmolConstants
 
preDefining - Variable in class org.jmol.script.ScriptCompiler
 
predragBinding - Variable in class org.jmol.viewer.ActionManager
 
preferencesDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PreferencesDialog - Class in org.openscience.jmol.app.jmolpanel
 
PreferencesDialog(JmolPanel, JFrame, GuiMap, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
PreferencesDialog.PrefsAction - Class in org.openscience.jmol.app.jmolpanel
 
PreferencesDialog.PrefsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
 
prefsAction - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
preloadClassIndex - Variable in class org.jmol.applet.AppletWrapper
 
preloadClassNames - Variable in class org.jmol.applet.AppletWrapper
 
preloadImage - Variable in class org.jmol.applet.AppletWrapper
 
preloadImageName - Variable in class org.jmol.applet.AppletWrapper
 
preloadImagePainted - Variable in class org.jmol.applet.AppletWrapper
 
preloadImageReadyForDisplay - Variable in class org.jmol.applet.AppletWrapper
 
preloadTextMessage - Variable in class org.jmol.applet.AppletWrapper
 
preloadThreadCount - Variable in class org.jmol.applet.AppletWrapper
 
preProcessPlanes - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
preserveState - Variable in class org.jmol.modelset.AtomCollection
 
preservestate - Static variable in class org.jmol.script.Token
 
preserveState - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pressed - Variable in class org.jmol.viewer.ActionManager
 
PRESSED - Static variable in class org.jmol.viewer.binding.Binding
 
pressedAtomIndex - Variable in class org.jmol.viewer.ActionManager
 
pressedCount - Variable in class org.jmol.viewer.ActionManager
 
prev - Static variable in class org.jmol.script.Token
 
prevAtom - Variable in class org.jmol.smiles.SmilesGenerator
 
prevFrame - Variable in class org.jmol.viewer.Viewer
 
PREVIOUS - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
 
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.MeshCollection
 
previousClassName - Variable in class org.jmol.applet.AppletWrapper
 
previousMeshID - Variable in class org.jmol.shape.MeshCollection
 
previousScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
previousSpaceGroup - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
previousUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
previousX - Variable in class org.jmol.viewer.TransformManager
 
previousY - Variable in class org.jmol.viewer.TransformManager
 
prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
prevSp2Atoms - Variable in class org.jmol.smiles.SmilesGenerator
 
prevZoomSetting - Variable in class org.jmol.viewer.TransformManager
 
pRight - Variable in class org.jmol.g3d.Hermite3D
 
primitiveCode - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
primitiveData - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
primitiveHallSymbol - Variable in class org.jmol.symmetry.HallInfo
 
primitives - Variable in class org.jmol.smiles.SmilesAtom
 
primitives - Variable in class org.jmol.smiles.SmilesBond
 
primitiveToCryst - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
primitiveToIndex - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
principalAxis - Variable in class org.jmol.symmetry.PointGroup
 
principalPlane - Variable in class org.jmol.symmetry.PointGroup
 
principalQuantumNumber - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
print() - Method in class org.jmol.script.ScriptEvaluator
 
print - Static variable in class org.jmol.script.Token
 
print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
print() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
added print command, so that it can be used by RasmolScriptHandler
printAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
printActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
printProgressbarMessage(Graphics) - Method in class org.jmol.applet.Jmol
 
priorRow - Variable in class org.jmol.export.image.PngEncoder
 
privateKey - Variable in class org.jmol.export.___Exporter
 
privateKey - Variable in class org.jmol.export.Export3D
 
privateKey - Variable in class org.jmol.export.image.ImageCreator
 
privateKey - Variable in class org.jmol.shapesurface.Isosurface
 
privateKey - Variable in class org.jmol.viewer.Viewer
 
probe - Static variable in class org.jmol.script.Token
 
proc - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
process(Point3f) - Method in interface org.jmol.api.QuantumCalculationInterface
 
process(int, int, float) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
Data mapping function to radically increase speed and reduce memory requirements of mapping data when the mapping comes from the same data set as the points, so isosurface creation and data mapping can be carried out both in the first (and only) pass.
process() - Method in class org.jmol.quantum.MepCalculation
 
process() - Method in class org.jmol.quantum.MOCalculation
 
process() - Method in class org.jmol.quantum.NciCalculation
 
process(int, int, float) - Method in class org.jmol.quantum.NciCalculation
Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point.
process(Point3f) - Method in class org.jmol.quantum.QuantumCalculation
 
process() - Method in class org.jmol.quantum.QuantumCalculation
 
process - Variable in class org.jmol.script.ParallelProcessor.RunProcess
 
process - Static variable in class org.jmol.script.Token
 
processAtom() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
processAtomicCharges() - Method in class org.jmol.adapter.readers.simple.MopacReader
Reads the section in MOPAC files with atomic charges.
processAtomObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processAtoms() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processAtoms(int, int, int, int) - Method in class org.jmol.quantum.NciCalculation
At each grid point we need to calculate the sum of the atom-based promolecular data.
processAtomSiteLoopBlock(boolean) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
reads atom data in any order
processAtomTypeLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
processBasisObject(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processBinaryDocument(BinaryDocument) - Method in class org.jmol.adapter.readers.more.BinaryReader
 
processBinaryDocument(BinaryDocument) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
processBirth(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processBondObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processBonds() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processCellParameter() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
unit cell parameters -- two options, so we use MOD 6
processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
incorporates double-click gesture
processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processChangeSync(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processCharges() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processChemCompLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
a general name definition field.
processChemicalInfo(String) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
reads some of the more interesting info into specific atomSetAuxiliaryInfo elements
processCmdfAtoms() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
processComponentKeyEvent(KeyEvent) - Method in class org.jmol.console.AppletConsole.ControlEnterTextArea
 
processConnectorObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processCoord() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processCoordinates() - Method in class org.jmol.adapter.readers.simple.MopacReader
Reads the section in MOPAC files with cartesian coordinates.
processCtab(boolean) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
processDataParameter() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
initialize a new atom set
processDeath(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processDeletedModelAtoms(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
processEndElement2(String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processes - Variable in class org.jmol.script.ParallelProcessor
 
processEvent(int, int, int, int, Point3f, long) - Method in class org.jmol.api.JmolViewer
 
processEvent(int, int, int, int, Point3f, long) - Method in class org.jmol.multitouch.ActionManagerMT
 
processEvent(int, int, int, int, Point3f, long) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
processEvent(int, Event) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
Translate the specialized Sparsh UI information into a format that Jmol's ActionManager can understand without any special classes.
processEvent(int, int, int, int, Point3f, long) - Method in class org.jmol.viewer.ActionManager
 
processEvent(int, int, int, int, Point3f, long) - Method in class org.jmol.viewer.Viewer
 
processFile(String, File, File, boolean, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
processGeomBondLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
reads bond data -- N_ijk symmetry business is ignored, so we only indicate bonds within the unit cell to just the original set of atoms.
processHeader() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processInfo() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processInputCoords() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
processKeyEvent(KeyEvent) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
 
processKeyEvent(KeyEvent) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
Custom key event processing for command 0 implementation.
processLigandBondLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
processLocalTransform() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processLock - Variable in class org.jmol.script.ParallelProcessor.RunProcess
 
processLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
processes loop_ blocks of interest or skips the data
processMessage(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
processMol() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
processMolecularOrbitalObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processMolecule() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
processMolSdHeader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
processMove(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processName - Variable in class org.jmol.script.ParallelProcessor.Process
 
processNextMeasure(Measurement) - Method in interface org.jmol.api.JmolMeasurementClient
 
processNextMeasure(Measurement) - Method in class org.jmol.modelset.MeasurementData
if this is the client, then this method is called by MeasurementData when a measurement is ready
processNextMeasure(Measurement) - Method in class org.jmol.shape.Measures
 
processNonpolyData() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
processNonpolyLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
a HETERO name definition field.
processOneCubical(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
processOneCubical(int, int[], int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
processPoints() - Method in class org.jmol.quantum.MOCalculation
 
processPoints() - Method in class org.jmol.quantum.QuantumCalculation
 
processScript(Object[]) - Method in class org.jmol.viewer.StatusManager
 
processShapeCommand(int) - Method in class org.jmol.script.ScriptEvaluator
 
processShell(int) - Method in class org.jmol.quantum.MOCalculation
 
processSlater(int) - Method in class org.jmol.quantum.MOCalculation
 
processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
processStartElement2(String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
processStructConfLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
identifies ranges for HELIX and TURN
processStructSheetRangeLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
identifies sheet ranges
processStructSiteBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
identifies structure sites
processSupportedRecord(int) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
processSymmetryOperationsLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
retrieves symmetry operations
processSymmetrySpaceGroupName() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
done by AtomSetCollectionReader
processTokenList(short, boolean) - Method in class org.jmol.script.ScriptCompiler
 
processTotalEnergy() - Method in class org.jmol.adapter.readers.simple.MopacReader
 
processTriangles(int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
processTriangles(int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
the PDB transformation matrix cartesian --> fractional
processVibrationObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processXml(XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processXml(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
processXml(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
procSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
producer - Variable in class org.jmol.export.image.ImageEncoder
 
programInfo - Variable in class org.jmol.atomdata.AtomData
 
progressbarMsgs - Static variable in class org.jmol.applet.Jmol
 
projectOntoAxis(Point3f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
 
prompt(String, String, String[], boolean) - Method in interface org.jmol.api.JmolPromptInterface
 
prompt(String, String, String[], boolean) - Method in class org.jmol.console.JmolPrompt
 
prompt() - Method in class org.jmol.script.ScriptEvaluator
 
prompt - Static variable in class org.jmol.script.Token
 
prompt(String, String, String[], boolean) - Method in class org.jmol.viewer.Viewer
 
prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
 
prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
 
prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
prop - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
PROP_ANIMATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_APPLET_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ATOM_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ATOM_LIST - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_AUXILIARY_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_BOND_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_BOUNDBOX_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_CENTER_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_CHAIN_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_CONSOLE_TEXT - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_COUNT - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_DATA_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ERROR_MESSAGE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_EVALUATE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_EXTRACT_MODEL - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILECONTENTS - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILECONTENTS_PATH - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILEHEADER - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILENAME - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_IMAGE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ISOSURFACE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_JMOL_STATUS - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_JMOL_VIEWER - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_LIGAND_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MEASUREMENT_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MENU - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MESSAGE_QUEUE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MINIMIZATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MODEL_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MOLECULE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MOUSE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ORIENTATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_POINTGROUP_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_POLYMER_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_SHAPE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_STATE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_TRANSFORM_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
propagateNeighborPointIndexes(int, int, int, int, int[][], int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
properties - Variable in class org.jmol.export.history.HistoryFile
The data stored in the history file.
properties - Variable in class org.jmol.modelset.Model
 
propertiesTextArea - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
property - Static variable in class org.jmol.script.Token
 
propertyatomnumbercolumncount - Static variable in class org.jmol.script.Token
 
propertyatomnumberfield - Static variable in class org.jmol.script.Token
 
propertyChange(PropertyChangeEvent) - Method in class org.jmol.export.dialog.FilePreview
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
 
propertyColorEncoder - Variable in class org.jmol.util.ColorEncoder
 
propertyColorEncoder - Variable in class org.jmol.viewer.ColorManager
 
propertycolorscheme - Static variable in class org.jmol.script.Token
 
propertyColorScheme - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
propertyCount - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
propertydatacolumncount - Static variable in class org.jmol.script.Token
 
propertydatafield - Static variable in class org.jmol.script.Token
 
propertyDistanceMax - Variable in class org.jmol.jvxl.readers.Parameters
 
PROPERTYFLAGS - Static variable in class org.jmol.script.Token
 
propertyItemCounts - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
PropertyManager - Class in org.jmol.viewer
The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
PropertyManager() - Constructor for class org.jmol.viewer.PropertyManager
 
propertyOf - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
propertySmoothing - Variable in class org.jmol.jvxl.readers.Parameters
 
propertySmoothingPower - Variable in class org.jmol.jvxl.readers.Parameters
 
propertyTypes - Static variable in class org.jmol.viewer.PropertyManager
 
props - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
propselector - Static variable in class org.jmol.script.Token
 
protein - Static variable in class org.jmol.script.Token
 
proteinShape(int) - Method in class org.jmol.script.ScriptEvaluator
 
proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
 
ProteinStructure - Class in org.jmol.modelsetbio
 
ProteinStructure(AlphaPolymer, EnumStructure, int, int, int) - Constructor for class org.jmol.modelsetbio.ProteinStructure
 
proteinstructurePending - Variable in class org.jmol.shapebio.RocketsRenderer
 
proteinStructureTainted - Variable in class org.jmol.modelset.ModelCollection
 
pS - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
psi - Variable in class org.jmol.modelset.Group
 
psi - Static variable in class org.jmol.script.Token
 
psi_l - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_l - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_m - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_m - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_monteCarloCount - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_n - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_n - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_normalization - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_Znuc - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_Znuc - Variable in class org.jmol.jvxl.readers.Parameters
 
psiContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
PsiReader - Class in org.jmol.adapter.readers.quantum
Reader for Psi3 output files.
PsiReader() - Constructor for class org.jmol.adapter.readers.quantum.PsiReader
 
pt - Variable in enum org.jmol.constant.EnumVdw
 
pt - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
pt - Variable in class org.jmol.modelset.LabelToken
 
pt - Variable in class org.jmol.shape.CageRenderer
 
pt - Variable in class org.jmol.shape.EchoRenderer
 
pt - Variable in class org.jmol.shapebio.BioShapeRenderer
 
pt - Variable in class org.jmol.util.ContactPair
 
pt - Variable in class org.jmol.util.ZipUtil.GZipData
 
pt - Variable in class org.jmol.viewer.FileManager.ArrayDataReader
 
pt - Variable in class org.jmol.viewer.FileManager.VectorDataReader
 
pt - Variable in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
pt - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
pt0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
pt0 - Variable in class org.jmol.script.ScriptFlowContext
 
pt0 - Variable in class org.jmol.script.ScriptFunction
 
pt0 - Static variable in class org.jmol.script.ScriptVariable
 
pt0 - Static variable in class org.jmol.shape.Axes
 
pt0 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
pt0f - Variable in class org.jmol.shapespecial.DrawRenderer
 
pt0i - Variable in class org.jmol.shapespecial.DrawRenderer
 
pt1 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
pt1 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
pt1 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
pt1 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
pt1 - Variable in class org.jmol.shapesurface.Contact
 
pt1f - Variable in class org.jmol.shape.MeshRenderer
 
pt1i - Variable in class org.jmol.shape.MeshRenderer
 
pt2 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
pt2 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
pt2 - Variable in class org.jmol.shapesurface.Contact
 
pt2f - Variable in class org.jmol.shape.MeshRenderer
 
pt2i - Variable in class org.jmol.shape.MeshRenderer
 
pt3i - Variable in class org.jmol.shape.MeshRenderer
 
pt4Value(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
 
PT_BITSET - Static variable in class org.jmol.shapespecial.Draw
 
PT_CHARGE - Static variable in class org.jmol.minimize.Minimizer
 
PT_CONNECT - Static variable in class org.jmol.minimize.Minimizer
 
PT_COORD - Static variable in class org.jmol.shapespecial.Draw
 
PT_ELEMENT - Static variable in class org.jmol.minimize.Minimizer
 
PT_IDENTIFIER - Static variable in class org.jmol.shapespecial.Draw
 
PT_MODEL_BASED_POINTS - Static variable in class org.jmol.shapespecial.Draw
 
PT_MODEL_INDEX - Static variable in class org.jmol.shapespecial.Draw
 
ptA - Variable in class org.jmol.export.Export3D
 
ptAi - Variable in class org.jmol.export.Export3D
 
ptAtom - Variable in class org.jmol.shape.EchoRenderer
 
ptB - Variable in class org.jmol.export.Export3D
 
ptBi - Variable in class org.jmol.export.Export3D
 
ptC - Variable in class org.jmol.export.Export3D
 
ptCenter - Variable in class org.jmol.shape.Mesh
 
ptCenter - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
ptCenters - Variable in class org.jmol.shapespecial.DrawMesh
 
ptCommand - Variable in class org.jmol.script.ScriptFlowContext
 
ptConnect - Variable in class org.jmol.shapebio.CartoonRenderer
 
ptD - Variable in class org.jmol.export.Export3D
 
ptDefault - Variable in class org.jmol.script.ScriptFlowContext
 
ptDefaultLattice - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ptFloat - Variable in class org.jmol.adapter.readers.more.MdCrdReader
 
ptid - Variable in class org.jmol.script.ScriptMathProcessor
 
ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ptLine - Variable in class org.jmol.script.ScriptFlowContext
 
ptList - Variable in class org.jmol.shapespecial.Draw
 
ptMark - Variable in class org.jmol.viewer.FileManager.ArrayDataReader
 
ptMark - Variable in class org.jmol.viewer.FileManager.VectorDataReader
 
ptMax - Variable in class org.jmol.export._IdtfExporter
 
ptMin - Variable in class org.jmol.export._IdtfExporter
 
ptMoveToCenter - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
ptMoveToCenter - Variable in class org.jmol.viewer.TransformManager11
 
ptNewSetModifier - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
ptNext - Variable in class org.jmol.shapebio.BioShapeRenderer
 
ptNext - Variable in class org.jmol.viewer.ActionManager.Gesture
 
ptOffset - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ptOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ptOffset - Variable in class org.jmol.util.MeshSurface
 
ptOffset - Variable in class org.jmol.viewer.RepaintManager
 
pTopLeft - Variable in class org.jmol.g3d.Hermite3D
 
pTopRight - Variable in class org.jmol.g3d.Hermite3D
 
ptOriginShift - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
ptPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
 
ptPsi - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
ptRef - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
pts - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
pts - Variable in class org.jmol.modelset.Measurement
 
ptS1 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ptS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ptSemi - Variable in class org.jmol.script.ScriptCompiler
 
ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
ptTemp - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ptTemp - Variable in class org.jmol.export._ObjExporter
 
ptTemp - Variable in class org.jmol.g3d.Sphere3D
 
ptTemp - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
ptTemp - Variable in class org.jmol.jvxl.data.VolumeData
 
ptTemp - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
ptTemp - Variable in class org.jmol.modelset.ModelCollection
 
ptTemp - Variable in class org.jmol.modelsetbio.AminoMonomer
 
ptTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
ptTemp - Variable in class org.jmol.shape.Axes
 
ptTemp - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
ptTemp1 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ptTemp2 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ptTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ptTempi - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
ptTest1 - Variable in class org.jmol.viewer.TransformManager
 
ptTest2 - Variable in class org.jmol.viewer.TransformManager
 
ptTest3 - Variable in class org.jmol.viewer.TransformManager
 
ptTrans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
ptValue(ScriptVariable, boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
ptValue(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
 
ptx - Variable in class org.jmol.script.ScriptMathProcessor
 
ptXY - Variable in class org.jmol.shape.Sticks
 
ptXY - Variable in class org.jmol.shapespecial.Draw
 
ptXY - Variable in class org.jmol.shapesurface.Isosurface
 
ptXyzTemp - Variable in class org.jmol.jvxl.data.VolumeData
 
ptXyzTemp - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
ptY0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
ptZ0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
purging - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
purine - Static variable in class org.jmol.script.Token
 
PURPLE - Static variable in class org.jmol.g3d.Graphics3D
 
push - Static variable in class org.jmol.script.Token
 
pushContext(ContextToken) - Method in class org.jmol.script.ScriptEvaluator
 
pushCount - Variable in class org.jmol.script.ScriptCompiler
 
pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
 
pushHoldRepaint() - Method in class org.jmol.viewer.RepaintManager
 
pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
 
pushHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
 
put(int, int) - Method in class org.jmol.util.Int2IntHash
 
putBox(int, float[]) - Method in class org.jmol.shape.Labels
 
Putbyte(byte, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
putCoord(Vector3d, double[]) - Static method in class org.jmol.minimize.Util
 
putFileContents(File, String) - Method in class org.openscience.chimetojmol.ChimePanel
 
putIf(char) - Method in class org.jmol.script.ScriptMathProcessor
 
putLabel(int, Text) - Method in class org.jmol.shape.Labels
 
putOp(Token) - Method in class org.jmol.script.ScriptMathProcessor
 
Putword(int, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
putX(ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
 
Pwr2 - Static variable in class org.jmol.util.TriangleData
 
Pwr2 - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
pyrimidine - Static variable in class org.jmol.script.Token
 

Q

q - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
q - Variable in class org.jmol.shape.Mesh
 
q0 - Variable in class org.jmol.util.Quaternion
 
q1 - Variable in class org.jmol.util.Quaternion
 
q2 - Variable in class org.jmol.util.Quaternion
 
q3 - Variable in class org.jmol.util.Quaternion
 
qchemContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
QchemReader - Class in org.jmol.adapter.readers.quantum
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
QchemReader() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader
 
QchemReader.MOInfo - Class in org.jmol.adapter.readers.quantum
 
QchemReader.MOInfo() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
qColor - Static variable in class org.jmol.modelsetbio.BioPolymer
 
QConst - Static variable in class org.jmol.modelset.HBond
 
qeImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
qm_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_moLinearCombination - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_moNumber - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_nAtoms - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_GAUSSIAN - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_NCI_PRO - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_NCI_SCF - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_SLATER - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_UNKNOWN - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_VOLUME_DATA - Static variable in class org.jmol.jvxl.readers.Parameters
 
qmAtoms - Variable in class org.jmol.quantum.QuantumCalculation
 
qmOrbitalCount - Variable in class org.jmol.jvxl.readers.Parameters
 
qmOrbitalType - Variable in class org.jmol.jvxl.readers.Parameters
 
qPanelJPEG - Variable in class org.jmol.export.dialog.Dialog
 
qPanelPNG - Variable in class org.jmol.export.dialog.Dialog
 
qpc - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
qpt2 - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
qSetupDone - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
qSliderJPEG - Variable in class org.jmol.export.dialog.Dialog
 
qSliderPNG - Variable in class org.jmol.export.dialog.Dialog
 
QtableNumber - Variable in class org.jmol.util.JpegInfo
 
qTemp - Static variable in class org.jmol.util.Quaternion
 
Quadric - Class in org.jmol.util
 
Quadric() - Constructor for class org.jmol.util.Quadric
 
quadruple(int, short[]) - Static method in class org.jmol.geodesic.Geodesic
 
Quality - Variable in class org.jmol.util.JpegEncoder
 
qualityJ - Variable in class org.jmol.export.dialog.Dialog
 
qualityJPG - Static variable in class org.jmol.export.dialog.Dialog
 
qualityJPG - Variable in class org.jmol.viewer.StatusManager
 
qualityJPG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
qualityP - Variable in class org.jmol.export.dialog.Dialog
 
qualityPNG - Static variable in class org.jmol.export.dialog.Dialog
 
qualityPNG - Variable in class org.jmol.viewer.StatusManager
 
qualityPNG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
quantize(float, boolean) - Method in class org.jmol.util.ColorEncoder
gets the value at the color boundary for this color range fraction
quantize(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
 
quantizeBlock(double[][], double[]) - Static method in class org.jmol.util.DCT
 
quantum - Variable in class org.jmol.util.DCT
Image Quality (0-100) - default 80 (good image / good compression)
quantum_chrominance - Variable in class org.jmol.util.DCT
Quantitization Matrix for chrominance.
quantum_luminance - Variable in class org.jmol.util.DCT
Quantitization Matrix for luminace.
QuantumCalculation - Class in org.jmol.quantum
 
QuantumCalculation() - Constructor for class org.jmol.quantum.QuantumCalculation
 
QuantumCalculation.QMAtom - Class in org.jmol.quantum
 
QuantumCalculation.QMAtom(int, Atom, float[], float[], float[], float[], float[], float[]) - Constructor for class org.jmol.quantum.QuantumCalculation.QMAtom
 
QuantumCalculationInterface - Interface in org.jmol.api
 
QuantumPlaneCalculationInterface - Interface in org.jmol.api
Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readers
quaternion - Static variable in class org.jmol.script.Token
 
Quaternion - Class in org.jmol.util
 
Quaternion() - Constructor for class org.jmol.util.Quaternion
 
Quaternion(Quaternion) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(Tuple3f, float) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(Matrix3f) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(AxisAngle4f) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(Point4f) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(float, float, float, float) - Constructor for class org.jmol.util.Quaternion
 
quaternionframe - Static variable in class org.jmol.script.Token
 
quaternionFrame - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
queueAtom(int, Point3fi) - Method in class org.jmol.viewer.ActionManager
 
queueThreads - Variable in class org.jmol.viewer.ScriptManager
 
quit - Static variable in class org.jmol.script.Token
 
qZero - Static variable in class org.jmol.util.Quaternion
 

R

r - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
r - Variable in class org.jmol.quantum.SlaterData
 
r0 - Variable in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
rab - Variable in class org.jmol.minimize.forcefield.Calculation
 
rad - Static variable in class org.jmol.script.Token
 
RAD_TO_DEG - Static variable in class org.jmol.minimize.forcefield.Calculations
 
RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
 
radialPart(double) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
RADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
radiansPerDegree - Static variable in class org.jmol.smiles.SmilesMeasure
 
radiansPerDegree - Static variable in class org.jmol.util.Measure
 
radiansPerDegree - Static variable in class org.jmol.viewer.JmolConstants
 
radical - Static variable in class org.jmol.script.Token
 
radii - Variable in class org.jmol.util.ContactPair
 
radiiIP2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radius - Variable in class org.jmol.adapter.smarter.Atom
 
radius - Variable in class org.jmol.bspt.CubeIterator
 
radius - Variable in class org.jmol.g3d.Cylinder3D
 
radius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
radius - Static variable in class org.jmol.script.Token
 
radius - Variable in class org.jmol.shapespecial.Polyhedra
 
radius - Variable in class org.jmol.symmetry.PointGroup
 
radius2 - Variable in class org.jmol.g3d.Cylinder3D
 
RADIUS_MAX - Static variable in class org.jmol.modelset.Atom
 
RADIUS_MAX - Static variable in class org.jmol.shape.Shape
 
RADIUS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for vector radius.
RADIUS_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Initial value of vector radius.
radiusData - Variable in class org.jmol.atomdata.AtomData
 
RadiusData - Class in org.jmol.atomdata
 
RadiusData() - Constructor for class org.jmol.atomdata.RadiusData
 
RadiusData(float, RadiusData.EnumType, EnumVdw) - Constructor for class org.jmol.atomdata.RadiusData
 
RadiusData(float[]) - Constructor for class org.jmol.atomdata.RadiusData
 
radiusData - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
radiusData - Variable in class org.jmol.modelset.MeasurementData
 
radiusData - Variable in class org.jmol.shape.Measures
 
RadiusData.EnumType - Enum in org.jmol.atomdata
 
RadiusData.EnumType() - Constructor for enum org.jmol.atomdata.RadiusData.EnumType
 
radiusHermites - Variable in class org.jmol.shapebio.BioShapeRenderer
 
radiusI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radiusP - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radiusSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
ramachandran - Static variable in class org.jmol.script.Token
 
random - Variable in class org.jmol.g3d.Graphics3D
 
random - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
random - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
random - Static variable in class org.jmol.script.Token
 
randomizeUnitVector(Vector3d) - Static method in class org.jmol.minimize.Util
 
randomPoint() - Static method in class org.jmol.shapespecial.Draw
 
randomPoint - Static variable in class org.jmol.shapespecial.Polyhedra
 
randomSeed - Variable in class org.jmol.jvxl.readers.Parameters
 
range - Static variable in class org.jmol.script.Token
 
range - Variable in class org.jmol.shapebio.BioShape
 
rangeAll - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeBohrOrAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
 
rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeSelected - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeselected - Static variable in class org.jmol.script.Token
 
rangeSelected - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
rasmol - Static variable in class org.jmol.script.Token
 
RASMOL - Static variable in class org.jmol.util.ColorEncoder
 
rasmolBinding - Variable in class org.jmol.viewer.ActionManager
 
RasmolBinding - Class in org.jmol.viewer.binding
 
RasmolBinding() - Constructor for class org.jmol.viewer.binding.RasmolBinding
 
rasmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
rasmolHeteroSetting - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
rasmolHydrogenSetting - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
rasmolOverrides - Static variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
rasmolScale - Static variable in class org.jmol.util.ColorEncoder
 
rasterCount - Variable in class org.jmol.g3d.Cylinder3D
 
rasterize(Platform3D, boolean) - Method in class org.jmol.g3d.Text3D
 
RAW_RGB - Static variable in class org.jmol.g3d.Graphics3D
 
RAW_RGB_INT - Static variable in class org.jmol.g3d.Colix3D
 
rd - Variable in class org.jmol.viewer.Viewer
 
rdLast - Variable in class org.jmol.shapespecial.Dots
 
rdVDW - Static variable in class org.jmol.shapesurface.Contact
 
read(char[]) - Method in class org.jmol.viewer.FileManager.ArrayDataReader
 
read(char[]) - Method in class org.jmol.viewer.FileManager.VectorDataReader
 
read() - Method in class org.openscience.jvxl.MonitorInputStream
 
read(byte[]) - Method in class org.openscience.jvxl.MonitorInputStream
 
read(byte[], int, int) - Method in class org.openscience.jvxl.MonitorInputStream
 
read3Vectors(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block
readableTypes - Static variable in class org.jmol.viewer.PropertyManager
 
readAllData - Variable in class org.jmol.jvxl.readers.Parameters
 
readAndSetVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readAparam() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
readArchive(String, boolean, int, boolean) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readArchive() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readArchiveHeader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readAtom(String[], boolean) - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
readAtomCountAndOrigin() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
readAtomCountAndSetNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readAtomData(float) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readAtomicOrbitalOrder() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readAtomicPos(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readAtomNames() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Reads the output coordinates section into a new AtomSet.
readAtoms(boolean) - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readAtoms() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
 
readAtoms() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
 
readAtoms() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readAtoms() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
readAtoms() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
readAtomsCartGeomThenCell() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
readAtomSet(String, boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readAtomsInAngstromCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readAtSign() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readBasisInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readBasisNormalized() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readBinaryHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readBonds(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
readBonds(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readBonds(int) - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readBonds() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readBonds() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
 
readBonds(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
 
readBrickLayer() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
readBuf(char[]) - Method in class org.jmol.viewer.FileManager.DataReader
 
readByte() - Method in class org.jmol.util.BinaryDocument
 
readByteArray(byte[]) - Method in class org.jmol.util.BinaryDocument
 
readByteArray(byte[], int, int) - Method in class org.jmol.util.BinaryDocument
 
readCalculationInfo(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readCalculationType() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readCellParam() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
readCellParam(boolean) - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
readCellParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readCellParams(boolean) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readCellThenAtomsCartesian() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
readCharges() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readCifData(BufferedReader) - Static method in class org.jmol.util.CifDataReader
 
readColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readColorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readConstraints() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readControlInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readCoord() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.quantum.AdfReader
Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.quantum.DgridReader
Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.simple.AmpacReader
Reads a set of coordinates
readCrystalInfo() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readCrystallographicCoords() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readData() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readData(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readData() - Method in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
readData() - Method in class org.jmol.util.CompoundDocument.CmpDocHeader
 
readData31(String, String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readData46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readDimensionality() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readDipole() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readDocument() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
readDocument() - Method in class org.jmol.adapter.readers.more.BinaryReader
 
readDots() - Method in class org.jmol.jvxl.readers.KinemageReader
 
readDouble() - Method in class org.jmol.util.BinaryDocument
 
readEFPInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readElementNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readEmbeddedScript() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
readEnergy() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
reader - Variable in class org.jmol.util.CifDataReader
A special tokenizer class for dealing with quoted strings in CIF files.
reader - Variable in class org.jmol.viewer.FileManager.FileReader
 
readerClosed - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readerSets - Static variable in class org.jmol.adapter.smarter.Resolver
 
readESym(boolean) - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readEventCount - Variable in class org.openscience.jvxl.MonitorInputStream
 
readExtents(int) - Method in class org.jmol.jvxl.readers.JaguarReader
read the extentx=, extenty=, extentz= lines and cache them then read the npts= line and construct the necessary data
readFile31() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readFile46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readFileData() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readFinalCell() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readFloat() - Method in class org.jmol.util.BinaryDocument
 
readFloatArray() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
readFragments() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readFreq() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
readFreqsAndModes() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.AdfReader
Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Reads the AtomSet and projected frequencies in the frequency section.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.QchemReader
Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.simple.AmpacReader
Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.simple.MopacReader
Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readFrequency() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readGeometryOptimization() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readGradient() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readGradients() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Reads the energy gradients section into a new AtomSet.
readHeader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readHeader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readHeader() - Method in class org.jmol.util.CompoundDocument
 
readInitialCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readInputAtoms() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readInputHeader() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readInputRecords() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readInt() - Method in class org.jmol.util.BinaryDocument
 
readJaguarMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readKeywords() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
readLatticeAbc() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readLatticeCart() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readLatticeVector(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
readLEInt() - Method in class org.jmol.util.BinaryDocument
 
readLELong() - Method in class org.jmol.util.BinaryDocument
 
readLengthUnit(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readLine() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
readLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
readLine() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readLine() - Method in interface org.jmol.api.JmolLineReader
 
readLine() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
readLine() - Method in class org.jmol.util.CifDataReader
 
readLine() - Method in class org.jmol.viewer.FileManager.ArrayDataReader
 
readLine() - Method in class org.jmol.viewer.FileManager.VectorDataReader
 
readLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readLineWithNewline() - Method in class org.jmol.adapter.smarter.LimitedLineReader
 
readLong() - Method in class org.jmol.util.BinaryDocument
 
readMagneticMoments() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readMdyn() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readMolecularOrbital() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readMolecularOrbital() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readMolecularOrbitalAnalysis(boolean) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
readMolecularOrbitals(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readMolecularOrbitals(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
readMolecularOrbitals - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readMolecularOrbitalVectors() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
readMOs() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readMOs(boolean, QchemReader.MOInfo[]) - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readMultipole(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
readNonCommentLine() - Method in class org.jmol.util.LimitedLineReader
 
readOrbitalData(boolean) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
readOutput() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readOutputAtoms() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readOutputCharges() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readOutputUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readParameters() - Method in class org.jmol.jvxl.readers.ApbsReader
 
readParameters() - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
readParameters() - Method in class org.jmol.jvxl.readers.CubeReader
 
readParameters() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
readParameters() - Method in class org.jmol.jvxl.readers.JaguarReader
nothing much here
readParameters() - Method in class org.jmol.jvxl.readers.JvxlReader
 
readParameters() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readParameters() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
 
readParameters() - Method in class org.jmol.jvxl.readers.PltFormattedReader
 
readParameters() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readParameters() - Method in class org.jmol.jvxl.readers.XplorReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Reads partial charges and assigns them only to the last atom set.
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Reads partial charges and assigns them only to the last atom set.
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.simple.AmpacReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readPhononFractionalCoord() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPhononFrequencies() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPhononTrajectories() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPhononUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPolygons() - Method in class org.jmol.jvxl.readers.KinemageReader
 
readPolygons() - Method in class org.jmol.jvxl.readers.MsmsReader
 
readPolygons() - Method in class org.jmol.jvxl.readers.ObjReader
 
readPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readPOSITION() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readPositionsAbs() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPositionsFrac() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPrimitiveMapping() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
create arrays that maps primitive atoms to conventional atoms in a 1:1 fashion.
readProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readProperty() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readPsiMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readQchemMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readResInfo(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readROHFonly - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
readSCFDone() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Interprets the SCF Done: section.
readSCFDone() - Method in class org.jmol.adapter.readers.quantum.PsiReader
Interprets the SCF Done: section.
readSecondOrderData() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
readShift() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readShort() - Method in class org.jmol.util.BinaryDocument
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readSpaceGroup() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readSpins() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readString(int) - Method in class org.jmol.util.BinaryDocument
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSurfaceData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readSymmetries() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readSymmetry() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Read the symmetry information and set the property.
readSymmetry() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
readThisModel - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
readTitleLines() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
readTotal() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Interpret a line starting with a line with "Total" in it.
readTotalAtomicCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readTransform() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readTransform() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readTransformationMatrix() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readUniqueAtoms() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readUnitCell() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
readUnitCell() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readUnnormalizedBasis() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readUnsignedShort() - Method in class org.jmol.util.BinaryDocument
 
readUserData(int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
readVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVectors() - Method in class org.jmol.jvxl.readers.KinemageReader
 
readVertices() - Method in class org.jmol.jvxl.readers.KinemageReader
 
readVertices() - Method in class org.jmol.jvxl.readers.MsmsReader
 
readVertices() - Method in class org.jmol.jvxl.readers.ObjReader
 
readVertices() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readVibFreqs() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVolumeFileSurfaceData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVolumePrimCell() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readVolumetricHeader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVoxelDataIndividually(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
realloc(int[]) - Method in class org.jmol.g3d.Cylinder3D
 
realloc(float[]) - Method in class org.jmol.g3d.Cylinder3D
 
reallocRasterArrays(int) - Method in class org.jmol.g3d.Triangle3D
 
reallocRgb16s(Rgb16[], int) - Method in class org.jmol.g3d.Triangle3D
 
rebond() - Method in class org.jmol.api.JmolViewer
 
rebond() - Method in class org.jmol.viewer.Viewer
 
rebond(boolean) - Method in class org.jmol.viewer.Viewer
 
rebond() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
recalc() - Method in class org.jmol.shape.Object2d
 
recalc() - Method in class org.jmol.shape.Text
 
recalcAltVertices - Variable in class org.jmol.shape.Mesh
 
reCalculate(BitSet, Matrix3f) - Method in class org.jmol.geodesic.EnvelopeCalculation
problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
recalculateLeadMidpointsAndWingVectors(int) - Method in class org.jmol.modelset.ModelCollection
 
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelset.Polymer
 
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
recalculatePositionDependentQuantities(BitSet, Matrix4f) - Method in class org.jmol.modelset.ModelSet
 
recallCommand(boolean) - Method in class org.jmol.console.AppletConsole.ControlEnterTextArea
 
recallCommand(boolean) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
Recall command history.
recentFiles - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
recentFilesAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
RecentFilesDialog - Class in org.openscience.jmol.app.jmolpanel
Manages a list of recently opened files.
RecentFilesDialog(Frame) - Constructor for class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
Creates a hidden recent files dialog
recordData(float) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
recordStatus(String) - Method in class org.jmol.viewer.StatusManager
 
recordTime(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
Rectangle - Class in org.jmol.util
 
Rectangle() - Constructor for class org.jmol.util.Rectangle
 
rectClip - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
rectRubber - Variable in class org.jmol.viewer.ActionManager
 
red - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
RED - Static variable in class org.jmol.g3d.Graphics3D
 
redo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
redoButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
redomove - Static variable in class org.jmol.script.Token
 
reduceFilename(String) - Static method in class org.jmol.viewer.ModelManager
 
reference - Variable in class org.jmol.modelset.TickInfo
 
reference - Static variable in class org.jmol.script.Token
 
referenceCenter - Variable in class org.jmol.export.___Exporter
 
referencePlaneOffset - Variable in class org.jmol.viewer.TransformManager
 
reformatDistanceIfSelected() - Method in class org.jmol.modelset.Measurement
 
reformatDistances() - Method in class org.jmol.shape.Measures
 
refresh(int, String) - Method in class org.jmol.api.JmolViewer
 
refresh() - Method in class org.jmol.modelset.Measurement
 
refresh() - Method in class org.jmol.script.ScriptEvaluator
 
refresh - Static variable in class org.jmol.script.Token
 
refresh() - Method in class org.jmol.viewer.RepaintManager
 
refresh(int, String) - Method in class org.jmol.viewer.Viewer
initiate a repaint/update sequence if it has not already been requested.
refreshing - Static variable in class org.jmol.script.Token
 
refreshing - Variable in class org.jmol.viewer.Viewer
 
refreshMeasures(boolean) - Method in class org.jmol.viewer.Viewer
 
refreshShapeTrajectories(int, BitSet, Matrix4f) - Method in class org.jmol.viewer.ShapeManager
 
registerAllValues(StateManager.GlobalSettings, boolean) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
rehash() - Method in class org.jmol.util.Int2IntHash
 
reinitializeLightingAndColor() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
RELATIVE_DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
RELATIVE_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
release() - Method in interface org.jmol.api.AtomIndexIterator
 
release() - Method in class org.jmol.bspt.CubeIterator
nulls internal references
release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
releaseBufferForClearing() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
releaseBuffers() - Method in class org.jmol.g3d.Graphics3D
 
releaseBuffers() - Method in class org.jmol.g3d.Platform3D
 
RELEASED - Static variable in class org.jmol.viewer.binding.Binding
 
releaseModelSet() - Method in class org.jmol.modelset.AtomCollection
 
releaseModelSet() - Method in class org.jmol.modelset.BondCollection
 
releaseModelSet() - Method in class org.jmol.modelset.ModelCollection
 
releaseModelSet() - Method in class org.jmol.modelset.ModelSet
 
releaseScreenImage() - Method in class org.jmol.api.JmolViewer
 
releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
 
releaseScreenImage() - Method in class org.jmol.viewer.Viewer
 
releaseShape(int) - Method in class org.jmol.viewer.ShapeManager
 
remapColors(ColorEncoder, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
remaps colors based on a new color scheme or translucency level
remark290() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
remark350() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
rememberCheckbox(String, JMenuItem) - Method in class org.jmol.popup.SimplePopup
 
remoteAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
remoteAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
remove - Static variable in class org.jmol.script.Token
 
remove(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
removeAll(Object) - Method in class org.jmol.popup.SimplePopup
 
removeAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
removeBinding(Iterator<String>, String) - Method in class org.jmol.viewer.binding.Binding
 
removeCommand() - Method in class org.jmol.util.CommandHistory
 
removeCommand(int) - Method in class org.jmol.util.CommandHistory
 
removeCommand() - Method in class org.jmol.viewer.Viewer
Removes one command from the command history
removeJmolParameter(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
removeMenuItem(Object, int) - Method in class org.jmol.popup.SimplePopup
 
removeMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.export.JmolFileDropper
 
removeProteinStructure(int, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
 
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
 
removeUnnecessaryBonds(Atom, boolean) - Method in class org.jmol.modelset.BondCollection
 
removeUserVariable(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
removeUserVariable(String) - Method in class org.jmol.viewer.Viewer
 
renameMenu(Object, String) - Method in class org.jmol.popup.SimplePopup
 
render(short, short, boolean, boolean, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Cylinder3D
 
render(int[], boolean, int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.g3d.Sphere3D
 
render() - Method in class org.jmol.shape.AxesRenderer
 
render() - Method in class org.jmol.shape.BallsRenderer
 
render() - Method in class org.jmol.shape.BbcageRenderer
 
render(int, Point3f[], Point3f[], int, int, int, float) - Method in class org.jmol.shape.CageRenderer
 
render() - Method in class org.jmol.shape.EchoRenderer
 
render() - Method in class org.jmol.shape.FrankRenderer
 
render() - Method in class org.jmol.shape.HalosRenderer
 
render() - Method in class org.jmol.shape.HoverRenderer
 
render() - Method in class org.jmol.shape.LabelsRenderer
 
render() - Method in class org.jmol.shape.MeasuresRenderer
 
render() - Method in class org.jmol.shape.MeshRenderer
 
render(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.shape.ShapeRenderer
 
render() - Method in class org.jmol.shape.ShapeRenderer
 
render() - Method in class org.jmol.shape.StarsRenderer
 
render() - Method in class org.jmol.shape.SticksRenderer
 
render(JmolRendererInterface, float, float, boolean, float[]) - Method in class org.jmol.shape.Text
 
render() - Method in class org.jmol.shape.UccageRenderer
 
render() - Method in class org.jmol.shapebio.BioShapeRenderer
 
render() - Method in class org.jmol.shapespecial.DipolesRenderer
 
render() - Method in class org.jmol.shapespecial.DotsRenderer
 
render() - Method in class org.jmol.shapespecial.DrawRenderer
 
render() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
render() - Method in class org.jmol.shapespecial.GeoSurfaceRenderer
 
render() - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
render() - Method in class org.jmol.shapespecial.VectorsRenderer
 
render() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
render() - Method in class org.jmol.shapesurface.MolecularOrbitalRenderer
 
render(Graphics3D, ModelSet, boolean) - Method in class org.jmol.viewer.RepaintManager
 
render() - Method in class org.jmol.viewer.Viewer
 
render1(Atom) - Method in class org.jmol.shape.HalosRenderer
 
render1(Mesh) - Method in class org.jmol.shape.MeshRenderer
 
render1(Atom, short) - Method in class org.jmol.shape.StarsRenderer
 
render1(int) - Method in class org.jmol.shape.UccageRenderer
 
render1() - Method in class org.jmol.shapebio.CartoonRenderer
 
render1() - Method in class org.jmol.shapebio.RocketsRenderer
 
render1() - Method in class org.jmol.shapebio.StrandsRenderer
 
render1(Dots) - Method in class org.jmol.shapespecial.DotsRenderer
 
render1(Mesh) - Method in class org.jmol.shapespecial.DrawRenderer
 
render1(Atom, Object[]) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
render1(Polyhedra.Polyhedron, short, Point3i[]) - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
render1(Graphics3D, ModelSet, boolean) - Method in class org.jmol.viewer.RepaintManager
 
render1(Object, Object, int, int) - Method in class org.jmol.viewer.Viewer
 
render1Strand(Point3i[]) - Method in class org.jmol.shapebio.StrandsRenderer
 
render2(boolean) - Method in class org.jmol.shape.MeshRenderer
 
render2(boolean) - Method in class org.jmol.shapespecial.DrawRenderer
 
render2(boolean) - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
render2Strand(boolean, float, float) - Method in class org.jmol.shapebio.MeshRibbonRenderer
 
renderAngle(boolean) - Method in class org.jmol.shape.MeasuresRenderer
 
renderArc(Point3f, int, int) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderArcs(Point3f) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderArrowHead(Point3f, Point3f, float, boolean, boolean, boolean) - Method in class org.jmol.shapespecial.DrawRenderer
 
renderArrowHeads - Variable in class org.jmol.shapebio.RocketsRenderer
 
renderAsRockets - Variable in class org.jmol.shapebio.CartoonRenderer
 
renderAxes() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderBackground() - Method in interface org.jmol.api.JmolRendererInterface
 
renderBackground() - Method in class org.jmol.export.Export3D
 
renderBackground() - Method in class org.jmol.g3d.Graphics3D
 
renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
 
renderBall() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.BackboneRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.CartoonRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.MeshRibbonRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.RibbonsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.RocketsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.StrandsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.TraceRenderer
 
renderBits(short, short, boolean, boolean, byte, int, float, float, float, float, float, float) - Method in class org.jmol.g3d.Cylinder3D
 
renderBond() - Method in class org.jmol.shape.SticksRenderer
 
renderCone(short, boolean, byte, int, float, float, float, float, float, float, boolean, boolean) - Method in class org.jmol.g3d.Cylinder3D
 
renderCone(int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderContourLines() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderConvex(short, FastBitSet, int) - Method in class org.jmol.shapespecial.DotsRenderer
generic renderer -- dots and geosurface
renderConvex(short, FastBitSet, int) - Method in class org.jmol.shapespecial.GeoSurfaceRenderer
 
renderDipoleVector(Dipole) - Method in class org.jmol.shapespecial.DipolesRenderer
 
renderDistance(boolean) - Method in class org.jmol.shape.MeasuresRenderer
 
renderDots(int) - Method in class org.jmol.shapespecial.DotsRenderer
also called by GeoSurface when in motion
renderDots(Point3f) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderEdges - Variable in class org.jmol.shapebio.CartoonRenderer
 
renderEllipsoid(Ellipsoids.Ellipsoid) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderers - Variable in class org.jmol.viewer.RepaintManager
 
renderFlatEndcap(boolean) - Method in class org.jmol.g3d.Cylinder3D
 
renderFlatEndcapPrecisely(boolean) - Method in class org.jmol.g3d.Cylinder3D
 
renderFrameTitle(String) - Method in class org.jmol.shape.EchoRenderer
 
renderHandles() - Method in class org.jmol.shapespecial.DrawRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderHermiteConic(int, boolean) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderHermiteCylinder(Point3i[], int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderHermiteRibbon(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Hermite3D
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderHermiteRope(boolean, int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Hermite3D
 
renderInfo(SymmetryInterface) - Method in class org.jmol.shape.UccageRenderer
 
renderInfo() - Method in class org.jmol.shapespecial.DrawRenderer
 
renderInfo() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderInfo() - Method in class org.jmol.shapesurface.MolecularOrbitalRenderer
 
rendering - Variable in class org.jmol.jvxl.data.JvxlData
 
renderLabel(String, float, float, float, float, float) - Method in class org.jmol.shape.AxesRenderer
 
renderLarge() - Method in class org.jmol.g3d.Sphere3D
 
renderLenotisWesthofEdges(NucleicMonomer, short) - Method in class org.jmol.shapebio.CartoonRenderer
 
renderLine(Point3f, Point3f, int, Point3i, Point3i, boolean) - Method in class org.jmol.shape.FontLineShapeRenderer
 
renderLonePair(boolean) - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderMeasurement(int, Measurement, boolean) - Method in class org.jmol.shape.MeasuresRenderer
 
renderMesh(int, int) - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
RenderMode - Variable in class org.openscience.jmol.app.webexport.Molecules
 
RenderMode - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
renderNormals() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderNucleic() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderNucleicBaseStep(NucleicMonomer, short, Point3i) - Method in class org.jmol.shapebio.CartoonRenderer
 
renderOffScreen(String, Font3D, Object, int, int, int) - Method in interface org.jmol.api.ApiPlatform
 
renderOffScreen(String, Font3D, Object, int, int, int) - Static method in class org.jmol.awt.Image
 
renderOffScreen(String, Font3D, Object, int, int, int) - Method in class org.jmol.awt.Platform
 
renderParallelPair(boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Hermite3D
 
renderPending() - Method in class org.jmol.shapebio.RocketsRenderer
 
renderPendingMeasurement(MeasurementPending) - Method in class org.jmol.shape.MeasuresRenderer
 
renderPendingRocketSegment(int, Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.shapebio.RocketsRenderer
 
renderPendingSheet(Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.shapebio.RocketsRenderer
 
renderPendingWithCursor(int, MeasurementPending) - Method in class org.jmol.shape.MeasuresRenderer
 
renderPoints() - Method in class org.jmol.shape.MeshRenderer
 
renderPoints() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderQuadrant(int, int) - Method in class org.jmol.g3d.Sphere3D
 
renderQuadrantClipped(int, int, int) - Method in class org.jmol.g3d.Sphere3D
 
renderQuadrantUnclipped(int, int, int) - Method in class org.jmol.g3d.Sphere3D
 
renderRing5() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderRing6() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderRockets() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderScreenImage(JmolViewer, Object, Object) - Method in interface org.jmol.api.ApiPlatform
 
renderScreenImage(Object, int, int) - Method in class org.jmol.api.JmolSimpleViewer
 
renderScreenImage(Object, Object, int, int) - Method in class org.jmol.api.JmolViewer
an added class for rendering stereo in two independent applets
renderScreenImage(Object, Object, Object) - Method in class org.jmol.api.JmolViewer
old -- not used in 12.2
renderScreenImage(JmolViewer, Object, Object) - Static method in class org.jmol.awt.Display
legacy apps will use this
renderScreenImage(JmolViewer, Object, Object) - Method in class org.jmol.awt.Platform
legacy apps will use this
renderScreenImage(Object, Object, int, int) - Method in class org.jmol.viewer.Viewer
 
renderScreenImage(Object, int, int) - Method in class org.jmol.viewer.Viewer
 
renderShapeClipped(int[]) - Method in class org.jmol.g3d.Sphere3D
 
renderShapeUnclipped(int[]) - Method in class org.jmol.g3d.Sphere3D
 
renderSimpleLabel(JmolRendererInterface, Font3D, String, short, short, float[], int, int, int, int, float, int, boolean, short, boolean) - Static method in class org.jmol.shape.Text
 
renderSpecialSegment(Monomer, short, short) - Method in class org.jmol.shapebio.RocketsRenderer
 
renderSphericalEndcaps() - Method in class org.jmol.g3d.Cylinder3D
 
renderSurface(FastBitSet) - Method in class org.jmol.shapespecial.GeoSurfaceRenderer
 
renderTorsion(boolean) - Method in class org.jmol.shape.MeasuresRenderer
 
renderTriangle() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.shape.MeshRenderer
 
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderVector(Atom) - Method in class org.jmol.shapespecial.VectorsRenderer
 
renderWireframe - Variable in class org.jmol.shape.SticksRenderer
 
renderXyArrow(int) - Method in class org.jmol.shapespecial.DrawRenderer
 
repaint(Object) - Method in interface org.jmol.api.ApiPlatform
 
repaint(Object) - Static method in class org.jmol.awt.Display
 
repaint(Object) - Method in class org.jmol.awt.Platform
 
repaint() - Method in class org.jmol.viewer.Viewer
 
repaintClock() - Method in class org.jmol.applet.AppletWrapper
 
repaintDone() - Method in class org.jmol.viewer.AnimationManager
 
repaintDone() - Method in class org.jmol.viewer.RepaintManager
 
RepaintManager - Class in org.jmol.viewer
 
RepaintManager(Viewer, ShapeManager) - Constructor for class org.jmol.viewer.RepaintManager
 
repaintManager - Variable in class org.jmol.viewer.Viewer
 
repaintPending - Variable in class org.jmol.viewer.RepaintManager
 
repaintwaitms - Static variable in class org.jmol.script.Token
 
repaintWaitMs - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
repeatCheckBox - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
replace - Static variable in class org.jmol.script.Token
 
replace(int, int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
replaceAllCharacters(String, String, String) - Static method in class org.jmol.util.TextFormat
Does a clean replace of any of the characters in str with strTo If strTo contains strFrom, then only a single pass is done.
replaceAllCharacters(String, String, char) - Static method in class org.jmol.util.TextFormat
Does a clean replace of any of the characters in str with chrTo If strTo contains strFrom, then only a single pass is done.
replaceCommand(Token) - Method in class org.jmol.script.ScriptCompiler
 
replaceCommand(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
Replaces current command on script.
replaceQuotedStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
 
replaceStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
 
report(String, boolean) - Method in class org.jmol.minimize.Minimizer
 
report(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
reportAll - Variable in class org.jmol.shape.Sticks
 
reportSelection(String) - Method in class org.jmol.viewer.Viewer
 
repositionWindow(String, Component, int, int, boolean) - Method in class org.jmol.export.history.HistoryFile
Uses the informations in the history to reposition the window.
repositionWindow(String, Component) - Method in class org.jmol.export.history.HistoryFile
Uses the informations in the history to reposition the window.
requestFocusInWindow(Object) - Method in interface org.jmol.api.ApiPlatform
 
requestFocusInWindow(Object) - Static method in class org.jmol.awt.Display
 
requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
 
requestRepaintAndWait() - Method in class org.jmol.viewer.RepaintManager
 
requestRepaintAndWait() - Method in class org.jmol.viewer.Viewer
 
REQUIRE_PROGRESSBAR - Static variable in class org.jmol.applet.Jmol
 
reset() - Method in class org.jmol.bspt.Bspt
 
reset() - Method in class org.jmol.script.ScriptEvaluator
 
reset - Static variable in class org.jmol.script.Token
 
reset() - Method in class org.jmol.util.BoxInfo
 
reset(int) - Method in class org.jmol.util.CommandHistory
Resets instance.
reset() - Method in class org.jmol.viewer.FileManager.ArrayDataReader
 
reset() - Method in class org.jmol.viewer.FileManager.VectorDataReader
 
reset(boolean) - Method in class org.jmol.viewer.Viewer
 
reset() - Method in class org.openscience.jvxl.MonitorInputStream
 
resetAromatic() - Method in class org.jmol.modelset.BondCollection
 
resetAromatic() - Method in class org.jmol.viewer.Viewer
 
resetAxes() - Method in class org.jmol.modelsetbio.ProteinStructure
 
resetAxisCoordinates() - Method in class org.jmol.shape.SticksRenderer
 
resetBioshapes(BitSet) - Method in class org.jmol.viewer.ShapeManager
 
resetBioshapes(BitSet) - Method in class org.jmol.viewer.Viewer
 
resetBoundCount() - Method in class org.jmol.modelset.Model
 
resetDefaults(String[]) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
resetElementColors() - Method in class org.jmol.viewer.ColorManager
 
resetError() - Method in class org.jmol.viewer.Viewer
 
resetFlag - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
resetForMapping(boolean) - Method in class org.jmol.jvxl.readers.Parameters
reset some parameters at the "MAP" keyword
resetFrankMenu() - Method in class org.jmol.popup.JmolPopup
 
resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
 
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
resetIndexPlane(int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
resetIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
resetKey - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
resetMeasurement() - Method in class org.jmol.viewer.ActionManager
 
resetMolecules() - Method in class org.jmol.modelset.BondCollection
 
resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager
something has arisen that requires resetting of the navigation point.
resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager11
 
resetNeeded - Variable in class org.jmol.multitouch.ActionManagerMT
 
resetObjects() - Method in class org.jmol.shapespecial.Draw
 
resetParameterStringValue(String, StateManager.GlobalSettings) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
resetPlane(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
resetShapes() - Method in class org.jmol.viewer.ShapeManager
 
resetShapes() - Method in class org.jmol.viewer.Viewer
 
resetSlab() - Method in class org.jmol.util.MeshSurface
 
resetTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
resetVoxelData(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
resetXYCenter(int, int) - Method in class org.jmol.viewer.TransformManager
 
residue - Static variable in class org.jmol.script.Token
 
residueChar - Variable in class org.jmol.smiles.SmilesAtom
 
residueName - Variable in class org.jmol.smiles.SmilesAtom
 
residueSpecCodeGenerated - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
resizeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
resizeByteArray(byte[], int) - Method in class org.jmol.export.image.PngEncoder
Increase or decrease the length of a byte array.
resizeDisplay(int, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
resizeImage(int, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
resizeInnerPanel(String) - Method in interface org.jmol.api.JmolStatusListener
 
resizeInnerPanel(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
resno - Static variable in class org.jmol.script.Token
 
resolution - Variable in class org.jmol.jvxl.readers.Parameters
 
resolution - Static variable in class org.jmol.script.Token
 
resolveEntity(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.DummyResolver
 
resolveEntity(String, String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
resolveEntity(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
Resolver - Class in org.jmol.adapter.smarter
 
Resolver() - Constructor for class org.jmol.adapter.smarter.Resolver
 
Resolver - Class in org.jmol.modelsetbio
 
Resolver() - Constructor for class org.jmol.modelsetbio.Resolver
 
Resolver.BondSorter - Class in org.jmol.modelsetbio
 
Resolver.BondSorter() - Constructor for class org.jmol.modelsetbio.Resolver.BondSorter
 
resourceName - Variable in class org.jmol.quantum.MepCalculation
 
resources - Variable in class org.jmol.export._IdtfExporter
 
restorativeForceAndAngleRadians(Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndDistance(Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndOutOfPlaneAngleRadians(Vector3d, Vector3d, Vector3d, Vector3d, Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndTorsionAngleRadians(Vector3d, Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
restore() - Method in class org.jmol.script.ScriptEvaluator
 
restore - Static variable in class org.jmol.script.Token
 
restore() - Method in class org.jmol.viewer.StateManager.Connections
 
restore(float, boolean) - Method in class org.jmol.viewer.StateManager.Orientation
 
restoreBonds(String) - Method in class org.jmol.viewer.StateManager
 
restoreBonds(String) - Method in class org.jmol.viewer.Viewer
 
restoreCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
 
restoreCoordinates() - Method in class org.jmol.minimize.Minimizer
 
restoreModelOrientation(int) - Method in class org.jmol.viewer.Viewer
 
restoreModelRotation(int) - Method in class org.jmol.viewer.Viewer
 
restoreOrientation(String, float, boolean) - Method in class org.jmol.viewer.StateManager
 
restoreOrientation(String, float) - Method in class org.jmol.viewer.Viewer
 
restorePopupMenu() - Method in class org.jmol.popup.JmolPopup
 
restorePopupMenu() - Method in class org.jmol.popup.SimplePopup
 
restoreRotation(String, float) - Method in class org.jmol.viewer.Viewer
 
restoreScriptContext(ScriptContext, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
restoreSelection(String) - Method in class org.jmol.viewer.StateManager
 
restoreSelection(String) - Method in class org.jmol.viewer.Viewer
 
restrict() - Method in class org.jmol.script.ScriptEvaluator
 
restrict - Static variable in class org.jmol.script.Token
 
restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
RESU - Static variable in class org.jmol.util.ColorEncoder
 
resume - Static variable in class org.jmol.script.Token
 
resumeAnimation() - Method in class org.jmol.viewer.AnimationManager
 
resumeButton - Variable in class org.jmol.console.ScriptEditor
 
resumePausedExecution() - Method in class org.jmol.script.ScriptEvaluator
 
resumeScriptExecution() - Method in class org.jmol.viewer.Viewer
 
returnCmd(ScriptVariable) - Method in class org.jmol.script.ScriptEvaluator
 
returncmd - Static variable in class org.jmol.script.Token
 
returnToken() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
returnValue - Variable in class org.jmol.script.ScriptFunction
 
reverse - Static variable in class org.jmol.script.Token
 
reverseAnimation() - Method in class org.jmol.viewer.AnimationManager
 
reverseChirality(String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
reverseChirality(String) - Method in class org.jmol.smiles.SmilesMatcher
 
reversecolor - Static variable in class org.jmol.script.Token
 
revNumber - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
rewind - Static variable in class org.jmol.script.Token
 
REWIND - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
rewindAnimation() - Method in class org.jmol.viewer.AnimationManager
 
rfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
rFill(StringBuffer, String, String) - Static method in class org.jmol.util.TextFormat
 
rgb - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
rgb - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
rgb(int, int, int) - Static method in class org.jmol.g3d.Shade3D
 
Rgb16 - Class in org.jmol.g3d
 
Rgb16() - Constructor for class org.jmol.g3d.Rgb16
 
Rgb16(int) - Constructor for class org.jmol.g3d.Rgb16
 
rgb16sE - Variable in class org.jmol.g3d.Triangle3D
 
rgb16sGouraud - Variable in class org.jmol.g3d.Triangle3D
 
rgb16sW - Variable in class org.jmol.g3d.Triangle3D
 
rgb16t1 - Variable in class org.jmol.g3d.Triangle3D
 
rgb16t2 - Variable in class org.jmol.g3d.Triangle3D
 
rgb2 - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
rgbColorModel - Static variable in class org.jmol.awt.Image
 
rgbFractionalFromArgb(int, char) - Static method in class org.jmol.export.___Exporter
 
rgbFractionalFromColix(short, char) - Method in class org.jmol.export.___Exporter
 
rgbModel - Static variable in class org.jmol.export.image.ImageEncoder
 
rgbPixels - Variable in class org.jmol.export.image.GifEncoder
 
RGBtoHSL(float, float, float, float[]) - Static method in class org.jmol.util.ColorEncoder
 
rhoMin - Variable in class org.jmol.quantum.NciCalculation
 
rhoMolecules - Variable in class org.jmol.quantum.NciCalculation
 
rhoParam - Variable in class org.jmol.quantum.NciCalculation
 
rhoPlot - Variable in class org.jmol.quantum.NciCalculation
 
ribbon - Static variable in class org.jmol.script.Token
 
ribbonaspectratio - Static variable in class org.jmol.script.Token
 
ribbonAspectRatio - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ribbonborder - Static variable in class org.jmol.script.Token
 
ribbonBorder - Variable in class org.jmol.shapebio.BioShapeRenderer
 
ribbonBorder - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ribbonBottomScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
 
Ribbons - Class in org.jmol.shapebio
 
Ribbons() - Constructor for class org.jmol.shapebio.Ribbons
 
RibbonsRenderer - Class in org.jmol.shapebio
 
RibbonsRenderer() - Constructor for class org.jmol.shapebio.RibbonsRenderer
 
ribbonTopScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
 
right - Static variable in class org.jmol.script.Token
 
RIGHT - Static variable in class org.jmol.viewer.binding.Binding
 
rightAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
rightbrace - Static variable in class org.jmol.script.Token
 
rightDifference(Quaternion) - Method in class org.jmol.util.Quaternion
 
rightOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
rightparen - Static variable in class org.jmol.script.Token
 
rightPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
rightsquare - Static variable in class org.jmol.script.Token
 
ring5OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
ring5Points - Variable in class org.jmol.shapebio.CartoonRenderer
 
ring5Screens - Variable in class org.jmol.shapebio.CartoonRenderer
 
ring6OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
ring6Points - Variable in class org.jmol.shapebio.CartoonRenderer
 
ring6Screens - Variable in class org.jmol.shapebio.CartoonRenderer
 
ringBonds - Variable in class org.jmol.smiles.SmilesParser
 
ringConnections - Variable in class org.jmol.smiles.SmilesSearch
 
ringConnectivity - Variable in class org.jmol.smiles.SmilesAtom
 
ringCounts - Variable in class org.jmol.smiles.SmilesSearch
 
ringData - Variable in class org.jmol.smiles.SmilesSearch
 
ringDataMax - Variable in class org.jmol.smiles.SmilesSearch
 
ringMembership - Variable in class org.jmol.smiles.SmilesAtom
 
ringSets - Variable in class org.jmol.smiles.SmilesGenerator
 
ringSets - Variable in class org.jmol.smiles.SmilesSearch
 
ringSize - Variable in class org.jmol.smiles.SmilesAtom
 
rmaxx - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rmaxy - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rmaxz - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rminx - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rminy - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rminz - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rna - Static variable in class org.jmol.script.Token
 
rnl - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
rocket - Static variable in class org.jmol.script.Token
 
rocketbarrels - Static variable in class org.jmol.script.Token
 
rocketBarrels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Rockets - Class in org.jmol.shapebio
 
Rockets() - Constructor for class org.jmol.shapebio.Rockets
 
RocketsRenderer - Class in org.jmol.shapebio
 
RocketsRenderer() - Constructor for class org.jmol.shapebio.RocketsRenderer
 
ROOT2 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
ROOT3 - Static variable in class org.jmol.adapter.readers.quantum.JaguarReader
 
ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
 
rootDir - Variable in class org.openscience.chimetojmol.ChimePanel
 
rootEntry - Variable in class org.jmol.util.CompoundDocument
 
rootPickingStyle - Variable in class org.jmol.viewer.ActionManager
 
rotate(boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
rotate - Static variable in class org.jmol.script.Token
 
rotate45 - Static variable in class org.jmol.script.Token
 
ROTATE_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
ROTATE_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
rotateAboutPointsInternal(Point3f, Point3f, float, float, boolean, boolean, BitSet, boolean, Vector3f, List<Point3f>) - Method in class org.jmol.viewer.TransformManager
 
rotateAboutPointsInternal(Point3f, Point3f, float, float, boolean, BitSet, Vector3f, List<Point3f>) - Method in class org.jmol.viewer.Viewer
 
rotateArcBall(float, float, float) - Method in class org.jmol.viewer.TransformManager
 
rotateArcBall(int, int, float) - Method in class org.jmol.viewer.Viewer
 
rotateAxisAngle(Vector3f, float) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngle(AxisAngle4f, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleAtCenter(Point3f, Vector3f, float, float, boolean, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleAtCenter(Point3f, Vector3f, float, float, boolean, BitSet) - Method in class org.jmol.viewer.Viewer
 
rotateAxisAngleRadiansFixed(float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleRadiansInternal(float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateBondIndex - Variable in class org.jmol.viewer.Viewer
 
rotateEllipsoid(int, Point3f, Vector3f[], Point3f, Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
rotateEllipsoid(int, Point3f, Vector3f[], UnitCell, Point3f, Point3f) - Method in class org.jmol.symmetry.SpaceGroup
 
rotateEllipsoid(int, Point3f, Vector3f[], Point3f, Point3f) - Method in class org.jmol.symmetry.Symmetry
 
rotateEllipsoid(Point3f, Vector3f[], UnitCell, Point3f, Point3f) - Method in class org.jmol.symmetry.SymmetryOperation
 
rotateFront() - Method in class org.jmol.api.JmolViewer
 
rotateFront() - Method in class org.jmol.viewer.TransformManager
 
rotateFront() - Method in class org.jmol.viewer.Viewer
 
rotatePoint(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
rotatePoint(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
rotatePrev1 - Variable in class org.jmol.viewer.Viewer
 
rotatePrev2 - Variable in class org.jmol.viewer.Viewer
 
rotateSelected - Static variable in class org.jmol.script.Token
 
rotateSelected(float, float, BitSet) - Method in class org.jmol.viewer.Viewer
 
rotateX(int) - Method in class org.jmol.api.JmolViewer
 
rotateX(float) - Method in class org.jmol.api.JmolViewer
 
rotateX(float) - Method in class org.jmol.viewer.TransformManager
 
rotateX(float) - Method in class org.jmol.viewer.Viewer
 
rotateX(int) - Method in class org.jmol.viewer.Viewer
 
rotateXRadians(float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateXYBy(float, float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateXYBy(float, float) - Method in class org.jmol.viewer.Viewer
 
rotateY(int) - Method in class org.jmol.api.JmolViewer
 
rotateY(float) - Method in class org.jmol.api.JmolViewer
 
rotateY(float) - Method in class org.jmol.viewer.TransformManager
 
rotateY(float) - Method in class org.jmol.viewer.Viewer
 
rotateY(int) - Method in class org.jmol.viewer.Viewer
 
rotateYRadians(float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateZ(float) - Method in class org.jmol.api.JmolViewer
 
rotateZ(float) - Method in class org.jmol.viewer.TransformManager
 
rotateZ(float) - Method in class org.jmol.viewer.Viewer
 
rotateZBy(int, int, int) - Method in class org.jmol.viewer.TransformManager
 
rotateZBy(int, int, int) - Method in class org.jmol.viewer.Viewer
 
rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
 
rotation - Static variable in class org.jmol.script.Token
 
rotation - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
Rotation - Class in org.jmol.symmetry
 
Rotation() - Constructor for class org.jmol.symmetry.Rotation
 
Rotation(String, String) - Constructor for class org.jmol.symmetry.Rotation
 
rotationAxis - Variable in class org.jmol.shapesurface.LcaoCartoon
 
rotationAxis - Variable in class org.jmol.viewer.TransformManager
 
rotationCenterDefault - Variable in class org.jmol.viewer.TransformManager
 
rotationMatrix - Variable in class org.jmol.viewer.StateManager.Orientation
 
rotationOrder - Variable in class org.jmol.symmetry.Translation
 
rotationradius - Static variable in class org.jmol.script.Token
 
rotationRadius - Variable in class org.jmol.viewer.StateManager.Orientation
 
rotationRadiusDefault - Variable in class org.jmol.viewer.TransformManager
 
rotationRadiusDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
rotationRate - Variable in class org.jmol.viewer.TransformManager
 
rotationShift12ths - Variable in class org.jmol.symmetry.Translation
 
rotationTerms - Variable in class org.jmol.symmetry.HallInfo
 
rotCode - Variable in class org.jmol.symmetry.Rotation
 
round(double) - Static method in class org.jmol.export.___Exporter
 
round(Tuple3f) - Static method in class org.jmol.export.___Exporter
 
route - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
row - Static variable in class org.jmol.script.Token
 
ROYGB - Static variable in class org.jmol.util.ColorEncoder
 
rpower - Static variable in class org.jmol.quantum.NciCalculation
 
rScaled - Variable in class org.jmol.g3d.Rgb16
 
rubberband - Static variable in class org.jmol.script.Token
 
rubberbandSelectionMode - Variable in class org.jmol.viewer.ActionManager
 
run() - Method in class org.jmol.applet.ClassPreloader
 
run() - Method in class org.jmol.applet.TickerThread
 
run() - Method in class org.jmol.applet.WrappedAppletLoader
 
run() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
run() - Method in class org.jmol.minimize.Minimizer.MinimizationThread
 
run() - Method in class org.jmol.script.ParallelProcessor.RunProcess
 
run() - Method in class org.jmol.viewer.ActionManager.HoverWatcher
 
run() - Method in class org.jmol.viewer.ActionManager.TimeoutThread
 
run() - Method in class org.jmol.viewer.AnimationManager.AnimationThread
 
run() - Method in class org.jmol.viewer.FileManager.DOMReader
 
run() - Method in class org.jmol.viewer.FileManager.FileReader
 
run() - Method in class org.jmol.viewer.FileManager.FilesReader
 
run() - Method in class org.jmol.viewer.ScriptManager.CommandWatcher
 
run() - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
run() - Method in class org.jmol.viewer.TransformManager.MotionThread
 
run() - Method in class org.jmol.viewer.TransformManager.SpinThread
 
run() - Method in class org.jmol.viewer.TransformManager.VibrationThread
 
run() - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog.PageLoader
 
run() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ExecuteCommandThread
 
run() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
run() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
 
run() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JsonNioServerThread
 
run() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JsonNioThread
 
run() - Method in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog.PageLoader
 
runAllProcesses(Viewer, boolean) - Method in class org.jmol.script.ParallelProcessor
 
runButton - Variable in class org.jmol.console.JmolConsole
 
runButton - Variable in class org.jmol.console.ScriptEditor
 
runFunction(ScriptFunction, String, List<ScriptVariable>, ScriptVariable, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
runFunction(ScriptFunction, List<ScriptVariable>, ScriptVariable) - Method in class org.jmol.script.ScriptEvaluator
 
runNextScript() - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
runPovCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
runProcess(ParallelProcessor.Process, ShapeManager) - Method in class org.jmol.script.ParallelProcessor
 
runScript(String, StringBuffer) - Method in class org.jmol.script.ScriptEvaluator
runs a script and sends selected output to a provided StringBuffer
runScript(String) - Method in class org.jmol.script.ScriptEvaluator
 
runScript(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
runScriptImmediately(String) - Method in class org.jmol.viewer.Viewer
 
runStatus - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
RWB - Static variable in class org.jmol.util.ColorEncoder
 

S

s0 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
s1 - Variable in class org.jmol.shape.SticksRenderer
 
s1 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
s10 - Static variable in class org.jmol.symmetry.PointGroup
 
s12 - Static variable in class org.jmol.symmetry.PointGroup
 
s2 - Variable in class org.jmol.shape.SticksRenderer
 
s2 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
s3 - Static variable in class org.jmol.symmetry.PointGroup
 
s4 - Static variable in class org.jmol.symmetry.PointGroup
 
s5 - Static variable in class org.jmol.symmetry.PointGroup
 
s6 - Static variable in class org.jmol.symmetry.PointGroup
 
s8 - Static variable in class org.jmol.symmetry.PointGroup
 
safeTruncate(float, int) - Static method in class org.jmol.util.TextFormat
 
sameAs(int[], Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
sameAs(int[], Point3fi[], int, int) - Method in class org.jmol.modelset.Measurement
 
sameAs(int, int) - Method in class org.jmol.modelset.Measurement
 
sampleModelBitMasks - Static variable in class org.jmol.awt.Image
 
sasurface - Static variable in class org.jmol.script.Token
 
SAT - Variable in class org.jmol.util.CompoundDocument
 
save() - Method in class org.jmol.export.history.HistoryFile
Saves properties to the history file.
save() - Method in class org.jmol.script.ScriptEvaluator
 
save - Static variable in class org.jmol.script.Token
 
SAVE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
save() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
save() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
saveAmbient - Variable in class org.jmol.g3d.Graphics3D
 
saveBonds(String) - Method in class org.jmol.viewer.StateManager
 
saveBonds(String) - Method in class org.jmol.viewer.Viewer
 
saveButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
saveButton - Variable in class org.openscience.jmol.app.webexport.Molecules
 
saveButton - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
saveButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
saveChooser - Static variable in class org.jmol.export.dialog.Dialog
 
saveChooser - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
saveCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
 
saveCoordinates() - Method in class org.jmol.minimize.Minimizer
 
saveCoordinates(String, BitSet) - Method in class org.jmol.viewer.StateManager
 
saveCoordinates(String, BitSet) - Method in class org.jmol.viewer.Viewer
 
saved - Variable in class org.jmol.viewer.StateManager
 
saveDiffuse - Variable in class org.jmol.g3d.Graphics3D
 
saveField - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
saveHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Just saves the path settings from this session.
saveHistory() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
saveList() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
Saves the list to the history file.
saveModelOrientation(int, StateManager.Orientation) - Method in class org.jmol.modelset.ModelCollection
 
saveModelOrientation() - Method in class org.jmol.viewer.Viewer
 
saveName - Variable in class org.jmol.viewer.StateManager.Connections
 
saveName - Variable in class org.jmol.viewer.StateManager.Orientation
 
saveOrientation(String) - Method in class org.jmol.viewer.StateManager
 
saveOrientation(String) - Method in class org.jmol.viewer.Viewer
 
savePathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
saveproteinstructurestate - Static variable in class org.jmol.script.Token
 
saveProteinStructureState - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
saveSelection(String, BitSet) - Method in class org.jmol.viewer.StateManager
 
saveSelection(String) - Method in class org.jmol.viewer.Viewer
 
saveState(String) - Method in class org.jmol.viewer.StateManager
 
saveState(String) - Method in class org.jmol.viewer.Viewer
 
saveStructure(String) - Method in class org.jmol.viewer.StateManager
 
saveStructure(String) - Method in class org.jmol.viewer.Viewer
 
saveVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
saveXYZCollection() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Saves the currently active collection as a multistep XYZ file.
say(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
sb - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
sb - Variable in class org.jmol.util.OutputStringBuffer
 
sbConect - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
sbIgnored - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
sbSelected - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
sbTemp - Variable in class org.jmol.export._IdtfExporter
 
scalarDictRef - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scalarDictValue - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scalarTitle - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scale(int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
scale - Variable in class org.jmol.jvxl.readers.Parameters
 
scale - Variable in class org.jmol.modelset.TickInfo
 
scale - Static variable in class org.jmol.script.Token
 
scale - Variable in class org.jmol.shape.Axes
 
scale - Variable in class org.jmol.shape.Mesh
 
scale - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
scale - Variable in class org.jmol.symmetry.PointGroup
 
scale3d - Variable in class org.jmol.jvxl.data.JvxlData
 
scale3d - Variable in class org.jmol.jvxl.readers.Parameters
 
scale3d - Static variable in class org.jmol.script.Token
 
scale3d - Variable in class org.jmol.shapesurface.Isosurface
 
scale3d - Variable in class org.jmol.util.MeshSurface
 
scale3D - Variable in class org.jmol.viewer.TransformManager
 
scale3DAngstromsPerInch - Variable in class org.jmol.viewer.TransformManager
 
SCALE_FLAG - Static variable in class org.jmol.shape.Labels
 
SCALE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for vector scale.
SCALE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Precision of the vector scale slider
SCALE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Initial value of vector scale.
scaleangstromsperinch - Static variable in class org.jmol.script.Token
 
scaleBox(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
 
scaleDefaultPixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
 
scaledHeightVector - Variable in class org.jmol.shapebio.RocketsRenderer
 
scaleDrawing(DrawMesh, float) - Static method in class org.jmol.shapespecial.Draw
 
scaledWidthVector - Variable in class org.jmol.shapebio.RocketsRenderer
 
scaleFitToScreen(boolean) - Method in class org.jmol.viewer.TransformManager
 
scaleFitToScreen(boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
scalePixelsPerAngstrom - Variable in class org.jmol.export.___Exporter
 
scalePixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
 
scalePixelsPerMicron - Variable in class org.jmol.shape.Labels
 
scalePixelsPerMicron - Variable in class org.jmol.shape.MeshRenderer
 
scalePixelsPerMicron - Variable in class org.jmol.shape.Object2d
 
scalePrimitiveData(int, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
Perform implementation-specific scaling.
scaleSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
scaleToPerspective(int, float) - Method in class org.jmol.viewer.TransformManager
 
scaleToPerspective(int, float) - Method in class org.jmol.viewer.Viewer
 
scaleToScreen(int, int) - Method in class org.jmol.modelset.Group
 
scaleToScreen(int, int) - Method in class org.jmol.viewer.TransformManager
 
scaleToScreen(int, int) - Method in class org.jmol.viewer.Viewer
 
scanForOffsets(int, int[], byte[]) - Static method in class org.jmol.modelsetbio.Monomer
 
scanPoint - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
The scan point, where -1 denotes no scan information.
schemes - Variable in class org.jmol.util.ColorEncoder
 
score - Variable in class org.jmol.util.ContactPair
 
screenA - Variable in class org.jmol.shapebio.RocketsRenderer
 
screenArrowBot - Variable in class org.jmol.shapebio.BioShapeRenderer
 
screenArrowBotPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
 
screenArrowHead - Variable in class org.jmol.shapespecial.VectorsRenderer
 
screenArrowTop - Variable in class org.jmol.shapebio.BioShapeRenderer
 
screenArrowTopPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
 
screenB - Variable in class org.jmol.shapebio.RocketsRenderer
 
screenC - Variable in class org.jmol.shapebio.RocketsRenderer
 
screenCoordinates - Variable in class org.jmol.shapespecial.DotsRenderer
 
screenCorners - Variable in class org.jmol.shapebio.RocketsRenderer
 
screenDiameter - Variable in class org.jmol.util.Point3fi
 
screenDotCount - Variable in class org.jmol.shapespecial.DotsRenderer
 
screenHeight - Variable in class org.jmol.export.___Exporter
 
screenHeight - Static variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
screenHeight - Variable in class org.jmol.viewer.TransformManager
 
screenLevel - Variable in class org.jmol.shapespecial.DotsRenderer
 
screenPixelCount - Variable in class org.jmol.viewer.TransformManager
 
screens - Variable in class org.jmol.shape.AxesRenderer
 
screens - Variable in class org.jmol.shape.CageRenderer
 
screens - Variable in class org.jmol.shape.MeshRenderer
 
screens - Variable in class org.jmol.shapespecial.DipolesRenderer
 
screens - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
screenSize - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
screenVectorEnd - Variable in class org.jmol.shapespecial.VectorsRenderer
 
screenWidth - Variable in class org.jmol.export.___Exporter
 
screenWidth - Static variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
screenWidth - Variable in class org.jmol.viewer.TransformManager
 
screenX - Variable in class org.jmol.util.Point3fi
 
screenY - Variable in class org.jmol.util.Point3fi
 
screenZ - Variable in class org.jmol.util.Point3fi
 
script(String) - Method in class org.jmol.api.JmolViewer
 
script(String) - Method in class org.jmol.applet.Jmol
 
script(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
script - Variable in class org.jmol.jvxl.readers.Parameters
 
script - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
script - Variable in class org.jmol.script.ScriptContext
 
script - Variable in class org.jmol.script.ScriptEvaluator
 
script(int, String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
script - Variable in class org.jmol.script.ScriptFunction
 
script - Static variable in class org.jmol.script.Token
 
script - Variable in class org.jmol.shape.Object2d
 
script - Variable in class org.jmol.shapesurface.Isosurface
 
script - Variable in class org.jmol.viewer.ActionManager.TimeoutThread
 
script(String) - Method in class org.jmol.viewer.Viewer
 
script - Variable in class org.openscience.jmol.app.JmolApp
 
script - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
script1 - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
script1 - Variable in class org.openscience.jmol.app.JmolApp
 
script2 - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
script2 - Variable in class org.openscience.jmol.app.JmolApp
 
SCRIPT_CHECK - Static variable in class org.jmol.applet.Jmol
 
SCRIPT_COMPLETED - Static variable in class org.jmol.script.ScriptEvaluator
 
SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JmolConstants
 
SCRIPT_NOWAIT - Static variable in class org.jmol.applet.Jmol
 
SCRIPT_WAIT - Static variable in class org.jmol.applet.Jmol
 
SCRIPT_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
scriptAppendix - Variable in class org.jmol.shapesurface.Isosurface
 
scriptButtonPercent - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
ScriptButtons - Class in org.openscience.jmol.app.webexport
 
ScriptButtons(JmolViewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.ScriptButtons
 
scriptCallback(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
from StatusManager
scriptCheck(String) - Method in class org.jmol.api.JmolViewer
 
scriptCheck(String) - Method in class org.jmol.applet.Jmol
 
scriptCheck(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
scriptCheck(String, boolean) - Method in class org.jmol.viewer.Viewer
 
scriptCheck(String) - Method in class org.jmol.viewer.Viewer
 
scriptCommand - Static variable in class org.jmol.script.Token
 
scriptCommand - Variable in class org.jmol.shape.Mesh
 
ScriptCompilationTokenParser - Class in org.jmol.script
 
ScriptCompilationTokenParser() - Constructor for class org.jmol.script.ScriptCompilationTokenParser
 
ScriptCompiler - Class in org.jmol.script
 
ScriptCompiler(Viewer) - Constructor for class org.jmol.script.ScriptCompiler
 
ScriptCompiler(ScriptCompiler) - Constructor for class org.jmol.script.ScriptCompiler
 
ScriptContext - Class in org.jmol.script
 
ScriptContext() - Constructor for class org.jmol.script.ScriptContext
 
scriptDelay - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
scriptEcho(String) - Method in class org.jmol.viewer.Viewer
 
scriptEditor - Variable in class org.jmol.console.JmolConsole
 
ScriptEditor - Class in org.jmol.console
 
ScriptEditor() - Constructor for class org.jmol.console.ScriptEditor
 
ScriptEditor(JmolViewer, JFrame, JmolConsole) - Constructor for class org.jmol.console.ScriptEditor
 
scriptEditor - Variable in class org.jmol.viewer.Viewer
 
ScriptEditor.EditorDocument - Class in org.jmol.console
 
ScriptEditor.EditorDocument() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument
 
ScriptEditor.EditorDocument.MyUndoableEditListener - Class in org.jmol.console
 
ScriptEditor.EditorDocument.MyUndoableEditListener() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
 
ScriptEditor.EditorTextPane - Class in org.jmol.console
 
ScriptEditor.EditorTextPane() - Constructor for class org.jmol.console.ScriptEditor.EditorTextPane
 
scriptEditorVisible - Variable in class org.jmol.viewer.Viewer
 
ScriptEvaluator - Class in org.jmol.script
 
ScriptEvaluator(Viewer) - Constructor for class org.jmol.script.ScriptEvaluator
 
ScriptEvaluator.ScriptException - Exception in org.jmol.script
 
ScriptEvaluator.ScriptException(String, String) - Constructor for exception org.jmol.script.ScriptEvaluator.ScriptException
 
scriptExtensions - Variable in class org.jmol.script.ScriptCompiler
 
scriptExtensions - Variable in class org.jmol.script.ScriptContext
 
scriptExtensions - Variable in class org.jmol.script.ScriptEvaluator
 
scriptFilename - Variable in class org.openscience.jmol.app.JmolApp
 
scriptFilePrefixes - Static variable in class org.jmol.viewer.FileManager
 
ScriptFlowContext - Class in org.jmol.script
 
ScriptFlowContext(ScriptCompiler, ContextToken, int, ScriptFlowContext) - Constructor for class org.jmol.script.ScriptFlowContext
 
ScriptFunction - Class in org.jmol.script
 
ScriptFunction(String, int) - Constructor for class org.jmol.script.ScriptFunction
 
scriptIndex - Variable in class org.jmol.viewer.Viewer
 
scriptLevel - Variable in class org.jmol.script.ScriptContext
 
scriptLevel - Variable in class org.jmol.script.ScriptEvaluator
 
scriptLevelMax - Static variable in class org.jmol.script.ScriptEvaluator
 
ScriptManager - Class in org.jmol.viewer
 
ScriptManager(Viewer) - Constructor for class org.jmol.viewer.ScriptManager
 
scriptManager - Variable in class org.jmol.viewer.Viewer
 
ScriptManager.CommandWatcher - Class in org.jmol.viewer
 
ScriptManager.CommandWatcher() - Constructor for class org.jmol.viewer.ScriptManager.CommandWatcher
 
ScriptManager.ScriptQueueRunnable - Class in org.jmol.viewer
 
ScriptManager.ScriptQueueRunnable(boolean, int) - Constructor for class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
ScriptMathProcessor - Class in org.jmol.script
 
ScriptMathProcessor(ScriptEvaluator, boolean, boolean, boolean) - Constructor for class org.jmol.script.ScriptMathProcessor
 
scriptNoWait(String) - Method in class org.jmol.applet.Jmol
 
scriptNoWait(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
scriptProcessor(String, String, int) - Method in class org.jmol.applet.Jmol
 
scriptqueue - Static variable in class org.jmol.script.Token
 
scriptQueue - Variable in class org.jmol.viewer.ScriptManager
 
scriptQueueRunning - Variable in class org.jmol.viewer.ScriptManager
 
scriptReportingLevel - Variable in class org.jmol.script.ScriptEvaluator
 
scriptreportinglevel - Static variable in class org.jmol.script.Token
 
scriptStatus(String) - Method in class org.jmol.viewer.Viewer
 
scriptStatus(String, String) - Method in class org.jmol.viewer.Viewer
 
scriptStatus(String, String, int, String) - Method in class org.jmol.viewer.Viewer
 
scriptStatusOrBuffer(String) - Method in class org.jmol.script.ScriptEvaluator
 
ScriptVariable - Class in org.jmol.script
 
ScriptVariable() - Constructor for class org.jmol.script.ScriptVariable
 
ScriptVariable(int) - Constructor for class org.jmol.script.ScriptVariable
 
ScriptVariable(int, int, Object) - Constructor for class org.jmol.script.ScriptVariable
 
ScriptVariable(int, Object) - Constructor for class org.jmol.script.ScriptVariable
 
ScriptVariable(int, int) - Constructor for class org.jmol.script.ScriptVariable
 
ScriptVariable(BitSet, int) - Constructor for class org.jmol.script.ScriptVariable
 
ScriptVariable(Token) - Constructor for class org.jmol.script.ScriptVariable
 
ScriptVariable.Sort - Class in org.jmol.script
 
ScriptVariable.Sort(int) - Constructor for class org.jmol.script.ScriptVariable.Sort
 
scriptWait(String) - Method in class org.jmol.api.JmolViewer
 
scriptWait(String) - Method in class org.jmol.applet.Jmol
 
scriptWait(String, String) - Method in class org.jmol.applet.Jmol
 
scriptWait(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
scriptWait(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
 
scriptWait(String) - Method in class org.jmol.viewer.Viewer
 
scriptWaitOutput(String) - Method in class org.jmol.applet.Jmol
 
scriptWaitOutput(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
 
scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
 
SDIM - Static variable in class org.jmol.g3d.Sphere3D
 
Se - Variable in class org.jmol.util.JpegInfo
 
search - Static variable in class org.jmol.script.Token
 
search - Variable in class org.jmol.smiles.SmilesMeasure
 
search(boolean) - Method in class org.jmol.smiles.SmilesSearch
the start of the search.
searchForTurns(AlphaPolymer.Code[], float[], EnumStructure[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
secondCharOnly - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
sectorPower - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
sectorSize - Variable in class org.jmol.util.CompoundDocument
 
seed - Static variable in class org.jmol.g3d.Shade3D
 
SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
 
seek(long) - Method in class org.jmol.util.BinaryDocument
 
segments - Variable in class org.jmol.modelsetbio.ProteinStructure
 
seitzMatrix - Variable in class org.jmol.symmetry.Rotation
 
seitzMatrix12ths - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
seitzMatrixInv - Variable in class org.jmol.symmetry.Rotation
 
select(int) - Method in class org.jmol.script.ScriptEvaluator
 
select - Static variable in class org.jmol.script.Token
 
select(BitSet, Boolean, boolean) - Method in class org.jmol.viewer.SelectionManager
 
select(BitSet, boolean, Boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
select - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
selectAll() - Method in class org.jmol.api.JmolViewer
 
selectAll(boolean) - Method in class org.jmol.viewer.SelectionManager
 
selectAll() - Method in class org.jmol.viewer.Viewer
 
selectallmodels - Static variable in class org.jmol.script.Token
 
selectAllModels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
selectAtoms(BitSet) - Method in class org.jmol.modelset.Group
 
selectBonds(BitSet) - Method in class org.jmol.viewer.Viewer
 
selectDisplayedTrajectories(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
selected - Static variable in class org.jmol.script.Token
 
selected - Variable in class org.jmol.smiles.SmilesAtom
 
selectedAtomCount - Variable in class org.jmol.smiles.SmilesSearch
 
selectedBonds - Variable in class org.jmol.shape.Sticks
 
selectedFileName - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
selectedfloat - Static variable in class org.jmol.script.Token
 
selectedGroupCount - Variable in class org.jmol.modelset.Chain
 
selectedIndex - Variable in class org.jmol.modelset.Group
 
selectedMeasurementRow - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
selectedMoleculeCount - Variable in class org.jmol.modelset.ModelCollection
 
selectedMolecules - Variable in class org.jmol.modelset.ModelCollection
 
selectedMonomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
 
selectedOctant - Variable in class org.jmol.g3d.Sphere3D
 
selectedOctant - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
selectedPoints - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
selectedTrajectory - Variable in class org.jmol.modelset.Model
 
selectField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
selecthetero - Static variable in class org.jmol.script.Token
 
selecthydrogen - Static variable in class org.jmol.script.Token
 
selection - Static variable in class org.jmol.script.Token
 
selectionChanged(BitSet) - Method in interface org.jmol.api.JmolSelectionListener
Called when the selected atoms change
selectionChanged(boolean) - Method in class org.jmol.viewer.SelectionManager
 
selectionHalo(int) - Method in class org.jmol.script.ScriptEvaluator
 
selectionHaloEnabled - Variable in class org.jmol.modelset.ModelSet
 
selectionhalos - Static variable in class org.jmol.script.Token
 
SelectionManager - Class in org.jmol.viewer
 
SelectionManager(Viewer) - Constructor for class org.jmol.viewer.SelectionManager
 
selectionManager - Variable in class org.jmol.viewer.Viewer
 
selectionWorking - Variable in class org.jmol.viewer.ActionManager
 
selectItem(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
 
selectItem(Token) - Static method in class org.jmol.script.ScriptVariable
 
selectItem(ScriptVariable, int) - Static method in class org.jmol.script.ScriptVariable
 
selectItem(Token, int) - Static method in class org.jmol.script.ScriptVariable
 
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
selectSeqcodeRange(int, int, int, BitSet) - Method in class org.jmol.modelset.Chain
 
selectSeqcodeRange(int, int, char, BitSet, boolean) - Method in class org.jmol.modelset.Model
 
selectSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
semicolon - Static variable in class org.jmol.script.Token
 
send(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
from JmolPanel and SYNC command
sendConsoleEcho(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
sendConsoleEcho(String) - Method in class org.jmol.console.AppletConsole
 
sendConsoleEcho(String) - Method in class org.jmol.console.JmolConsole
 
sendConsoleEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
sendConsoleMessage(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
sendConsoleMessage(String) - Method in class org.jmol.console.AppletConsole
 
sendConsoleMessage(String) - Method in class org.jmol.console.JmolConsole
 
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
sendJsTextareaStatus(String) - Method in class org.jmol.applet.Jmol
 
sendJsTextStatus(String) - Method in class org.jmol.applet.Jmol
 
sendKeyBuffer() - Method in class org.jmol.awt.Mouse
 
sendMessage(JsonNioService.JSONObject, String, NIOSocket) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
sendNioMessage(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
sendScript(String, String, boolean, boolean) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
sep - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
SEQ_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
seqcode - Variable in class org.jmol.modelset.Group
 
seqcode - Static variable in class org.jmol.script.Token
 
seqcodes - Variable in class org.jmol.modelset.ModelLoader
 
sequence - Static variable in class org.jmol.script.Token
 
SEQUENCE_NUMBER_FLAG - Static variable in class org.jmol.modelset.Group
 
SEQUENCE_NUMBER_SHIFT - Static variable in class org.jmol.modelset.Group
 
sequenceNumber - Variable in class org.jmol.adapter.smarter.Atom
 
serial - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
SERIAL_NO - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
serialArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
serialID - Variable in class org.jmol.adapter.smarter.Structure
 
serialID - Variable in class org.jmol.modelsetbio.ProteinStructure
 
serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Orbitals
 
serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Test
 
serverConnection - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
serverService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
serverSocket - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
serverThread - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
service - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
service - Variable in class org.openscience.molecularplayground.MPJmolApp
 
SERVICE_LOST - Static variable in class org.jmol.multitouch.ActionManagerMT
 
set(ModelCollection, int, int, int, Point3f, float, RadiusData) - Method in interface org.jmol.api.AtomIndexIterator
 
set(Point3f, float) - Method in interface org.jmol.api.AtomIndexIterator
 
set(Bspt) - Method in class org.jmol.bspt.CubeIterator
 
set(Point3f, Point3i) - Static method in class org.jmol.g3d.Hermite3D
 
set(int) - Method in class org.jmol.g3d.Rgb16
 
set(Rgb16) - Method in class org.jmol.g3d.Rgb16
 
set() - Method in class org.jmol.minimize.MinAtom
 
set(ModelCollection, int, int, int, Point3f, float, RadiusData) - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
set(Point3f, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
set(Point3f, float) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
 
set(int) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
 
set(JmolViewer) - Method in class org.jmol.popup.SimplePopup
 
set() - Method in class org.jmol.script.ScriptEvaluator
 
set(ScriptVariable, boolean) - Method in class org.jmol.script.ScriptVariable
creates a NEW version of the variable
set - Static variable in class org.jmol.script.Token
 
set(String, String, Atom[], float, short, float, int, float, Point3f, Vector3f) - Method in class org.jmol.shapespecial.Dipole
 
set(Point3f, Point3f) - Method in class org.jmol.shapespecial.Dipole
 
set(float) - Method in class org.jmol.shapespecial.Dipole
 
set(Point3f, Point3f, float) - Method in class org.jmol.shapespecial.Dipole
 
set(Point3f, Vector3f) - Method in class org.jmol.shapespecial.Dipole
 
set(Atom, Atom, float) - Method in class org.jmol.shapespecial.Dipole
 
set(SmilesBond) - Method in class org.jmol.smiles.SmilesBond
 
set(int, boolean) - Method in class org.jmol.smiles.SmilesBond
 
set(SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
set(PointGroup, Atom[], BitSet, boolean, float, float) - Method in class org.jmol.symmetry.PointGroup
 
set(int) - Method in class org.jmol.util.FastBitSet
 
set(int, boolean) - Method in class org.jmol.util.FastBitSet
 
set(int, int) - Method in class org.jmol.util.FastBitSet
 
set(int, int, boolean) - Method in class org.jmol.util.FastBitSet
 
set(float, float, float) - Method in interface org.jmol.util.JmolNode
 
set(Quaternion) - Method in class org.jmol.util.Quaternion
 
set(Point4f) - Method in class org.jmol.util.Quaternion
{x y z w} --> {q1 q2 q3 q0} and factored
set(Tuple3f, float) - Method in class org.jmol.util.Quaternion
q = (cos(theta/2), sin(theta/2) * n)
set(AxisAngle4f) - Method in class org.jmol.util.Quaternion
 
set(Matrix3f) - Method in class org.jmol.util.Quaternion
 
set(int, int, int, long) - Method in class org.jmol.viewer.ActionManager.MotionPoint
 
set(long, int, int, int) - Method in class org.jmol.viewer.ActionManager.Mouse
 
set(int, String) - Method in class org.jmol.viewer.ActionManager.TimeoutThread
 
set(float, Point3f, Matrix3f, float, float, float, float, Point3f, float, float, float) - Method in class org.jmol.viewer.TransformManager.MotionThread
 
set2D() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
set2dZ(int, int) - Method in class org.jmol.modelset.ModelLoader
 
set3dContourVector(List<Object>, int[][], Point3f[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.
setAaTokenCompiled() - Method in class org.jmol.script.ScriptCompiler
 
setABC(int) - Method in class org.jmol.util.MeshSurface
 
setAbstractButtonLabels(Map<String, AbstractButton>, Map<String, String>) - Static method in class org.jmol.console.KeyJMenuItem
 
setAction(int, long) - Method in class org.jmol.viewer.ActionManager.Gesture
 
setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
Changes the activation state for a logging level.
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
adaptable via subclassing
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.more.P2nReader
 
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.more.PqrReader
 
setAdjustForWindow(boolean) - Method in class org.jmol.shape.Object2d
 
setAlignment(int, int) - Method in class org.jmol.shape.Labels
 
setAlignment(String) - Method in class org.jmol.shape.Object2d
 
setAlignment(int) - Method in class org.jmol.shape.Object2d
 
setAll(int) - Static method in class org.jmol.util.BitSetUtil
 
setAllFractionalRelative(boolean) - Method in class org.jmol.symmetry.UnitCell
 
setAllowStatusReporting(boolean) - Method in class org.jmol.viewer.StatusManager
 
setAmbientPercent(int) - Static method in class org.jmol.g3d.Graphics3D
fractional distance from black for ambient color
setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.g3d.Rgb16
 
setAngleUnits(int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setAnimation(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationDirection(int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationDirection(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationFps(int) - Method in class org.jmol.api.JmolViewer
 
setAnimationFps(int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationLast() - Method in class org.jmol.viewer.AnimationManager
 
setAnimationNext() - Method in class org.jmol.viewer.AnimationManager
 
setAnimationOff(boolean) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setAnimationPrevious() - Method in class org.jmol.viewer.AnimationManager
 
setAnimationRange(int, int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
 
setAnimationRelative(int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationReplayMode(EnumAnimationMode, float, float) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationReplayMode(EnumAnimationMode, float, float) - Method in class org.jmol.viewer.Viewer
 
setAnisoBorU(Atom, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAnisotropy(Point3f) - Method in class org.jmol.jvxl.readers.Parameters
 
setAntialias(boolean) - Method in class org.jmol.viewer.TransformManager
 
setAntialias(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setAppendNew(boolean) - Method in class org.jmol.viewer.Viewer
 
setAppletContext(String, URL, URL, String) - Method in class org.jmol.api.JmolViewer
 
setAppletContext(URL, URL, String) - Method in class org.jmol.viewer.FileManager
 
setAppletContext(String, URL, URL, String) - Method in class org.jmol.viewer.Viewer
 
setAppletPath(String, boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setAppletProxy(String) - Method in class org.jmol.viewer.FileManager
 
setAppletWrapper(AppletWrapper) - Method in class org.jmol.applet.Jmol
 
setAppletWrapper(AppletWrapper) - Method in interface org.jmol.applet.WrappedApplet
 
setApplySymmetryToBonds(boolean) - Method in class org.jmol.viewer.Viewer
 
setAtom2(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
setAtom2dZ(Atom, Atom, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.modelset.ModelLoader
 
setAtomArray() - Method in class org.jmol.smiles.SmilesSearch
 
setAtomBitSet(BitSet) - Method in class org.jmol.modelset.Chain
 
setAtomCoord(Atom, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoord(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoord(BitSet, int, Object) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoord(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoord(BitSet, int, Object) - Method in class org.jmol.modelset.ModelSet
 
setAtomCoord(int, float, float, float) - Method in class org.jmol.viewer.Viewer
 
setAtomCoord(BitSet, int, Object) - Method in class org.jmol.viewer.Viewer
 
setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoordRelative(BitSet, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoordRelative(Tuple3f, BitSet) - Method in class org.jmol.modelset.ModelSet
 
setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.viewer.Viewer
 
setAtomCoordRelative(Tuple3f, BitSet) - Method in class org.jmol.viewer.Viewer
 
setAtomData(int, String, String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setAtomData(int, String, String, boolean) - Method in class org.jmol.viewer.Viewer
 
setAtomI(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setAtomicAndIsotopeNumber(int) - Method in class org.jmol.modelset.Atom
 
setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the atomic mass of the atom.
setAtomicOrbital(float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setAtomLabel(String, int) - Method in class org.jmol.viewer.ShapeManager
 
setAtomLabel(String, int) - Method in class org.jmol.viewer.Viewer
 
setAtomName(Atom, String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
 
setAtomName(int, String) - Method in class org.jmol.modelset.AtomCollection
 
setAtomName(String) - Method in class org.jmol.smiles.SmilesAtom
 
setAtomNames(Properties) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomNamesAndNumbers(int, int, AtomCollection) - Method in class org.jmol.modelset.ModelCollection
 
setAtomNumber(int, int) - Method in class org.jmol.modelset.AtomCollection
 
setAtomPickingOption(String) - Method in class org.jmol.viewer.ActionManager
 
setAtomPickingOption(String) - Method in class org.jmol.viewer.Viewer
 
setAtomPositions() - Method in class org.jmol.minimize.Minimizer
 
setAtomProperties() - Method in class org.jmol.modelset.ModelLoader
 
setAtomProperty(BitSet, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.AtomCollection
 
setAtomProperty(BitSet, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelCollection
 
setAtomProperty(BitSet, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
 
setAtomProperty(BitSet, int, int, float, String, float[], String[]) - Method in class org.jmol.viewer.Viewer
 
setAtomSetAtomProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetAuxiliaryInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets auxiliary information for the AtomSet
setAtomSetAuxiliaryInfo(String, Object, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets auxiliary information for an AtomSet
setAtomSetCollectionAuxiliaryInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetCollectionPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the partial atomic charges based on atomSetCollection auxiliary info
setAtomSetEnergy(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetFrequency(String, String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetInfo() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
setAtomSetInfoMd() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
setAtomSetModelProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and moleular energies
setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the name for the current AtomSet
setAtomSetNames(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the atom set names of the last n atomSets
setAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the number for the current AtomSet
setAtomSetPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the partial atomic charges based on atomSet auxiliary info
setAtomSetProperties(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the same properties for the last n atomSets.
setAtomSetProperty(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the a property for the an AtomSet
setAtomSetSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomShapeSize(int, float) - Method in class org.jmol.script.ScriptEvaluator
 
setAtomSymmetry(BitSet) - Method in class org.jmol.modelset.Atom
 
setAtomType(int, String) - Method in class org.jmol.modelset.AtomCollection
 
setAtomVibrationVector(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAttr(String, float) - Method in class org.jmol.export._MayaExporter
 
setAttr(String, int) - Method in class org.jmol.export._MayaExporter
 
setAttr(String, Tuple3f) - Method in class org.jmol.export._MayaExporter
 
setAttributes() - Method in class org.jmol.console.ScriptEditor
 
setAutoBond(boolean) - Method in class org.jmol.api.JmolViewer
 
setAutoBond(boolean) - Method in class org.jmol.viewer.Viewer
 
setAutoscrolls(Object) - Method in class org.jmol.popup.SimplePopup
 
setAxes(DrawMesh) - Static method in class org.jmol.shapespecial.Draw
 
setAxes(float) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
setAxesModeMolecular(boolean) - Method in class org.jmol.viewer.Viewer
 
setAxesModeUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
 
setAxesOrientationRasmol(boolean) - Method in class org.jmol.api.JmolViewer
 
setAxesOrientationRasmol(boolean) - Method in class org.jmol.viewer.Viewer
 
setAxesScale(float) - Method in class org.jmol.viewer.Viewer
 
setBackgroundArgb(int) - Method in class org.jmol.g3d.Graphics3D
sets background color to the specified argb value
setBackgroundColor(int) - Method in class org.jmol.g3d.Platform3D
 
setBackgroundImage(Object) - Method in class org.jmol.g3d.Graphics3D
 
setBackgroundImage(String, Object) - Method in class org.jmol.viewer.Viewer
 
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.AnimationManager
 
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Platform3D
 
setBanner(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
setBannerLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setBannerLabel(String) - Method in interface org.openscience.jmol.app.jmolpanel.JsonNioClient
 
setBannerLabel(String) - Method in class org.openscience.molecularplayground.MPJmolApp
 
setBaseSymmetryAtomCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setBbcage(float) - Method in class org.jmol.util.BoxInfo
 
setBf(int) - Method in class org.jmol.modelset.AtomCollection
 
setBFactor(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setBgcolix(int, short) - Method in class org.jmol.shape.Labels
 
setBgColix(short) - Method in class org.jmol.shape.Object2d
 
setBgColix(Object) - Method in class org.jmol.shape.Object2d
 
setBinding(Binding) - Method in class org.jmol.multitouch.ActionManagerMT
 
setBinding(Binding) - Method in class org.jmol.viewer.ActionManager
 
setBioAtom(char) - Method in class org.jmol.smiles.SmilesAtom
 
setBiomoleculeAtomCounts() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
setBioPolymer(BioPolymer, int) - Method in class org.jmol.modelsetbio.Monomer
 
setBit(int) - Static method in class org.jmol.util.BitSetUtil
 
setBitmap(String, Font3D, Graphics3D, boolean) - Method in class org.jmol.g3d.Text3D
 
setBitsetProperty(BitSet, int, int, float, Token) - Method in class org.jmol.script.ScriptEvaluator
 
setBond(Bond, int[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
 
setBondArray() - Method in class org.jmol.smiles.SmilesAtom
 
setBondDirections() - Method in class org.jmol.smiles.SmilesGenerator
Creates global BitSets bsBondsUp and bsBondsDown.
setBondingAndMolecules() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
(1) If GEOM_BOND records are present, we (a) use them to generate bonds (b) add H atoms to bonds if necessary (c) turn off autoBonding ("hasBonds") (2) If MOLECULAR, then we (a) use {1 1 1} if lattice is not defined (b) use atomSetCollection.bonds[] to construct a preliminary molecule and connect as we go (c) check symmetry for connections to molecule in any one of the 27 3x3 adjacent cells (d) move those atoms and their connected branch set (e) iterate as necessary to get all atoms desired (f) delete unselected atoms (g) set all coordinates as Cartesians (h) remove all unit cell information
setBondmode() - Method in class org.jmol.script.ScriptEvaluator
 
setBondOrder(int, char) - Method in class org.jmol.modelset.BondCollection
 
setBondPickingOption(String) - Method in class org.jmol.viewer.ActionManager
 
setBondPickingOption(String) - Method in class org.jmol.viewer.Viewer
 
setBonds(Bond[]) - Method in class org.jmol.modelset.Atom
 
setBonds(SmilesBond[]) - Method in class org.jmol.smiles.SmilesAtom
 
setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
 
setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
 
setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
 
setBooleanProperty(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setBooleanProperty(String, int, boolean) - Method in class org.jmol.viewer.Viewer
 
setBorder() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.modelset.ModelCollection
 
setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.util.BoxInfo
 
setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.viewer.Viewer
 
setBoundingBox() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setBoundingBox(Point3f, float) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.shape.Object2d
 
setBoxXY(float, float, float, float, float[], boolean) - Static method in class org.jmol.shape.Text
 
setBraceCount - Variable in class org.jmol.script.ScriptCompiler
 
setBranch2dZ(Atom, BitSet, BitSet, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.modelset.ModelLoader
 
setBs(Atom[], int, BitSet[], BitSet) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
iteratively run through connected atoms, adding them to the set
setBsHidden(BitSet) - Method in class org.jmol.modelset.AtomCollection
 
setBsVdw() - Method in class org.jmol.shapesurface.Isosurface
 
setButton(String) - Method in class org.jmol.console.JmolConsole
 
setButton(String) - Method in class org.jmol.console.ScriptEditor
 
setButton(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
setCalculationType() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolCallbackListener
 
setCallbackFunction(String, String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
setCallbackFunction(String, String) - Method in class org.jmol.console.JmolConsole
 
setCallbackFunction(String, String) - Method in class org.jmol.viewer.StatusManager
 
setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setCameraDepthPercent(float) - Method in class org.jmol.viewer.TransformManager
either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model
setCapOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setCE(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
 
setCell() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
setCellParams() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
setCenter(int) - Method in class org.jmol.shapespecial.DrawMesh
 
setCenter() - Method in class org.jmol.viewer.TransformManager
 
setCenterAt(String, Point3f) - Method in class org.jmol.viewer.TransformManager
 
setCenterAt(String, Point3f) - Method in class org.jmol.viewer.Viewer
 
setCenterBitSet(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
setCenters() - Method in class org.jmol.shapespecial.DrawMesh
 
setCenterSelected() - Method in class org.jmol.api.JmolViewer
 
setCenterSelected() - Method in class org.jmol.viewer.Viewer
 
setCharge(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the charge of the atom.
setCharges() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
setCheckBoxOption(JMenuItem, String, String) - Method in class org.jmol.modelkit.ModelKitPopup
 
setCheckBoxOption(JMenuItem, String, String) - Method in class org.jmol.popup.SimplePopup
 
setCheckBoxState(Object, boolean) - Method in class org.jmol.popup.SimplePopup
 
setCheckBoxValue(JMenuItem, String, boolean) - Method in class org.jmol.popup.JmolPopup
(1) setOption --> set setOption true or set setOption false
setCheckBoxValue(JMenuItem, String, boolean) - Method in class org.jmol.popup.SimplePopup
(1) setOption --> set setOption true or set setOption false
setCheckBoxValue(Object) - Method in class org.jmol.popup.SimplePopup
 
setCheckSpecial(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setChiralClass(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the chiral class of the atom.
setChiralOrder(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the chiral order of the atom.
setClickable(int) - Method in class org.jmol.modelset.Atom
 
setClipboard(Image) - Static method in class org.jmol.export.image.ImageSelection
Transfers image into the clipboard.
setClipboard(String) - Static method in class org.jmol.export.image.ImageSelection
Transfers text into the clipboard.
setCoeffs(boolean) - Method in class org.jmol.quantum.MOCalculation
 
setColix(short) - Method in interface org.jmol.api.JmolRendererInterface
sets current color from colix color index
setColix(short) - Method in class org.jmol.export.Export3D
sets current color from colix color index
setColix(short) - Method in class org.jmol.g3d.Graphics3D
sets current color from colix color index
setColix(short) - Method in class org.jmol.modelset.Bond
 
setColix(short) - Method in class org.jmol.modelset.Measurement
 
setColix(int, short, byte) - Method in class org.jmol.shape.Labels
 
setColix(short) - Method in class org.jmol.shape.MeshRenderer
 
setColix(short) - Method in class org.jmol.shape.Object2d
 
setColix(Object) - Method in class org.jmol.shape.Object2d
 
setColix(short, byte, int) - Method in class org.jmol.shape.Shape
 
setColix(short, byte, Atom) - Method in class org.jmol.shape.Shape
 
setColix(short, int, Bond) - Method in class org.jmol.shape.Shape
 
setColix(short, byte, BitSet) - Method in class org.jmol.shapebio.BioShape
 
setColix(short) - Method in class org.jmol.util.MeshSurface
 
setColixAndPalette(short, byte, int) - Method in class org.jmol.shape.AtomShape
 
setColixAtom(short) - Method in class org.jmol.modelset.Atom
 
setColixBackgroundContrast(int) - Method in class org.jmol.viewer.ColorManager
 
setColixDipole(short, int, BitSet) - Method in class org.jmol.shapespecial.Dipoles
 
setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setColor(int) - Method in interface org.jmol.api.JmolRendererInterface
 
setColor(int) - Method in class org.jmol.export.Export3D
 
setColor(int) - Method in class org.jmol.g3d.Graphics3D
 
setColor(short) - Method in class org.jmol.shape.Measures
 
setColorBackground(String) - Method in class org.jmol.api.JmolViewer
 
setColorBackground(String) - Method in class org.jmol.viewer.Viewer
 
setColorByScore(float, int) - Method in class org.jmol.shapesurface.Contact
 
setColorCommand() - Method in class org.jmol.shapesurface.IsosurfaceMesh
just sets the color command for this isosurface.
setColorModel(ColorModel) - Method in class org.jmol.export.image.ImageEncoder
 
setColorNoisy(int) - Method in class org.jmol.g3d.Graphics3D
 
setColorOptions(StringBuffer, int, int, int) - Method in class org.jmol.script.ScriptEvaluator
 
setColorScheme(String, boolean) - Method in class org.jmol.util.ColorEncoder
 
setColorsFromJvxlData(int) - Method in class org.jmol.shapesurface.IsosurfaceMesh
from Isosurface.notifySurfaceGenerationCompleted() starting with Jmol 12.1.50, JVXL files contain color, translucency, color scheme information, and vertex color mappings (as from COLOR ISOSURFACE {hydrophobic} WHITE), returning these settings when the JVXL file is opened.
setCommand(Token) - Method in class org.jmol.script.ScriptCompiler
 
setCommonDefaults() - Method in class org.jmol.viewer.StateManager
 
setCompressionLevel(int) - Method in class org.jmol.export.image.PngEncoder
Set the compression level to use
setConformation(BitSet) - Method in class org.jmol.modelset.Model
 
setConformation(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
setConformation(BitSet) - Method in class org.jmol.modelset.Polymer
 
setConformation(BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
setConformation() - Method in class org.jmol.viewer.Viewer
 
setConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
 
setConsole(JmolAppConsoleInterface) - Method in class org.jmol.api.JmolViewer
sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(viewer, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java
setConsoleTextPane(AppConsole.ConsoleTextPane) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
setConstraints(List<Object[]>) - Method in class org.jmol.minimize.forcefield.Calculations
 
setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
 
setContactBitSets(BitSet, BitSet, boolean, float, RadiusData, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
setContacts(Object[]) - Method in class org.jmol.shapesurface.Contact
 
setContext(ScriptContext) - Method in class org.jmol.console.ScriptEditor
 
setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setContourVector(List<Object>, int, BitSet, float, short, int, StringBuffer) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setCount(int) - Method in class org.jmol.modelset.Measurement
 
setCount(int) - Method in class org.jmol.modelset.MeasurementPending
 
setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelCollection
 
setCrystallographicDefaults() - Method in class org.jmol.viewer.StateManager
 
setCurrent(int) - Method in class org.jmol.viewer.ActionManager.Mouse
 
setCurrent(long, int, int, int) - Method in class org.jmol.viewer.ActionManager
 
setCurrentAtomSetIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setCurrentColorRange(String) - Method in class org.jmol.viewer.Viewer
 
setCurrentColorRange(float[], BitSet) - Method in class org.jmol.viewer.Viewer
 
setCurrentColorRange(float, float) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelIndex(int) - Method in class org.jmol.viewer.AnimationManager
 
setCurrentModelIndex(int, boolean) - Method in class org.jmol.viewer.AnimationManager
 
setCurrentModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelIndex(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setCurrentUnitCellOffset(int) - Method in class org.jmol.viewer.Viewer
 
setCurrentUnitCellOffset(Point3f) - Method in class org.jmol.viewer.Viewer
 
setCursor(int, Object) - Method in interface org.jmol.api.ApiPlatform
 
setCursor(int, Object) - Static method in class org.jmol.awt.Display
 
setCursor(int, Object) - Method in class org.jmol.awt.Platform
 
setCursor(int) - Method in class org.jmol.viewer.Viewer
 
setCursorWait(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
setCutoffAutomatic() - Method in class org.jmol.jvxl.readers.MapFileReader
 
setData(String, String, int, int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
setData(List<Object[]>, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.AngleCalc
 
setData(List<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
setData(List<Object[]>, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.ESCalc
 
setData(List<Object[]>, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.OOPCalc
 
setData(List<Object[]>, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.PairCalc
 
setData(List<Object[]>, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.TorsionCalc
 
setData(List<Object[]>, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.VDWCalc
 
setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.DataManager
 
setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
setDataDistanceToPlane(Point4f) - Method in interface org.jmol.api.VolumeDataInterface
 
setDataDistanceToPlane(Point4f) - Method in class org.jmol.jvxl.data.VolumeData
 
setDebugging() - Method in class org.jmol.script.ScriptEvaluator
 
setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
 
setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
 
setDefaultColors(boolean) - Method in class org.jmol.viewer.ColorManager
 
setDefaultColors(boolean) - Method in class org.jmol.viewer.Viewer
 
setDefaultLattice(Point3f) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setDefaultLattice(Point3f) - Method in class org.jmol.viewer.Viewer
 
setDefaultRendering(int) - Method in class org.jmol.modelset.ModelLoader
 
setDefaults - Variable in class org.jmol.shape.Labels
 
setDefaults(String) - Method in class org.jmol.viewer.Viewer
 
setDefaults() - Method in class org.jmol.viewer.Viewer
 
setDefaultStructure(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
setDefaultVdw(EnumVdw) - Method in class org.jmol.viewer.DataManager
 
setDefaultVdw(String) - Method in class org.jmol.viewer.Viewer
 
setDegree(int) - Method in class org.jmol.smiles.SmilesAtom
 
setDepth(Vector3f, Point3f, Point3f, Point3f, float) - Method in class org.jmol.g3d.Hermite3D
 
setDesiredQpt(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
setDialogLocation(Point) - Method in class org.jmol.export.dialog.FileChooser
 
setDialogSize(Dimension) - Method in class org.jmol.export.dialog.FileChooser
 
setDiffusePercent(int) - Static method in class org.jmol.g3d.Graphics3D
df in I = df * (N dot L) + sf * (R dot V)^p
setDimensions(int, int) - Method in class org.jmol.export.image.ImageEncoder
 
setDipole(String[]) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
setDipole() - Method in class org.jmol.shapespecial.Dipoles
 
setDipole(Atom, Atom, float, float) - Method in class org.jmol.shapespecial.Dipoles
 
setDirect() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
setDiscreteColixes(float[], short[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setDisplayMenuState() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setDoFixPeriodic() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
 
setDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setDrawing(int[]) - Method in class org.jmol.shapespecial.Draw
 
setDynamic(boolean) - Method in class org.jmol.modelset.Measurement
 
setDynamicMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
 
setE(double[], double) - Method in class org.jmol.quantum.MOCalculation
 
setEccentricity(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setEcho() - Method in class org.jmol.script.ScriptEvaluator
 
setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
 
setEchoStateActive(boolean) - Method in class org.jmol.viewer.Viewer
 
setEdges() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
setEdges() - Method in class org.jmol.shape.BbcageRenderer
 
setEdges() - Method in class org.jmol.shape.CageRenderer
 
setEdges() - Method in class org.jmol.shape.UccageRenderer
 
setEditorTextPane(ScriptEditor.EditorTextPane) - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
setElement(Atom, int) - Method in class org.jmol.modelset.AtomCollection
 
setElementArgb(int, int) - Method in class org.jmol.viewer.ColorManager
 
setElementArgb(int, int) - Method in class org.jmol.viewer.Viewer
 
setEllipsoid(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setEllipsoid(float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setEllipsoid(int, Object[]) - Method in class org.jmol.modelset.AtomCollection
 
setEllipsoidMatrix(Vector3f[], float[], Vector3f, Matrix3f) - Static method in class org.jmol.util.Quadric
 
setEnabled(JButton, boolean) - Method in class org.jmol.console.JmolConsole
 
setEncodeAlpha(boolean) - Method in class org.jmol.export.image.PngEncoder
Set the alpha encoding on or off.
setEnergies(String, String, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
setEnergy() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Interpret the Energy= line for non SCF type energy output
setEnergy(String, String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
setEnergy() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
setEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
setEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
setEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
setEqualPt - Variable in class org.jmol.script.ScriptCompiler
 
setError(Throwable) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setError(boolean) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
setErrorLineMessage(String, String, int, int, String) - Static method in class org.jmol.script.ScriptEvaluator
 
setErrorMessage(String) - Method in class org.jmol.script.ScriptEvaluator
 
setErrorMessage(String) - Method in class org.jmol.viewer.Viewer
 
setErrorMessage(String, String) - Method in class org.jmol.viewer.Viewer
 
setExplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of explicit hydrogen atoms bonded with this atom.
setFid(byte) - Method in class org.jmol.shape.Text
 
setFile() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
setFileData(Object) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setFileInfo(String[]) - Method in class org.jmol.viewer.FileManager
 
setFileInfo(String[]) - Method in class org.jmol.viewer.Viewer
 
setFileLoadStatus(String, String, String, String, int, boolean) - Method in class org.jmol.viewer.StatusManager
 
setFileLoadStatus(FileManager.EnumFileStatus, String, String, String, String) - Method in class org.jmol.viewer.Viewer
 
setFilename(String) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
setFilename(String) - Method in class org.jmol.console.ScriptEditor
 
setFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFilter(int) - Method in class org.jmol.export.image.PngEncoder
Set the filter to use
setFinalOperations(Point3f[], int, int, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setFinalOperations(Point3f[], int, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
setFinalOperations(Point3f[], int, int, boolean) - Method in class org.jmol.symmetry.Symmetry
 
setFixedRotationCenter(Point3f) - Method in class org.jmol.viewer.TransformManager
 
setFloatProperty(String, float) - Method in class org.jmol.api.JmolViewer
 
setFloatProperty(String, float) - Method in class org.jmol.script.ScriptEvaluator
 
setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
 
setFloatProperty(String, int, float) - Method in class org.jmol.viewer.Viewer
 
setFocus() - Method in class org.jmol.viewer.Viewer
 
setFont(byte) - Method in interface org.jmol.api.JmolRendererInterface
 
setFont(byte) - Method in class org.jmol.export.Export3D
 
setFont(byte) - Method in class org.jmol.g3d.Graphics3D
 
setFont(Font3D) - Method in class org.jmol.g3d.Graphics3D
 
setFont(int, byte) - Method in class org.jmol.shape.Labels
 
setFont(Font3D) - Method in class org.jmol.shape.Text
 
setFontScale(float) - Method in class org.jmol.shape.Text
 
setForcesUsingNumericalDerivative(MinAtom, int) - Method in class org.jmol.minimize.forcefield.ForceField
 
setFormalCharge(int) - Method in class org.jmol.modelset.Atom
 
setFormalCharges(BitSet, int) - Method in class org.jmol.modelset.AtomCollection
 
setFormalCharges(int) - Method in class org.jmol.viewer.Viewer
 
setFormats(String) - Method in class org.jmol.shape.Measures
 
setForVdwClash(boolean) - Method in class org.jmol.util.ContactPair
 
setFractionalCoord(int, float, boolean) - Method in class org.jmol.modelset.Atom
 
setFractionalCoord(Point3f, boolean) - Method in class org.jmol.modelset.Atom
 
setFractionalCoord(Point3f, Point3f, boolean) - Method in class org.jmol.modelset.Atom
 
setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFrameOffset(int) - Method in class org.jmol.viewer.TransformManager
 
setFrameOffset(int) - Method in class org.jmol.viewer.Viewer
 
setFrameOffsets(Point3f[]) - Method in class org.jmol.viewer.TransformManager
 
setFrameOffsets(BitSet) - Method in class org.jmol.viewer.Viewer
 
setFrameRangeVisible() - Method in class org.jmol.viewer.AnimationManager
 
setFrameTitle(BitSet, Object) - Method in class org.jmol.modelset.ModelCollection
 
setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
 
setFrameTitle(Object) - Method in class org.jmol.viewer.Viewer
 
setFrameVariables(int, int) - Method in class org.jmol.viewer.Viewer
 
setFrankMenu(String) - Method in class org.jmol.popup.JmolPopup
 
setFrankOn(boolean) - Method in class org.jmol.api.JmolViewer
 
setFrankOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setFreqValue(float, String[]) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
setFromBits(int, BitSet) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setFront(int, boolean) - Method in class org.jmol.shape.Labels
 
setFunction(ScriptFunction) - Method in class org.jmol.script.ScriptFlowContext
 
setFunction(ScriptFunction, String, int, int, short[], int[][], List<Token[]>) - Static method in class org.jmol.script.ScriptFunction
 
setFunctionXY(List<Object>) - Method in class org.jmol.jvxl.readers.Parameters
 
setFunctionXYZ(List<Object>) - Method in class org.jmol.jvxl.readers.Parameters
 
setGeneralBindings() - Method in class org.jmol.viewer.binding.JmolBinding
 
setGestureSwipeFactor(float) - Method in class org.jmol.viewer.ActionManager
 
setGhostOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setGlobal() - Method in class org.jmol.script.ScriptVariable
 
setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setGouraud(int, int, int) - Method in class org.jmol.g3d.Triangle3D
 
setGreyscaleMode(boolean) - Method in class org.jmol.g3d.Graphics3D
controls greyscale rendering
setGridLimitsForAtom(Point3f, float, Point3i, Point3i) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setGroup(Group) - Method in class org.jmol.modelset.Atom
 
setGroup(int, boolean) - Method in class org.jmol.shape.Labels
 
setGroupIndex(int) - Method in class org.jmol.modelset.Group
 
setGroupParameter(int, float) - Method in class org.jmol.modelset.Group
 
setHandler(XMLReader, XmlReader.JmolXmlHandler) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
setHaveHsAlready(boolean) - Method in interface org.jmol.api.JmolBioResolver
 
setHaveHsAlready(boolean) - Method in class org.jmol.modelsetbio.Resolver
 
setHaveStraightness(boolean) - Method in class org.jmol.modelset.AtomCollection
 
setHbond() - Method in class org.jmol.script.ScriptEvaluator
 
setHeader(String, String) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setHeader(String) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
setHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
 
setHeading(Point3f, Vector3f, int) - Method in class org.jmol.shapesurface.Isosurface
 
setHidden(boolean) - Method in class org.jmol.modelset.Measurement
 
setHideNotSelected(boolean) - Method in class org.jmol.viewer.SelectionManager
 
setHints(int) - Method in class org.jmol.export.image.ImageEncoder
 
setHoverLabel(String) - Method in class org.jmol.viewer.Viewer
 
setHydrogen(int, int, String, Point3f) - Method in class org.jmol.modelsetbio.Resolver
 
setHydrogenCount(SmilesSearch) - Method in class org.jmol.smiles.SmilesAtom
Finalizes the hydrogen count hydrogens in a SmilesMolecule.
setHydrophobicity(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setImage(Image) - Method in class org.jmol.export.image.PngEncoder
Set the image to be encoded
setImage(Object) - Method in class org.jmol.shape.Text
 
setImageDimensions(int, int) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Sets the output image dimensions.
setImageInfo(int, int, String) - Method in interface org.jmol.api.JmolDialogInterface
 
setImageInfo(int, int, String) - Method in class org.jmol.export.dialog.Dialog
 
setImplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of implicit hydrogen atoms bonded with this atom.
setIndex(int) - Method in class org.jmol.modelset.Bond
 
setIndex(int) - Method in class org.jmol.modelset.Measurement
 
setIndexes(DefaultMutableTreeNode) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Sets the indexes to the atomSetIndex values of each leaf of the node.
setIndices() - Method in class org.jmol.shape.Measures
 
setInfo(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
setInMotion(boolean) - Method in class org.jmol.viewer.AnimationManager
 
setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
 
setIntersectData() - Method in class org.jmol.shapespecial.Draw
 
setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
 
setIntProperty(String, int) - Method in class org.jmol.script.ScriptEvaluator
 
setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
 
setIntProperty(String, int, int) - Method in class org.jmol.viewer.Viewer
 
setIonicRadius(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setIsBigEndian(boolean) - Method in class org.jmol.util.BinaryDocument
 
setIsDna(boolean) - Method in class org.jmol.modelset.Chain
 
setIsPDB() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setIsRna(boolean) - Method in class org.jmol.modelset.Chain
 
setIteratorForAtom(AtomIndexIterator, int, float) - Method in interface org.jmol.atomdata.AtomDataServer
 
setIteratorForAtom(AtomIndexIterator, int, int, float, RadiusData) - Method in class org.jmol.modelset.ModelCollection
 
setIteratorForAtom(AtomIndexIterator, int, float) - Method in class org.jmol.viewer.Viewer
 
setIteratorForPoint(AtomIndexIterator, int, Point3f, float) - Method in interface org.jmol.atomdata.AtomDataServer
 
setIteratorForPoint(AtomIndexIterator, int, Point3f, float) - Method in class org.jmol.modelset.ModelCollection
 
setIteratorForPoint(AtomIndexIterator, int, Point3f, float) - Method in class org.jmol.viewer.Viewer
 
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.api.JmolViewer
 
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.StatusManager
 
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.Viewer
 
setJmolDataFrame(String, int, int) - Method in class org.jmol.modelset.ModelCollection
 
setJmolDataFrame(String, int, int) - Method in class org.jmol.viewer.Viewer
 
setJmolDefaults() - Method in class org.jmol.api.JmolViewer
 
setJmolDefaults() - Method in class org.jmol.viewer.StateManager
 
setJmolDefaults() - Method in class org.jmol.viewer.Viewer
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.api.JmolViewer
 
setJmolStatusListener(JmolStatusListener, JmolCallbackListener) - Method in class org.jmol.viewer.StatusManager
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
 
setJvxlColorMap(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
set up the jvxlData fields needed for either just the header (isAll = false) or the full file (isAll = true)
setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setJvxlDataRendering() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setJvxlInfo() - Method in class org.jmol.shapesurface.Isosurface
 
setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
setLabel(Object, String) - Method in class org.jmol.popup.SimplePopup
 
setLabel(String) - Method in class org.jmol.script.ScriptEvaluator
 
setLabel(LabelToken[][], String, int) - Method in class org.jmol.shape.Labels
 
setLabel(String, BitSet) - Method in class org.jmol.viewer.ShapeManager
 
setLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.BannerFrame
 
setLabels() - Method in class org.jmol.console.AppletConsole
 
setLanguagePath(String) - Static method in class org.jmol.i18n.GT
 
setLastError(String) - Static method in exception org.jmol.smiles.InvalidSmilesException
 
setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
set symmetry lattice type using Hall rotations
setLattice(int) - Method in class org.jmol.symmetry.SpaceGroup
 
setLattice(char, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
setLattice(int) - Method in class org.jmol.symmetry.Symmetry
 
setLatticeCells(int[], boolean, boolean, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setLatticeVectors() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
setLcao(String, int) - Method in class org.jmol.jvxl.readers.Parameters
 
setLcao() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setLcaoOn(boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setLcaoOn(int, boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setLength(Object, int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(String[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(float[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(int[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(short[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(byte[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(boolean[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLigandModel(String, String) - Method in class org.jmol.viewer.Viewer
 
setLighting(int) - Method in class org.jmol.shape.Mesh
 
setLine() - Method in class org.jmol.script.ScriptFlowContext
 
setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
setLinearOffsets() - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
setLineBits(float, float) - Method in class org.jmol.g3d.Line3D
 
setLoadFormat(String, char, boolean) - Method in class org.jmol.viewer.Viewer
 
setLoadParameters(Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
 
setLoadState(Map<String, Object>) - Method in class org.jmol.viewer.FileManager
 
setLobe(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setLocalPath(JmolViewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
called by getImageFileNameFromDialog called by getOpenFileNameFromDialog called by getSaveFileNameFromDialog called by classifyName for any full file load called from the CD command currentLocalPath is set in all cases and is used specifically for dialogs as a first try defaultDirectoryLocal is set only when not from a dialog and is used only in getLocalPathForWritingFile or from an open/save dialog.
setLogFile(String) - Method in class org.jmol.viewer.Viewer
 
setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
Replaces the current logger implementation by a new one.
setLogging() - Method in class org.jmol.applet.Jmol
 
setLoggingEnabled(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setLogLevel(int) - Static method in class org.jmol.util.Logger
Activates all logging levels up through a given level.
setLp(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setMad(short) - Method in class org.jmol.modelset.Bond
 
setMad(short, BitSet, float[]) - Method in class org.jmol.shapebio.BioShape
 
setMad(int, short) - Method in class org.jmol.shapebio.BioShape
 
setMadAtom(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
 
setMads(short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setMads(int, boolean) - Method in class org.jmol.shapebio.BioShapeRenderer
 
setMappingPlane(Point4f) - Method in class org.jmol.jvxl.data.VolumeData
 
setMapRanges(SurfaceReader, boolean) - Method in class org.jmol.jvxl.readers.Parameters
 
setMarBond(short) - Method in class org.jmol.api.JmolViewer
 
setMarBond(short) - Method in class org.jmol.viewer.Viewer
 
setMarchingSquares(MarchingSquares) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setMatchingAtom(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of a matching atom in a molecule.
setMatrices() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
setMatrix() - Method in class org.jmol.jvxl.data.VolumeData
 
setMatrix() - Method in class org.jmol.util.Quaternion
 
setMatrixFromXYZ(String) - Method in class org.jmol.symmetry.SymmetryOperation
 
setMaximumSize(int) - Method in class org.jmol.viewer.Viewer
 
setMaxSize(int) - Method in class org.jmol.util.CommandHistory
Resets maximum size of command queue.
setMeasureDistanceUnits(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setMeasureDistanceUnits(String) - Method in class org.jmol.viewer.Viewer
 
setMeasurementUnits(String) - Method in class org.jmol.script.ScriptEvaluator
 
setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setMep(float[], boolean) - Method in class org.jmol.jvxl.readers.Parameters
 
setMerged(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setMesh(String) - Method in class org.jmol.shape.MeshCollection
 
setMesh() - Method in class org.jmol.shapesurface.Isosurface
 
setMeshCreator(Object) - Method in class org.jmol.viewer.Viewer
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer viewer = applet.getViewer(); viewer.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
setMeshDisplayProperty(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
 
setMeshTokenProperty(Mesh, int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
 
setMinBondDistance(float) - Method in class org.jmol.api.JmolViewer
 
setMinBondDistance(float) - Method in class org.jmol.viewer.Viewer
 
setMinimizationOn(boolean) - Method in class org.jmol.minimize.Minimizer
 
setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setMinMax(int) - Method in class org.jmol.quantum.QuantumCalculation
 
setMinMaxLatticeParameters(Point3i, Point3i) - Method in interface org.jmol.api.SymmetryInterface
 
setMinMaxLatticeParameters(Point3i, Point3i) - Method in class org.jmol.symmetry.Symmetry
 
setMinMaxLatticeParameters(Point3i, Point3i) - Method in class org.jmol.symmetry.UnitCell
 
setMO(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
setMO(int, float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
setMOData(Map<String, Object>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setMoData(List<Object[]>, int, float[], int, boolean, int, String) - Method in class org.jmol.script.ScriptEvaluator
 
setModel(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
 
setModel(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
setModel(int) - Method in class org.jmol.shape.Object2d
 
setModelAuxiliaryInfo(int, Object, Object) - Method in class org.jmol.modelset.ModelCollection
 
setModelClickability() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setModelClickability() - Method in class org.jmol.shape.AtomShape
 
setModelClickability() - Method in class org.jmol.shape.Balls
 
setModelClickability() - Method in class org.jmol.shape.Labels
 
setModelClickability() - Method in class org.jmol.shape.Shape
 
setModelClickability() - Method in class org.jmol.shape.Sticks
 
setModelClickability() - Method in class org.jmol.shapebio.Backbone
 
setModelClickability() - Method in class org.jmol.shapebio.BioShape
 
setModelClickability() - Method in class org.jmol.shapebio.BioShapeCollection
 
setModelClickability() - Method in class org.jmol.shapespecial.Dots
 
setModelIndex(int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setModelIndex(short) - Method in class org.jmol.modelset.Measurement
 
setModelIndex(int) - Method in class org.jmol.modelset.ModelCollection.StateScript
 
setModelIndex() - Method in class org.jmol.shapespecial.Dipoles
 
setModelKitMode(boolean) - Method in class org.jmol.viewer.Viewer
 
setModelkitMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setModelNameNumberProperties(int, int, String, int, Properties, Map<String, Object>, String) - Method in class org.jmol.modelset.ModelLoader
 
setModelParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
setModelSet(ModelSet) - Method in class org.jmol.modelset.Chain
 
setModelSet(ModelSet) - Method in class org.jmol.modelset.Group
 
setModelSet(ModelSet) - Method in class org.jmol.shape.Shape
 
setModelVisibility() - Method in class org.jmol.viewer.ShapeManager
 
setModelVisibility() - Method in class org.jmol.viewer.Viewer
 
setModeMouse(int) - Method in class org.jmol.api.JmolViewer
 
setModeMouse(int) - Method in class org.jmol.viewer.ActionManager
only NONE (-1) is implemented; it just stops the hoverWatcher thread so that the viewer references are all removed
setModeMouse(int) - Method in class org.jmol.viewer.Viewer
 
setMonitor() - Method in class org.jmol.script.ScriptEvaluator
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
 
setMotionFixedAtoms(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
setMotionFixedAtoms(BitSet) - Method in class org.jmol.viewer.Viewer
 
setMOType(Map<String, Object>, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
setMouseDragFactor(float) - Method in class org.jmol.viewer.ActionManager
 
setMouseEnabled(boolean) - Method in class org.jmol.viewer.Viewer
 
setMouseMode() - Method in class org.jmol.awt.Mouse
 
setMouseMode() - Method in class org.jmol.viewer.ActionManager
 
setMouseWheelFactor(float) - Method in class org.jmol.viewer.ActionManager
 
setMovableBitSet(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
setMovableX(int) - Method in class org.jmol.shape.Object2d
 
setMovableXPercent(int) - Method in class org.jmol.shape.Object2d
 
setMovableY(int) - Method in class org.jmol.shape.Object2d
 
setMovableYPercent(int) - Method in class org.jmol.shape.Object2d
 
setMovableZ(int) - Method in class org.jmol.shape.Object2d
 
setMovableZPercent(int) - Method in class org.jmol.shape.Object2d
 
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
setNAltLocs(int) - Method in class org.jmol.modelset.Model
 
setName(String) - Method in class org.jmol.script.ScriptVariable
 
setNavFps(int) - Method in class org.jmol.viewer.TransformManager
 
setNavFps(int) - Method in class org.jmol.viewer.TransformManager11
 
setNavigationDepthPercent(float, float) - Method in class org.jmol.viewer.TransformManager
sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be <0 or >100)
setNavigationDepthPercent(float, float) - Method in class org.jmol.viewer.TransformManager11
 
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.TransformManager11
 
setNavigationDepthPercent(float, float) - Method in class org.jmol.viewer.Viewer
 
setNavigationMode(boolean) - Method in class org.jmol.viewer.TransformManager
 
setNavigationMode(boolean) - Method in class org.jmol.viewer.Viewer
 
setNavigationOffsetRelative(boolean) - Method in class org.jmol.viewer.TransformManager
 
setNavigationOffsetRelative(boolean) - Method in class org.jmol.viewer.TransformManager11
 
setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager
 
setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager11
 
setNavOn(boolean) - Method in class org.jmol.viewer.TransformManager
 
setNavOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setNavXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
 
setNavXYZ(float, float, float) - Method in class org.jmol.viewer.Viewer
 
setNci(boolean) - Method in class org.jmol.jvxl.readers.Parameters
 
setNeighbors(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
setNested(int, Object) - Method in class org.jmol.smiles.SmilesSearch
 
setNewRotationCenter(Point3f, boolean) - Method in class org.jmol.viewer.TransformManager
 
setNewRotationCenter(Point3f) - Method in class org.jmol.viewer.Viewer
 
setNewSetCommand(boolean, String) - Method in class org.jmol.script.ScriptCompiler
 
setNewWindowParametersForExport() - Method in class org.jmol.g3d.Graphics3D
 
setNext(String, String, int[], int) - Static method in class org.jmol.util.XmlReader
shift pointer to a new tag or field contents
setNInsertions(int) - Method in class org.jmol.modelset.Model
 
setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
used by CartoonRenderer (DNA surface) and GeoSurfaceRenderer (face) to assign a noisy shade to the surface it will render
setNoneSelected(boolean) - Method in class org.jmol.viewer.Viewer
 
setNonhydrogenDegree(int) - Method in class org.jmol.smiles.SmilesAtom
 
setNoPrompt() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
setNotionalUnitCell(float[], Matrix3f, Point3f) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setObjectArgb(String, int) - Method in class org.jmol.script.ScriptEvaluator
 
setObjectArgb(String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectColor(String, String) - Method in class org.jmol.viewer.Viewer
 
setObjectMad(int, String, int) - Method in class org.jmol.script.ScriptEvaluator
 
setObjectMad(int, String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectProperty() - Method in class org.jmol.script.ScriptEvaluator
 
setOccupancy(int, int) - Method in class org.jmol.modelset.AtomCollection
 
setOffset(int) - Method in interface org.jmol.api.SymmetryInterface
 
setOffset(int) - Method in class org.jmol.shape.Object2d
 
setOffset(int) - Method in class org.jmol.symmetry.Symmetry
 
setOffset(Point3f[], int, int) - Method in class org.jmol.symmetry.SymmetryOperation
 
setOffset(Point3f) - Method in class org.jmol.symmetry.UnitCell
 
setOffset(int) - Method in class org.jmol.symmetry.UnitCell
 
setOffsetPositions() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
setOffsets(int, int, boolean) - Method in class org.jmol.shape.Labels
 
setOrbital(int, float[]) - Method in class org.jmol.shapesurface.MolecularOrbital
 
setOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
setOrder(int) - Method in class org.jmol.modelset.Bond
 
setOrientation(Matrix3f) - Method in class org.jmol.symmetry.UnitCell
 
setOutputStream(BinaryDocument, OutputStream) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
setOutputStream(OutputStream) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
setOutputStream(BinaryDocument, OutputStream) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setOutputStream(OutputStream) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setOutputStream(BinaryDocument, OutputStream) - Method in class org.jmol.shapesurface.Isosurface
 
setOutputStream(OutputStream, Viewer, double) - Method in class org.jmol.util.BinaryDocument
 
setPaletteID(byte) - Method in class org.jmol.modelset.Atom
 
setPaletteID(byte) - Method in class org.jmol.modelset.Bond
 
setPaletteID(byte) - Method in class org.jmol.modelset.HBond
 
setPanel(JPanel) - Method in class org.openscience.jmol.app.jmolpanel.KioskFrame
 
setParallel(boolean) - Method in class org.jmol.viewer.Viewer
 
setparam - Static variable in class org.jmol.script.Token
 
setParameter(String, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
setParameter(String, Object) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setParameter is the main interface for surface generation.
setParameter(String, Object, BitSet) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setParameters(VolumeData, Parameters) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
setParameterValue(String, boolean) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setParameterValue(String, int) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setParameterValue(String, float) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setParameterValue(String, String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setParams(Map<String, FFParam>) - Method in class org.jmol.minimize.forcefield.Calculations
 
setParent(SmilesSearch) - Method in class org.jmol.smiles.SmilesSearch
 
setPartialCharge(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setPdb() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setPdbConectBonding(int, int, BitSet) - Method in class org.jmol.modelset.ModelSet
 
setPdbConectBonding(boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
setPendingMeasurement(MeasurementPending) - Method in class org.jmol.viewer.Viewer
 
setPercentVdwAtom(int) - Method in class org.jmol.api.JmolViewer
 
setPercentVdwAtom(int) - Method in class org.jmol.viewer.Viewer
 
setPerspectiveDepth(boolean) - Method in class org.jmol.api.JmolViewer
 
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.TransformManager
 
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.Viewer
 
setPerspectiveModel(int) - Method in class org.jmol.viewer.Viewer
 
setPhongExponent(int) - Static method in class org.jmol.g3d.Graphics3D
p in I = df * (N dot L) + sf * (R dot V)^p
setPhononVector(float[], Atom, Vector3f, Vector3f, Vector3f) - Method in class org.jmol.adapter.readers.xtal.CastepReader
transform complex vibration vector to a real vector by applying the appropriate translation, storing the results in v
setPickBindings() - Method in class org.jmol.viewer.binding.JmolBinding
 
setPicked(int) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setPicked(int) - Method in class org.jmol.viewer.Viewer
 
setPicking() - Method in class org.jmol.script.ScriptEvaluator
 
setPickingMode(int) - Method in class org.jmol.viewer.ActionManager
 
setPickingMode(String, int) - Method in class org.jmol.viewer.Viewer
 
setPickingStyle() - Method in class org.jmol.script.ScriptEvaluator
 
setPickingStyle(int) - Method in class org.jmol.viewer.ActionManager
 
setPickingStyle(String, int) - Method in class org.jmol.viewer.Viewer
 
setPixels(int, int, int, int, ColorModel, byte[], int, int) - Method in class org.jmol.export.image.ImageEncoder
 
setPixels(int, int, int, int, ColorModel, int[], int, int) - Method in class org.jmol.export.image.ImageEncoder
 
setPlane(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setPlaneDerivatives() - Method in class org.jmol.g3d.Sphere3D
 
setPlaneParameters(Point4f) - Method in interface org.jmol.api.VolumeDataInterface
 
setPlaneParameters(Point4f) - Method in class org.jmol.jvxl.data.VolumeData
 
setPlanes(float[][]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
Planes to use for holding raw file data.
setPlanes(float[][]) - Method in class org.jmol.quantum.NciCalculation
Raw file data planes are passed to us here from VolumeFileReader
setPoint(Point3f, Point3f, Vector3f, int) - Method in class org.jmol.g3d.Hermite3D
 
setPoint(float[], int, int, int) - Static method in class org.jmol.util.MeshSurface
 
setPointer(int, int) - Method in class org.jmol.shape.Labels
 
setPointer(int) - Method in class org.jmol.shape.Object2d
 
setPointGroup(SymmetryInterface, Atom[], BitSet, boolean, float, float) - Method in interface org.jmol.api.SymmetryInterface
 
setPointGroup(SymmetryInterface, Atom[], BitSet, boolean, float, float) - Method in class org.jmol.symmetry.Symmetry
 
setPoints(int, int) - Method in class org.jmol.shapespecial.Draw
 
setPolygon(int) - Method in class org.jmol.shapespecial.Draw
 
setPolygonColix(int, short) - Method in class org.jmol.util.MeshSurface
 
setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
 
setPopInDim(int, int) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setPosition(float) - Method in class org.jmol.shape.Text
 
setPositions() - Method in class org.jmol.adapter.readers.simple.AmpacReader
 
setPreliminary(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setPreserveState(boolean) - Method in class org.jmol.modelset.AtomCollection
 
setPrincipalAxis(int, int) - Method in class org.jmol.symmetry.PointGroup
 
setPrincipalPlane(int, int) - Method in class org.jmol.symmetry.PointGroup
 
setPrivateKeyForShape(int) - Method in class org.jmol.viewer.Viewer
 
setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
 
setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
 
setProperties(Hashtable<?, ?>) - Method in class org.jmol.export.image.ImageEncoder
 
setProperty(String, Object) - Method in interface org.jmol.api.MinimizerInterface
 
setProperty(String, Object) - Method in class org.jmol.minimize.Minimizer
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.AtomShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Axes
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Balls
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Echo
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.FontLineShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.FontShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Halos
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Hover
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Labels
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Measures
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.MeshCollection
 
setProperty(String, Object, Object2d) - Static method in class org.jmol.shape.Object2d
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Object2dShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Shape
may come from any source -- executed AFTER a shape's own setProperty method
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Sticks
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.TextShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapebio.Backbone
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Dipoles
 
setProperty(int, boolean, int, float) - Method in class org.jmol.shapespecial.Dipoles
 
setProperty(int, Dipole, int, float) - Method in class org.jmol.shapespecial.Dipoles
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Dots
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Draw
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Ellipsoids
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Polyhedra
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Vectors
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapesurface.Contact
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapesurface.Isosurface
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapesurface.MolecularOrbital
 
setPropertyColorRange(float[], BitSet, String) - Method in class org.jmol.viewer.ColorManager
 
setPropertyColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
 
setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.ColorManager
 
setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
setPropertySuper(String, Object, BitSet) - Method in class org.jmol.shapespecial.Draw
 
setPropertySuper(String, Object, BitSet) - Method in class org.jmol.shapesurface.Isosurface
 
setProteinStructureId(int) - Method in class org.jmol.modelset.Group
 
setProteinStructureId(int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setProteinStructureId(int) - Method in class org.jmol.modelsetbio.Monomer
 
setProteinStructureType(EnumStructure, int) - Method in class org.jmol.modelset.Group
 
setProteinStructureType(EnumStructure, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setProteinType(BitSet, EnumStructure) - Method in class org.jmol.modelset.ModelCollection
 
setProteinType(EnumStructure, BitSet) - Method in class org.jmol.viewer.Viewer
 
setPt0(int, boolean) - Method in class org.jmol.script.ScriptFlowContext
 
setQuality(int) - Method in class org.jmol.util.JpegEncoder
 
setRadical(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setRadius(float) - Method in class org.jmol.modelset.Atom
 
setRandom(boolean) - Method in class org.jmol.util.BinaryDocument
 
setRange(float, float, boolean) - Method in class org.jmol.util.ColorEncoder
 
setRanges(float, int) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setRasmolDefaults() - Method in class org.jmol.api.JmolViewer
 
setRasMolDefaults() - Method in class org.jmol.viewer.StateManager
 
setRasmolDefaults() - Method in class org.jmol.viewer.Viewer
 
setReader() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setRef(Quaternion) - Method in class org.jmol.util.Quaternion
 
setRefreshing(boolean) - Method in class org.jmol.viewer.Viewer
 
setRenderer(JmolRendererInterface) - Method in class org.jmol.export.___Exporter
 
setRgb(byte[], byte[], byte[]) - Method in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
setRingConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRingData(BitSet) - Method in class org.jmol.smiles.SmilesSearch
 
setRingMembership(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRingSize(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRotateBondIndex(int) - Method in class org.jmol.viewer.Viewer
 
setRotateMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setRotation(Matrix3f) - Method in class org.jmol.viewer.TransformManager
 
setRotationCenterAndRadiusXYZ(Point3f, boolean) - Method in class org.jmol.viewer.TransformManager
 
setRotationCenterAndRadiusXYZ(String, Point3f) - Method in class org.jmol.viewer.TransformManager
 
setRotationMatrix(Matrix3f) - Method in class org.jmol.g3d.Normix3D
 
setRotationMatrix(Matrix3f) - Method in class org.jmol.viewer.Viewer
 
setRotationPointXY(Point3f) - Method in class org.jmol.viewer.TransformManager
 
setRotationRadius(int, float) - Method in class org.jmol.modelset.ModelCollection
 
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.TransformManager
 
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.Viewer
 
setRubberbandArgb(int) - Method in class org.jmol.viewer.ColorManager
 
setRubberbandArgb(int) - Method in class org.jmol.viewer.Viewer
 
setScale(float) - Method in class org.jmol.shape.Axes
 
setScaleAngstromsPerInch(float) - Method in class org.jmol.viewer.TransformManager
 
setScalePixelsPerMicron(float) - Method in class org.jmol.shape.Object2d
 
setScalePixelsPerMicron(float) - Method in class org.jmol.shape.Text
 
setScaling() - Method in class org.jmol.shape.Labels
 
setScreenDimension(int, int) - Method in class org.jmol.api.JmolViewer
 
setScreenDimension(int, int) - Method in class org.jmol.viewer.Viewer
 
setScreenParameters(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
setScreenParameters(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager11
 
setScript(String) - Method in class org.jmol.script.ScriptFunction
 
setScript(String) - Method in class org.jmol.shape.Object2d
 
setScriptButtonPercent(int) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setScriptEcho(String, boolean) - Method in class org.jmol.viewer.StatusManager
 
setScriptEditor(ScriptEditor) - Method in class org.jmol.console.JmolConsole
 
setScriptExtensions() - Method in class org.jmol.script.ScriptEvaluator
 
setScriptFileReferences(String, String, String, String) - Static method in class org.jmol.viewer.FileManager
 
setScriptFileReferences(String, String, boolean) - Static method in class org.jmol.viewer.FileManager
Sets all local file references in a script file to point to files within dataPath.
setScriptInfo(String) - Method in class org.jmol.shapesurface.Isosurface
 
setScriptQueue(boolean) - Method in class org.jmol.viewer.Viewer
 
setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.StatusManager
 
setSelectBindings() - Method in class org.jmol.viewer.binding.DragBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.JmolBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.PfaatBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.RasmolBinding
 
setSelected(BitSet) - Method in class org.jmol.smiles.SmilesSearch
 
setSelected(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.SelectionManager
 
setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setSelectedFloats(float, BitSet, float[]) - Static method in class org.jmol.util.Parser
 
setSelectedOctant() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
setSelectedTranslation(BitSet, char, int) - Method in class org.jmol.viewer.RepaintManager
 
setSelectedValue(int, ScriptVariable) - Method in class org.jmol.script.ScriptVariable
 
setSelectionHaloEnabled(boolean) - Method in class org.jmol.modelset.ModelSet
 
setSelectionHalos(boolean) - Method in class org.jmol.api.JmolViewer
 
setSelectionHalos(boolean) - Method in class org.jmol.viewer.Viewer
 
setSelectionSet(BitSet) - Method in class org.jmol.api.JmolViewer
 
setSelectionSet(BitSet, Boolean) - Method in class org.jmol.viewer.SelectionManager
 
setSelectionSet(BitSet) - Method in class org.jmol.viewer.Viewer
 
setSelectionSubset(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
setSelectionSubset(BitSet) - Method in class org.jmol.viewer.Viewer
 
setShapeErrorState(int, String) - Method in class org.jmol.viewer.Viewer
 
setShapeId(int, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
setShapeModelSet(ModelSet) - Method in class org.jmol.viewer.ShapeManager
 
setShapeProperty(int, String, Object) - Method in class org.jmol.script.ScriptEvaluator
 
setShapeProperty(int, String, Object, BitSet) - Method in class org.jmol.script.ScriptEvaluator
 
setShapeProperty(String, Object, BitSet) - Method in class org.jmol.shape.Shape
specifically from modelSet.setShapeProperty, mostly from ScriptEvaluation, but not always -- definitely not from "super.setProperty"
setShapeProperty(int, String, Object, BitSet) - Method in class org.jmol.viewer.ShapeManager
 
setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
 
setShapeSize(int, int, BitSet) - Method in class org.jmol.script.ScriptEvaluator
 
setShapeSize(int, RadiusData) - Method in class org.jmol.script.ScriptEvaluator
 
setShapeSize(int, RadiusData, BitSet) - Method in class org.jmol.shape.Shape
 
setShapeSize(int, RadiusData, BitSet) - Method in class org.jmol.shapebio.Backbone
 
setShapeSize(int, RadiusData, BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
 
setShapeSize(int, int, RadiusData, BitSet) - Method in class org.jmol.viewer.ShapeManager
 
setShapeSize(int, int, BitSet) - Method in class org.jmol.viewer.Viewer
 
setShapeSize(int, RadiusData, BitSet) - Method in class org.jmol.viewer.Viewer
 
setShapeState(Map<String, BitSet>, Map<String, BitSet>) - Method in class org.jmol.shapebio.BioShape
 
setShapeTranslucency(int, String, String, float, BitSet) - Method in class org.jmol.script.ScriptEvaluator
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
 
setShapeVisibility(boolean) - Method in class org.jmol.modelset.Bond
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Group
 
setShapeVisibilityFlags(int) - Method in class org.jmol.modelset.Atom
 
setShapeVisibilityFlags(int) - Method in class org.jmol.modelset.Bond
 
setShowAxes(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowAxes(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowBbcage(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowBbcage(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowHydrogens(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowHydrogens(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowMeasurements(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowWithin(List<Point3f>, float, boolean) - Method in class org.jmol.shape.Mesh
 
setSilent(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setSingleItem(List<Object>) - Method in class org.jmol.shape.Measures
 
setSize(int, BitSet) - Method in class org.jmol.shape.AtomShape
 
setSize(RadiusData, BitSet) - Method in class org.jmol.shape.AtomShape
 
setSize(RadiusData, BitSet) - Method in class org.jmol.shape.Balls
 
setSize(int, BitSet) - Method in class org.jmol.shape.Measures
 
setSize(int, BitSet) - Method in class org.jmol.shape.Shape
 
setSize(RadiusData, BitSet) - Method in class org.jmol.shape.Shape
 
setSize(int, BitSet) - Method in class org.jmol.shape.Sticks
sets the size of a bond, or sets the selectedBonds set
setSize(RadiusData, BitSet) - Method in class org.jmol.shapespecial.Dots
 
setSize(int, BitSet) - Method in class org.jmol.shapespecial.Ellipsoids
 
setSlab(int) - Method in interface org.jmol.api.JmolRendererInterface
 
setSlab(int) - Method in class org.jmol.export.Export3D
 
setSlab(int) - Method in class org.jmol.g3d.Graphics3D
 
setSlab(BitSet, BitSet, String, String, float) - Method in class org.jmol.util.MeshSurface
 
setSlabAndDepthValues(int, int, boolean, int, int) - Method in class org.jmol.g3d.Graphics3D
clipping from the front and the back
setSlabData() - Method in class org.jmol.shapespecial.Draw
 
setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.TransformManager
set internal slab or depth from screen-based slab or depth
setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.Viewer
 
setSlabEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
 
setSlabRange(float) - Method in class org.jmol.viewer.TransformManager
 
setSlaters(boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
after the vectors intinfo and floatinfo are completed, we
setSlice(float, float, float, float, Point3f, Vector3f, boolean) - Method in class org.openscience.jmol.app.surfacetool.Slice
Sets the right plane and left plane bounding a slice.
setSlice(float, float, float, float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
Defines a slice within which isosurfaces (and in future? atoms) are displayed.
setSliceAnglefromZ(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSliceAngleXY(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSlicePosition(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSliceThickness(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSmilesBondCoordinates(SmilesAtom, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
 
setSmilesCoordinates(JmolNode, SmilesAtom, SmilesAtom, JmolNode[]) - Method in class org.jmol.smiles.SmilesSearch
 
setSmilesString(String) - Method in class org.jmol.viewer.Viewer
 
setSolvent(String, float) - Method in class org.jmol.jvxl.readers.Parameters
 
setSpaceGroup(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroup(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroup(boolean) - Method in class org.jmol.symmetry.Symmetry
 
setSpaceGroup(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
setSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setSpecular(boolean) - Static method in class org.jmol.g3d.Graphics3D
 
setSpecularExponent(int) - Static method in class org.jmol.g3d.Graphics3D
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of shades
setSpecularPercent(int) - Static method in class org.jmol.g3d.Graphics3D
sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything, really
setSpecularPower(int) - Static method in class org.jmol.g3d.Graphics3D
fractional distance to white for specular dot
setSphere(float) - Method in class org.jmol.jvxl.readers.Parameters
 
setSphereMatrix(Point3f, float, float, float, AxisAngle4f, Matrix4f) - Method in class org.jmol.export.__CartesianExporter
 
setSpin(String, int) - Method in class org.jmol.viewer.Viewer
 
setSpinFps(int) - Method in class org.jmol.viewer.TransformManager
 
setSpinOn(boolean) - Method in class org.jmol.viewer.TransformManager
 
setSpinOn(boolean, float, List<Point3f>, BitSet, boolean) - Method in class org.jmol.viewer.TransformManager
 
setSpinOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setSpinXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
 
setSsbond() - Method in class org.jmol.script.ScriptEvaluator
 
setsSuccessful - Variable in class org.jmol.jvxl.data.MeshData
 
setStateInfo(Map<String, BitSet>, int, String) - Static method in class org.jmol.shape.Shape
 
setStateInfo(Map<String, BitSet>, int, int, String) - Static method in class org.jmol.shape.Shape
 
setStateInfo(Map<String, BitSet>, int, int, String) - Static method in class org.jmol.viewer.StateManager
 
setStatement(int) - Method in class org.jmol.script.ScriptEvaluator
provides support for @x and @{....} in statements.
setStateScriptVersion(String) - Method in class org.jmol.viewer.Viewer
 
setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusBar
 
setStatusAppletReady(String, boolean) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomHovered(int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomHovered(int, String) - Method in class org.jmol.viewer.Viewer
 
setStatusAtomMoved(BitSet) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomPicked(int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomPicked(int, String) - Method in class org.jmol.viewer.Viewer
 
setStatusChanged(String, int, Object, boolean) - Method in class org.jmol.viewer.StatusManager
 
setStatusClicked(int, int, int, int, int) - Method in class org.jmol.viewer.StatusManager
 
setStatusFrameChanged() - Method in class org.jmol.viewer.AnimationManager
 
setStatusFrameChanged(int, int, int, int, int) - Method in class org.jmol.viewer.StatusManager
 
setStatusFrameChanged(int) - Method in class org.jmol.viewer.Viewer
 
setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.StatusManager
 
setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.Viewer
 
setStatusPicked(int, Point3f) - Method in class org.jmol.shape.MeshCollection
 
setStatusResized(int, int) - Method in class org.jmol.viewer.StatusManager
 
setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
 
setStereoDegrees(float) - Method in class org.jmol.viewer.TransformManager
 
setStereoGraphics(boolean) - Method in class org.jmol.applet.Jmol
 
setStereoGraphics(boolean) - Method in interface org.jmol.applet.JmolAppletInterface
 
setStereoMode(int[]) - Method in class org.jmol.viewer.TransformManager
 
setStereoMode(EnumStereoMode) - Method in class org.jmol.viewer.TransformManager
 
setStereoMode(int[], EnumStereoMode, float) - Method in class org.jmol.viewer.Viewer
 
setStrandCount() - Method in class org.jmol.shapebio.StrandsRenderer
 
setStrandCount(int, int) - Method in class org.jmol.viewer.Viewer
 
setStream(BufferedInputStream, boolean) - Method in class org.jmol.util.BinaryDocument
 
setStream(DataInputStream) - Method in class org.jmol.util.BinaryDocument
 
setString(String) - Method in class org.jmol.util.CifDataReader
sets a string to be parsed from the beginning
setStringNextLine() - Method in class org.jmol.util.CifDataReader
sets the string for parsing to be from the next line when the token buffer is empty, and if ';' is at the beginning of that line, extends the string to include that full multiline string.
setStringProperty(String, String) - Method in class org.jmol.api.JmolViewer
 
setStringProperty(String, String) - Method in class org.jmol.applet.Jmol
 
setStringProperty(String, String) - Method in class org.jmol.script.ScriptEvaluator
 
setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
 
setStringProperty(String, int, String) - Method in class org.jmol.viewer.Viewer
 
setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setStructure(BitSet, EnumStructure) - Method in class org.jmol.modelsetbio.AminoPolymer
 
setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.Monomer
 
setStructure(String) - Method in class org.jmol.popup.PopupResource
 
setStructureIds() - Method in class org.jmol.modelset.ModelCollection
 
setStructureList(Map<EnumStructure, float[]>) - Method in class org.jmol.modelset.ModelCollection
 
setStructureList(Map<EnumStructure, float[]>) - Method in class org.jmol.modelset.Polymer
 
setStructureList(Map<EnumStructure, float[]>) - Method in class org.jmol.modelsetbio.AminoPolymer
 
setStructureList(float[], EnumStructure) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setStructureList(float[], EnumStructure) - Method in class org.jmol.viewer.Viewer
 
setStructureTypes() - Method in class org.jmol.shapebio.BioShapeRenderer
 
setStrut(int, int, int, List<Atom>, BitSet, BitSet, List<Atom[]>, BitSet, BitSet, BitSet, int) - Static method in class org.jmol.modelsetbio.AlphaPolymer
 
setSuperCell(String, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSurfaceInfo(Point4f, int, String) - Method in class org.jmol.jvxl.data.JvxlData
 
setSurfaceInfoFromBitSet(BitSet, Point4f) - Method in class org.jmol.jvxl.data.JvxlData
 
setSurfaceToolParam() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSym(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
Sets the symbol of the atm.
setSymmetry() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
setSymmetryInfo(int, Map<String, Object>) - Method in interface org.jmol.api.SymmetryInterface
 
setSymmetryInfo(int, Map<String, Object>) - Method in class org.jmol.symmetry.Symmetry
 
setSymmetryInfo(Map<String, Object>) - Method in class org.jmol.symmetry.SymmetryInfo
 
setSymmetryMinMax(Point3f) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSymmetryOperator(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setSymmetryOps() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSymmetryRange(float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSync(String) - Method in class org.jmol.viewer.StatusManager
 
setSync() - Method in class org.jmol.viewer.Viewer
 
setSyncDriver(int) - Method in class org.jmol.viewer.StatusManager
 
setSyncDriver(int) - Method in class org.jmol.viewer.Viewer
 
setSyncStarting() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSyncTarget(int, boolean) - Method in class org.jmol.viewer.Viewer
 
settable - Static variable in class org.jmol.script.Token
 
setTag(char[], BitSet, char) - Method in class org.jmol.modelsetbio.AminoPolymer
 
setTainted(boolean) - Method in class org.jmol.viewer.Viewer
 
setTaintedAtoms(BitSet, byte) - Method in class org.jmol.modelset.AtomCollection
 
setTaintedAtoms(BitSet, byte) - Method in class org.jmol.viewer.Viewer
 
setTemp() - Method in class org.jmol.quantum.MOCalculation
 
setTempPoints(Point3f, Point3f, boolean) - Method in class org.jmol.export.__CartesianExporter
 
setTempVertex(Point3f, Point3f, Point3f) - Static method in class org.jmol.export.___Exporter
 
setTempZSlab(int) - Method in class org.jmol.g3d.Graphics3D
 
setText(String) - Method in class org.jmol.shape.Text
 
setThisScheme(String, int[]) - Method in class org.jmol.util.ColorEncoder
 
setTimeout(String, int, String) - Method in class org.jmol.viewer.ActionManager
 
setTimeout(String, int, String) - Method in class org.jmol.viewer.Viewer
 
setTitle() - Method in class org.jmol.console.JmolConsole
 
setToken(Viewer, String, LabelToken, int, int, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
sets a label token based on a label string
setTokenProperty(int, boolean) - Method in class org.jmol.shape.Mesh
 
setTokenProperty(int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
 
setTorsionData(Point3f, Point3f, Point3f, Point3f, SmilesSearch.VTemp, boolean) - Static method in class org.jmol.smiles.SmilesMeasure
 
setTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setTrajectory(BitSet) - Method in class org.jmol.modelset.ModelSet
 
setTrajectory(int) - Method in class org.jmol.modelset.ModelSet
 
setTrajectory(int) - Method in class org.jmol.viewer.Viewer
 
setTrajectory(BitSet) - Method in class org.jmol.viewer.Viewer
 
setTrajectoryName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setTransform(float, float, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setTransformManager(TransformManager) - Method in class org.jmol.viewer.Viewer
for an external application
setTransformManagerDefaults() - Method in class org.jmol.viewer.Viewer
 
setTranslationFractions() - Method in class org.jmol.viewer.TransformManager
 
setTranslations() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Atom
 
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Bond
 
setTranslucent(boolean, float) - Method in class org.jmol.shape.Mesh
 
setTranslucent(float, boolean) - Method in class org.jmol.shape.Object2d
 
setTranslucent(boolean, BitSet, float) - Method in class org.jmol.shapebio.BioShape
 
setTranslucent(boolean, float) - Method in class org.jmol.shapespecial.Dipole
 
setTranslucent(boolean, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setTranslucentCoverOnly(boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
setTranslucentCoverOnly(boolean) - Method in class org.jmol.export.Export3D
 
setTranslucentCoverOnly(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setTransparentColor(int) - Method in class org.jmol.export.image.PngEncoder
 
setTransparentCursor(Object) - Method in interface org.jmol.api.ApiPlatform
 
setTransparentCursor(Object) - Static method in class org.jmol.awt.Display
 
setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
 
setTriangleColixAndShadeIndex(short, int) - Method in class org.jmol.g3d.Graphics3D
 
setTriangleTranslucency(short, short, short) - Method in class org.jmol.g3d.Graphics3D
 
setUnitCell() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
setUnitCell(float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setUnitCell(float[]) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCell(float[]) - Method in class org.jmol.symmetry.Symmetry
 
setUnitCellAllFractionalRelative(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCellAllFractionalRelative(boolean) - Method in class org.jmol.symmetry.Symmetry
 
setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setUnitCellOffset(Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCellOffset(int, Point3f, int) - Method in class org.jmol.modelset.ModelCollection
 
setUnitCellOffset(Point3f) - Method in class org.jmol.symmetry.Symmetry
 
setUnitCellOrientation(Matrix3f) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCellOrientation(Matrix3f) - Method in class org.jmol.symmetry.Symmetry
 
setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
 
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
setup(String) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMepReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
 
setup(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setup(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setup() - Method in class org.jmol.minimize.forcefield.ForceField
 
setup(int, float[], Point3f[], BitSet) - Method in class org.jmol.quantum.MepCalculation
 
setupCalculation(VolumeDataInterface, BitSet, BitSet, BitSet[], String, Point3f[], int, List<int[]>, float[][], int[][], Object, float[], float[], float[][], float[], boolean, Point3f[], float[], int) - Method in interface org.jmol.api.QuantumCalculationInterface
 
setupCalculation() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
setupCalculation(VolumeDataInterface, BitSet, BitSet, BitSet[], String, Point3f[], int, List<int[]>, float[][], int[][], Object, float[], float[], float[][], float[], boolean, Point3f[], float[], int) - Method in class org.jmol.quantum.MOCalculation
 
setupCalculation(VolumeDataInterface, BitSet, BitSet, BitSet[], String, Point3f[], int, List<int[]>, float[][], int[][], Object, float[], float[], float[][], float[], boolean, Point3f[], float[], int) - Method in class org.jmol.quantum.NciCalculation
 
setupCalculations() - Method in class org.jmol.minimize.forcefield.Calculations
 
setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
setupCoordinates(float[], float[], BitSet, Point3f[], Point3f[], boolean) - Method in class org.jmol.quantum.QuantumCalculation
 
setupElectrostatics() - Method in class org.jmol.minimize.forcefield.Calculations
 
setupElectrostatics() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
setupInput() - Method in class org.jmol.console.AppletConsole
 
setupLabels() - Method in class org.jmol.console.AppletConsole
 
setupLabels() - Method in class org.jmol.console.JmolConsole
 
setupLabels() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
setupLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
setupMinimization() - Method in class org.jmol.minimize.Minimizer
 
setupOutput() - Method in class org.jmol.console.AppletConsole
 
setupUI(boolean) - Method in interface org.jmol.api.JmolDialogInterface
 
setupUI(boolean) - Method in class org.jmol.export.dialog.Dialog
 
setupUIManager() - Static method in class org.jmol.export.dialog.Dialog
Setup the UIManager (for i18n)
setUseMolecular(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setUseNumberLocalization(boolean) - Static method in class org.jmol.util.TextFormat
 
setUserAtomTypes() - Method in class org.jmol.adapter.readers.more.ForceFieldReader
 
setUserColors() - Method in class org.jmol.script.ScriptEvaluator
 
setUserScale(int[]) - Method in class org.jmol.util.ColorEncoder
 
setUserScale(int[]) - Method in class org.jmol.viewer.ColorManager
 
setUserScale(int[]) - Method in class org.jmol.viewer.Viewer
 
setUserVariable(String, ScriptVariable) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setUserVariable(String, ScriptVariable) - Method in class org.jmol.viewer.Viewer
 
setUserVdw(EnumVdw) - Method in class org.jmol.viewer.DataManager
 
setValence(int) - Method in class org.jmol.modelset.Atom
 
setValence(int) - Method in class org.jmol.smiles.SmilesAtom
 
setValue(String, String) - Method in class org.jmol.applet.Jmol
 
setValue(float) - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
setValueMinMax() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
setValues(LabelToken[], Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
 
setVariable(int, int, String, int) - Method in class org.jmol.script.ScriptEvaluator
 
setVariables(Map<String, ScriptVariable>, List<ScriptVariable>) - Method in class org.jmol.script.ScriptFunction
 
setVariables() - Method in class org.jmol.shape.MeshRenderer
 
setVectorAnisotropy(Vector3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVectorScale(float) - Method in class org.jmol.api.JmolViewer
 
setVectorScale(float) - Method in class org.jmol.viewer.Viewer
 
setVersion(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setVertexAnisotropy(Point3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVertexSets(boolean) - Method in class org.jmol.jvxl.data.MeshData
 
setVertexSource() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVibrationOff() - Method in class org.jmol.viewer.Viewer
 
setVibrationOn(boolean) - Method in class org.jmol.viewer.TransformManager
 
setVibrationPeriod(float) - Method in class org.jmol.api.JmolViewer
 
setVibrationPeriod(float) - Method in class org.jmol.viewer.TransformManager
sets the period of vibration -- period > 0: sets the period and turns vibration on -- period < 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)
setVibrationPeriod(float) - Method in class org.jmol.viewer.Viewer
 
setVibrationScale(float) - Method in class org.jmol.api.JmolViewer
 
setVibrationScale(float) - Method in class org.jmol.viewer.TransformManager
 
setVibrationScale(float) - Method in class org.jmol.viewer.Viewer
 
setVibrationsFromProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
setVibrationT(float) - Method in class org.jmol.viewer.TransformManager
 
setVibrationVector() - Method in class org.jmol.modelset.Atom
 
setVibrationVector(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setVibrationVector(int, int, float) - Method in class org.jmol.modelset.AtomCollection
 
setViewer(JmolViewer, double) - Method in interface org.jmol.api.JmolImageCreatorInterface
 
setViewer(JmolViewer, double) - Method in class org.jmol.export.image.ImageCreator
 
setViewer(Viewer, String) - Method in class org.jmol.multitouch.ActionManagerMT
 
setViewer(Viewer, String) - Method in class org.jmol.viewer.ActionManager
 
setViewer(Viewer, int, int) - Method in class org.jmol.viewer.TransformManager
 
setViewer(JmolViewer) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setViewer(JmolViewer) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setViewerG3dShapeID(Viewer, JmolRendererInterface, int) - Method in class org.jmol.shape.ShapeRenderer
 
setVisibility(boolean) - Method in class org.jmol.shape.Object2d
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Balls
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Bbcage
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Halos
 
setVisibilityFlags(int) - Method in class org.jmol.shape.Mesh
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.MeshCollection
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Object2dShape
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Shape
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapespecial.Dipoles
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapespecial.Draw
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapespecial.Ellipsoids
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapespecial.Polyhedra
 
setVisibilityInfo() - Method in class org.jmol.shape.Measures
 
setVisible(boolean) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
setVisible(boolean) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
setVisible(boolean) - Method in class org.jmol.console.AppletConsole
 
setVisible(boolean) - Method in class org.jmol.console.JmolConsole
 
setVisible(boolean) - Method in class org.jmol.console.ScriptEditor
 
setVisible(boolean) - Method in class org.jmol.modelset.Measurement
 
setVisible(boolean) - Method in class org.jmol.shapespecial.Polyhedra
 
setVisualRange(float) - Method in class org.jmol.viewer.TransformManager
 
setVolumeData() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVolumeData() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
setVolumeData() - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
setVolumeData() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
setVolumeData(VolumeData) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumeData() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setVolumeData(int, VolumeData, ContactPair, float, int) - Method in class org.jmol.shapesurface.Contact
 
setVolumeDataParams() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setVolumeForPlane() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVolumetricAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumetricOrigin(float, float, float) - Method in interface org.jmol.api.VolumeDataInterface
 
setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVolumetricOriginAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumetricVector(int, float, float, float) - Method in interface org.jmol.api.VolumeDataInterface
 
setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVolumetricXml() - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxel(int, int, int, int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVoxelCounts(int, int, int) - Method in interface org.jmol.api.VolumeDataInterface
 
setVoxelCounts(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelData(float[][][]) - Method in interface org.jmol.api.VolumeDataInterface
 
setVoxelData(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelData(int, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelMap() - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelMapValue(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
for sparse data mapping, as for a plane
setVoxelRange(int, float, float, float, int) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setVoxels() - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
setWebPageAuthor(String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setWidthHeight(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setWindow(JmolRendererInterface, float) - Method in class org.jmol.shape.Object2d
 
setWindowCentered(boolean) - Method in class org.jmol.viewer.TransformManager
 
setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
 
setXmlProperty(String, Object, BitSet) - Method in class org.jmol.shape.Shape
may NOT be over-ridden by shape; executed BEFORE shape's setProperty
setXY(int, int) - Method in class org.jmol.shape.Object2d
 
setXYZ(boolean) - Method in class org.jmol.quantum.QuantumCalculation.QMAtom
 
setXYZ(Point3f) - Method in class org.jmol.shape.Object2d
 
setXYZBohr(Point3f[]) - Method in class org.jmol.quantum.QuantumCalculation
 
setXYZBohr(float[], int, int, Point3f[]) - Method in class org.jmol.quantum.QuantumCalculation
 
setXYZs(int, int, int, int) - Method in class org.jmol.shape.Object2d
 
setZMargin(int) - Method in class org.jmol.g3d.Graphics3D
 
setZoomEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
 
setZs(int, int) - Method in class org.jmol.shape.Object2d
 
setZShadeEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
 
setZShadePower(int) - Static method in class org.jmol.g3d.Graphics3D
fractional distance from black for ambient color
setZslab() - Method in class org.jmol.script.ScriptEvaluator
 
setZslabPoint(Point3f) - Method in class org.jmol.viewer.TransformManager
 
setZslabPoint(Point3f) - Method in class org.jmol.viewer.Viewer
 
sfacElementSymbols - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
sg - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
sg - Variable in class org.jmol.shapesurface.Isosurface
 
sgIndex - Static variable in class org.jmol.symmetry.SpaceGroup
 
Shade3D - Class in org.jmol.g3d
All static functions.
Shade3D() - Constructor for class org.jmol.g3d.Shade3D
 
SHADE_SLAB_CLIPPED - Static variable in class org.jmol.g3d.Sphere3D
 
shadeIndexes - Variable in class org.jmol.g3d.Normix3D
 
shadeIndexes2Sided - Variable in class org.jmol.g3d.Normix3D
 
shadeIndexLast - Static variable in class org.jmol.g3d.Shade3D
 
shadeIndexMax - Static variable in class org.jmol.g3d.Shade3D
 
shadeIndexNoisyLimit - Static variable in class org.jmol.g3d.Shade3D
 
shadeIndexNormal - Static variable in class org.jmol.g3d.Shade3D
 
shades - Variable in class org.jmol.g3d.Sphere3D
 
shadesA - Variable in class org.jmol.g3d.Cylinder3D
 
shadesB - Variable in class org.jmol.g3d.Cylinder3D
 
shadesCurrent - Variable in class org.jmol.g3d.Graphics3D
 
shape - Static variable in class org.jmol.script.Token
 
Shape - Class in org.jmol.shape
Shape now encompasses: AtomShape (abstract) | Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface BioShapeCollection (abstract) | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Dipoles FontLineShape (abstract) | Axes, Bbcage, Frank, Uccage Measures MeshCollection (abstract) | | Draw Isosurface | LcaoCartoon, MolecularOrbital, Pmesh Sticks | Hsticks, Sssticks TextShape (abstract) | Echo, Hover
Shape() - Constructor for class org.jmol.shape.Shape
 
shape - Variable in class org.jmol.shape.ShapeRenderer
 
shape - Variable in class org.jmol.shapebio.BioShape
 
SHAPE_AXES - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_BALLS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_CARTOON - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_CONTACT - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_DOTS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_DRAW - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_ECHO - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_FRANK - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_HALOS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_HOVER - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_LABELS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MEASURES - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MO - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_PMESH - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_STARS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_STICKS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_STRANDS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_STRUTS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_TRACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_VECTORS - Static variable in class org.jmol.viewer.JmolConstants
 
shapeClassBases - Static variable in class org.jmol.viewer.JmolConstants
 
shapeCommand - Static variable in class org.jmol.script.Token
 
shapeID - Variable in class org.jmol.shape.Shape
 
shapeID - Variable in class org.jmol.shape.ShapeRenderer
 
shapely - Static variable in class org.jmol.script.Token
 
SHAPELY - Static variable in class org.jmol.util.ColorEncoder
 
shapeManager - Variable in class org.jmol.modelset.ModelCollection
 
shapeManager - Variable in class org.jmol.script.ParallelProcessor.RunProcess
 
shapeManager - Variable in class org.jmol.script.ScriptEvaluator
 
shapeManager - Variable in class org.jmol.viewer.RepaintManager
 
ShapeManager - Class in org.jmol.viewer
 
ShapeManager(Viewer) - Constructor for class org.jmol.viewer.ShapeManager
 
ShapeManager(Viewer, ModelSet) - Constructor for class org.jmol.viewer.ShapeManager
 
shapeManager - Variable in class org.jmol.viewer.Viewer
 
ShapeRenderer - Class in org.jmol.shape
 
ShapeRenderer() - Constructor for class org.jmol.shape.ShapeRenderer
 
shapes - Variable in class org.jmol.viewer.ShapeManager
 
shapeTokenIndex(int) - Static method in class org.jmol.viewer.JmolConstants
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Atom
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Bond
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Group
 
shapeVisibilityFlags - Variable in class org.jmol.viewer.StateManager.Connection
 
Sheet - Class in org.jmol.modelsetbio
 
Sheet(AlphaPolymer, int, int, int, EnumStructure) - Constructor for class org.jmol.modelsetbio.Sheet
 
sheet - Static variable in class org.jmol.script.Token
 
SHEET_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
sheetOffsets - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
 
sheetsmoothing - Static variable in class org.jmol.script.Token
 
sheetSmoothing - Variable in class org.jmol.shapebio.BioShapeRenderer
 
sheetSmoothing - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
shell - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
SHELL_D_CARTESIAN - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_D_SPHERICAL - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_F_CARTESIAN - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_F_SPHERICAL - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_L - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_P - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_S - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_SP - Static variable in class org.jmol.api.JmolAdapter
 
shellCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
shellCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
shellOrder - Static variable in class org.jmol.quantum.MOCalculation
 
shells - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
shells - Variable in class org.jmol.quantum.MOCalculation
 
shellsByUniqueAtom - Variable in class org.jmol.adapter.readers.quantum.PsiReader
 
shelxLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
ShelxReader - Class in org.jmol.adapter.readers.xtal
A reader for SHELX output (RES) files.
ShelxReader() - Constructor for class org.jmol.adapter.readers.xtal.ShelxReader
 
SHIFT - Static variable in class org.jmol.viewer.binding.Binding
 
SHIFT_MASK - Static variable in class org.jmol.api.Event
 
shortSectorPower - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
shortSectorSize - Variable in class org.jmol.util.CompoundDocument
 
shouldDisplay() - Method in class org.jmol.i18n.GT.Language
 
show(int, int, char) - Method in interface org.jmol.api.JmolModelKitInterface
 
show(int, int) - Method in interface org.jmol.api.JmolPopupInterface
 
show(int, int, char) - Method in class org.jmol.modelkit.ModelKit
 
show(int, int) - Method in class org.jmol.popup.JmolPopup
 
show(int, int, boolean) - Method in class org.jmol.popup.SimplePopup
 
show() - Method in class org.jmol.script.ScriptEvaluator
 
show - Static variable in class org.jmol.script.Token
 
show - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
show2D(String) - Method in class org.jmol.viewer.Viewer
 
showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Show an atom set from the indexes array
showAuxiliaryInfo(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
showaxes - Static variable in class org.jmol.script.Token
 
showAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
showboundbox - Static variable in class org.jmol.script.Token
 
showBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
showBox(JmolRendererInterface, short, int, int, int, int, int, int, float, boolean) - Static method in class org.jmol.shape.Text
 
showConsole(boolean) - Method in class org.jmol.viewer.Viewer
 
showContourLines - Variable in class org.jmol.shape.Mesh
 
showEditor(String[]) - Method in class org.jmol.viewer.Viewer
 
showfrank - Static variable in class org.jmol.script.Token
 
showFrankMenu(int, int) - Method in class org.jmol.popup.JmolPopup
 
showGridInfo() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
showhiddenselectionhalos - Static variable in class org.jmol.script.Token
 
showHiddenSelectionHalos - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showHide(boolean) - Method in class org.jmol.shape.Measures
 
showHide(Measurement, boolean) - Method in class org.jmol.shape.Measures
 
showhydrogens - Static variable in class org.jmol.script.Token
 
showHydrogens - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showHydrogens - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
showInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
showKey - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
showKey() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
showkeystrokes - Static variable in class org.jmol.script.Token
 
showKeyStrokes - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showmeasurements - Static variable in class org.jmol.script.Token
 
showMeasurements - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showMeasurements - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
showMessage(String) - Method in class org.jmol.viewer.Viewer
 
showModelSetDownload() - Method in class org.jmol.api.JmolViewer
 
showModelSetDownload() - Method in class org.jmol.viewer.Viewer
 
showMoleculesAndOrbitals - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
showmultiplebonds - Static variable in class org.jmol.script.Token
 
showMultipleBonds - Variable in class org.jmol.shape.SticksRenderer
 
showMultipleBonds - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
shownavigationpointalways - Static variable in class org.jmol.script.Token
 
showNavigationPointAlways - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showNumbers - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
showPaintTime - Variable in class org.jmol.applet.Jmol
 
showPaintTime - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
showParameter(String, boolean, int) - Method in class org.jmol.viewer.Viewer
 
showPoints - Variable in class org.jmol.shape.Mesh
 
showPopupMenu(int, int) - Method in class org.jmol.popup.SimplePopup
 
showPovrayPathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Show a file selector when the savePath button is pressed.
showProgress() - Method in class org.openscience.chimetojmol.ChimePanel
 
showProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Shows the properties in the propertiesPane of the AtomSetChooser window
showRebondTimes - Static variable in class org.jmol.modelset.ModelCollection
 
showSaveDialog(Component, JFileChooser, File) - Method in class org.jmol.export.dialog.Dialog
 
showSavePathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Show a file selector when the savePath button is pressed.
showscript - Static variable in class org.jmol.script.Token
 
showSelected - Variable in class org.jmol.viewer.Viewer
 
showSliceBoundaryPlanes(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
showSplashScreen() - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
showStatus(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
showStatus(String) - Method in interface org.openscience.jmol.app.SplashInterface
 
showString(String) - Method in class org.jmol.script.ScriptEvaluator
 
showString(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
showString(String, boolean) - Method in class org.jmol.viewer.Viewer
 
showTimeout(String) - Method in class org.jmol.viewer.ActionManager
 
showTimeout(String) - Method in class org.jmol.viewer.Viewer
 
showTimes(int, int, Graphics) - Method in class org.jmol.applet.Jmol
 
showTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
showTriangles - Variable in class org.jmol.shape.Mesh
 
showunitcell - Static variable in class org.jmol.script.Token
 
showUrl(String) - Method in interface org.jmol.api.JmolStatusListener
 
showUrl(String) - Method in class org.jmol.api.JmolViewer
 
showUrl(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
showUrl(String) - Method in class org.jmol.viewer.StatusManager
 
showUrl(String) - Method in class org.jmol.viewer.Viewer
 
showUrl(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
SID_DIR_start - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
SID_MSAT_next - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
SID_SSAT_start - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
sidechain - Static variable in class org.jmol.script.Token
 
SIDfirstSector - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
siestaContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
SiestaReader - Class in org.jmol.adapter.readers.xtal
SIESTA http://www.icmab.es/siesta/
SiestaReader() - Constructor for class org.jmol.adapter.readers.xtal.SiestaReader
 
sigma - Variable in class org.jmol.jvxl.readers.Parameters
 
sigma - Static variable in class org.jmol.script.Token
 
sign - Static variable in class org.jmol.script.Token
 
SignedOnly - Variable in class org.jmol.popup.SimplePopup
 
signFactor - Variable in class org.jmol.modelset.TickInfo
 
silent - Variable in class org.jmol.minimize.forcefield.Calculations
 
silent - Static variable in class org.jmol.script.Token
 
SILVER - Static variable in class org.jmol.g3d.Graphics3D
 
simpleAverage(Quaternion[]) - Static method in class org.jmol.util.Quaternion
Just a starting point.
SimpleMarchingCubes - Class in org.openscience.jvxl.simplewriter
 
SimpleMarchingCubes(VoxelDataCreator, VolumeData, Parameters, JvxlData, List<Point3f>, float[]) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
SimpleMarchingCubesOld - Class in org.openscience.jvxl.simplewriter
 
SimpleMarchingCubesOld(VoxelDataCreator, VolumeData, float, boolean, boolean) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
SimplePopup - Class in org.jmol.popup
 
SimplePopup() - Constructor for class org.jmol.popup.SimplePopup
 
SimplePopup(JmolViewer) - Constructor for class org.jmol.popup.SimplePopup
 
SimplePopup(JmolViewer, String, PopupResource, boolean) - Constructor for class org.jmol.popup.SimplePopup
 
SimplePopup.CheckboxMenuItemListener - Class in org.jmol.popup
 
SimplePopup.CheckboxMenuItemListener() - Constructor for class org.jmol.popup.SimplePopup.CheckboxMenuItemListener
 
SimplePopup.MenuItemListener - Class in org.jmol.popup
 
SimplePopup.MenuItemListener() - Constructor for class org.jmol.popup.SimplePopup.MenuItemListener
 
simpleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
simpleReplace(String, String, String) - Static method in class org.jmol.util.TextFormat
Does a clean replace of strFrom in str with strTo If strTo contains strFrom, then only a single pass is done.
SimpleUnitCell - Class in org.jmol.util
general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity
SimpleUnitCell(float[]) - Constructor for class org.jmol.util.SimpleUnitCell
 
simulationPhase - Variable in class org.jmol.multitouch.ActionManagerMT
 
simulator - Variable in class org.jmol.multitouch.ActionManagerMT
 
sin - Static variable in class org.jmol.script.Token
 
sinAlpha - Variable in class org.jmol.util.SimpleUnitCell
 
sinBeta - Variable in class org.jmol.util.SimpleUnitCell
 
sinGamma - Variable in class org.jmol.util.SimpleUnitCell
 
SINGLE_CLICK - Static variable in class org.jmol.viewer.binding.Binding
 
SINGLE_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
SingleModelOnly - Variable in class org.jmol.popup.SimplePopup
 
SinglePointGesture - Class in org.jmol.multitouch.sparshui
SINGLE_POINT_GESTURE only passes single-touch gestures.
SinglePointGesture() - Constructor for class org.jmol.multitouch.sparshui.SinglePointGesture
 
sinPhi - Variable in class org.jmol.g3d.Cylinder3D
 
site() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
site - Static variable in class org.jmol.script.Token
 
SITE_ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
SITE_COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
SITE_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
SITE_INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
SITE_SEQ_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
siteScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
sixdots - Static variable in class org.jmol.shape.SticksRenderer
 
size - Variable in class org.jmol.g3d.Text3D
 
size - Static variable in class org.jmol.script.Token
 
size() - Method in class org.jmol.util.FastBitSet
 
sizeCorrection - Variable in class org.jmol.g3d.Circle3D
 
sizeOf(Token) - Static method in class org.jmol.script.ScriptVariable
 
skip(long) - Method in class org.openscience.jvxl.MonitorInputStream
 
skipAtomSet(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
skipComments(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.MrcBinaryReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
skipFloats(int) - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
skipHeader() - Method in class org.jmol.jvxl.readers.MsmsReader
 
skipLoop() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
skips all associated loop data
skipping - Variable in class org.jmol.script.ScriptMathProcessor
 
skipPoints(int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
skipTag(String) - Method in class org.jmol.util.XmlReader
 
skipTo(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
skipTo(String, String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
skipTo(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
 
skipTo(String) - Method in class org.jmol.util.XmlReader
 
skipVoxels(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
slab - Variable in class org.jmol.export.Export3D
 
slab - Variable in class org.jmol.g3d.Graphics3D
 
slab - Variable in class org.jmol.g3d.Sphere3D
 
slab(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
slab - Static variable in class org.jmol.script.Token
 
slabbing - Variable in class org.jmol.shape.SticksRenderer
 
slabbingObject - Variable in class org.jmol.shape.Mesh
 
slabbingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
 
slabbyatom - Static variable in class org.jmol.script.Token
 
slabByAtom - Variable in class org.jmol.shape.SticksRenderer
 
slabByAtom - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
slabbymolecule - Static variable in class org.jmol.script.Token
 
slabByMolecule - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
slabByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
slabByPixels(int) - Method in class org.jmol.viewer.Viewer
 
slabColix - Variable in class org.jmol.util.MeshSurface
 
slabData - Variable in class org.jmol.shapespecial.Draw
 
slabDepthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
slabDepthByPixels(int) - Method in class org.jmol.viewer.Viewer
 
slabDepthChanged() - Method in class org.jmol.viewer.TransformManager
 
slabenabled - Static variable in class org.jmol.script.Token
 
slabEnabled - Variable in class org.jmol.viewer.TransformManager
 
slabInfo - Variable in class org.jmol.jvxl.data.JvxlData
 
slabInfo - Variable in class org.jmol.jvxl.readers.Parameters
 
slabInternal(Point4f, boolean) - Method in class org.jmol.viewer.TransformManager
 
slabInternal(Point4f, boolean) - Method in class org.jmol.viewer.Viewer
 
slabIsosurface(List<Object[]>) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
slabMeshType - Variable in class org.jmol.util.MeshSurface
 
slabOptions - Variable in class org.jmol.util.MeshSurface
 
slabPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
slabPlane - Variable in class org.jmol.viewer.TransformManager
 
slabPlaneOffset - Variable in class org.jmol.jvxl.readers.Parameters
 
slabPolygons(Object[]) - Method in class org.jmol.shapesurface.Isosurface
 
slabPolygons(List<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
 
slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSurface
 
slabrange - Static variable in class org.jmol.script.Token
 
slabRange - Variable in class org.jmol.viewer.TransformManager
 
slabReset() - Method in class org.jmol.viewer.TransformManager
 
slabReset() - Method in class org.jmol.viewer.Viewer
 
slabToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
slabToPercent(int) - Method in class org.jmol.viewer.Viewer
 
slabValue - Variable in class org.jmol.jvxl.data.JvxlData
 
slabValue - Variable in class org.jmol.viewer.TransformManager
 
slabZ - Variable in class org.jmol.export.___Exporter
 
slaterArray - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
SlaterData - Class in org.jmol.quantum
 
SlaterData(int, int, int, int, int, double, double) - Constructor for class org.jmol.quantum.SlaterData
 
SlaterReader - Class in org.jmol.adapter.readers.quantum
 
SlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader
 
SlaterReader.OrbitalSorter - Class in org.jmol.adapter.readers.quantum
 
SlaterReader.OrbitalSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
 
SlaterReader.SlaterSorter - Class in org.jmol.adapter.readers.quantum
 
SlaterReader.SlaterSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
 
slaters - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
slaters - Variable in class org.jmol.quantum.MOCalculation
 
sLeft - Variable in class org.jmol.g3d.Hermite3D
 
Slice - Class in org.openscience.jmol.app.surfacetool
 
Slice() - Constructor for class org.openscience.jmol.app.surfacetool.Slice
 
slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
sliceObject(String, int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
slicer - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
slicerFrame - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
sliceSelected() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SLIDE_ZOOM_X_PERCENT - Static variable in class org.jmol.viewer.ActionManager
 
slider - Variable in class org.jmol.export.dialog.Dialog.QualityListener
 
sliderPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SLIM - Static variable in class org.jmol.g3d.Sphere3D
 
slope - Variable in class org.jmol.g3d.Line3D
 
slopeKey - Variable in class org.jmol.g3d.Line3D
 
SlowBitSet - Class in org.jmol.util
 
SlowBitSet() - Constructor for class org.jmol.util.SlowBitSet
 
SmallAtomDot - Static variable in class org.openscience.jmol.app.webexport.Orbitals
 
smallmoleculemaxatoms - Static variable in class org.jmol.script.Token
 
smallMoleculeMaxAtoms - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
smartaromatic - Static variable in class org.jmol.script.Token
 
smartAromatic - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
SmarterJmolAdapter - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter() - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter
 
SmarterJmolAdapter.AtomIterator - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter.AtomIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
SmarterJmolAdapter.BondIterator - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter.BondIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
SmarterJmolAdapter.StructureIterator - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter.StructureIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
smiles - Static variable in class org.jmol.script.Token
 
smiles2dimageformat - Static variable in class org.jmol.script.Token
 
SmilesAromatic - Class in org.jmol.smiles
 
SmilesAromatic() - Constructor for class org.jmol.smiles.SmilesAromatic
 
SmilesAtom - Class in org.jmol.smiles
This class represents an atom in a SmilesMolecule.
SmilesAtom(int) - Constructor for class org.jmol.smiles.SmilesAtom
Constructs a SmilesAtom.
SmilesAtom(int, int, int, short, int) - Constructor for class org.jmol.smiles.SmilesAtom
 
SmilesBond - Class in org.jmol.smiles
Bond in a SmilesMolecule
SmilesBond(SmilesAtom, SmilesAtom, int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
SmilesBond constructor
SmilesBond(int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
 
SmilesGenerator - Class in org.jmol.smiles
Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.
SmilesGenerator() - Constructor for class org.jmol.smiles.SmilesGenerator
 
SmilesMatcher - Class in org.jmol.smiles
Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods
SmilesMatcher() - Constructor for class org.jmol.smiles.SmilesMatcher
 
smilesMatcher - Variable in class org.jmol.viewer.Viewer
 
SmilesMatcherInterface - Interface in org.jmol.api
 
SmilesMeasure - Class in org.jmol.smiles
 
SmilesMeasure(SmilesSearch, int, int, float, float, boolean) - Constructor for class org.jmol.smiles.SmilesMeasure
 
SmilesParser - Class in org.jmol.smiles
Parses a SMILES String to create a SmilesMolecule.
SmilesParser(boolean) - Constructor for class org.jmol.smiles.SmilesParser
 
SmilesSearch - Class in org.jmol.smiles
-- was SmilesMolecule, but this now includes more data than that and the search itself so as to keep this thread safe
SmilesSearch() - Constructor for class org.jmol.smiles.SmilesSearch
 
SmilesSearch.VTemp - Class in org.jmol.smiles
 
SmilesSearch.VTemp() - Constructor for class org.jmol.smiles.SmilesSearch.VTemp
 
smilesurlformat - Static variable in class org.jmol.script.Token
 
smilesUrlFormat - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
smoothingPower - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
 
solid - Static variable in class org.jmol.script.Token
 
solvent - Static variable in class org.jmol.script.Token
 
solvent_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
solvent_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
solventDistance(float, float, float, float, float) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
solventExtendedAtomRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
solventOn - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
solventprobe - Static variable in class org.jmol.script.Token
 
solventproberadius - Static variable in class org.jmol.script.Token
 
solventProbeRadius - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
solventRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
solventRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
someModelsHaveAromaticBonds - Variable in class org.jmol.modelset.ModelCollection
 
someModelsHaveFractionalCoordinates - Variable in class org.jmol.modelset.ModelCollection
 
someModelsHaveSymmetry - Variable in class org.jmol.modelset.ModelCollection
 
someModelsHaveUnitcells - Variable in class org.jmol.modelset.ModelLoader
 
sort(int) - Method in class org.jmol.bspt.Leaf
 
sort() - Method in class org.jmol.export.image.GifEncoder.ColorVector
 
sort - Static variable in class org.jmol.script.Token
 
sortedItem(List<String>, int) - Static method in class org.jmol.util.ArrayUtil
 
sortInorganic(JmolNode, List<JmolEdge>) - Method in class org.jmol.smiles.SmilesGenerator
We must sort the bond vector such that a diaxial pair is first and last.
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
sorts coefficients by atomic number for speed later
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.SlaterReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrReverse(int) - Method in class org.jmol.script.ScriptVariable
 
sortSurfaceSets() - Method in class org.jmol.jvxl.data.MeshData
 
source - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
sourceIndices - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
sp - Variable in class org.jmol.bspt.CubeIterator
 
SP_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
spacebeforesquare - Static variable in class org.jmol.script.Token
 
spacefill - Static variable in class org.jmol.script.Token
 
Spacefilling - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
spaceGroup - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
spaceGroup - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
spacegroup - Static variable in class org.jmol.script.Token
 
SpaceGroup - Class in org.jmol.symmetry
 
SpaceGroup(boolean) - Constructor for class org.jmol.symmetry.SpaceGroup
 
SpaceGroup(String) - Constructor for class org.jmol.symmetry.SpaceGroup
 
spaceGroup - Variable in class org.jmol.symmetry.Symmetry
 
spaceGroup - Variable in class org.jmol.symmetry.SymmetryInfo
 
spaceGroupDefinitions - Static variable in class org.jmol.symmetry.SpaceGroup
 
spaceGroupName - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
SpartanArchive - Class in org.jmol.adapter.readers.quantum
 
SpartanArchive(BasisFunctionReader) - Constructor for class org.jmol.adapter.readers.quantum.SpartanArchive
 
SpartanArchive(BasisFunctionReader, String, String) - Constructor for class org.jmol.adapter.readers.quantum.SpartanArchive
 
spartanArchive - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
spartanBinaryContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
spartanContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
SpartanInputReader - Class in org.jmol.adapter.readers.quantum
 
SpartanInputReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanInputReader
 
SpartanReader - Class in org.jmol.adapter.readers.quantum
 
SpartanReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanReader
 
spartanSmolLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
SpartanSmolReader - Class in org.jmol.adapter.readers.quantum
 
SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
spec_alternate - Static variable in class org.jmol.script.Token
 
spec_atom - Static variable in class org.jmol.script.Token
 
spec_chain - Static variable in class org.jmol.script.Token
 
spec_model - Static variable in class org.jmol.script.Token
 
spec_model2 - Static variable in class org.jmol.script.Token
 
spec_name_pattern - Static variable in class org.jmol.script.Token
 
spec_resid - Static variable in class org.jmol.script.Token
 
spec_seqcode - Static variable in class org.jmol.script.Token
 
spec_seqcode_range - Static variable in class org.jmol.script.Token
 
SPECIAL_AIMS - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ALCHEMY - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ARGUS_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ARGUS_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CASTEP - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CHEM3D_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CHEM3D_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CML_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CML_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_COLIX_MAX - Static variable in class org.jmol.g3d.Graphics3D
 
SPECIAL_CRYSTAL - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CUBE - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_FOLDINGXYZ - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_GENNBO - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_GROMACS - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_JME - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_MOL - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_MOLPRO_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_MOLPRO_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_MOPACGRAPHF - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ODYSSEY - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ODYSSEY_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ODYSSEY_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_QE_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_VASP_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_VASP_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_WIEN - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_XSD_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_XSD_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_XYZ - Static variable in class org.jmol.adapter.smarter.Resolver
 
specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
 
specialAtomNames - Static variable in class org.jmol.viewer.JmolConstants
 
specialLabel - Variable in class org.jmol.shape.Hover
 
specialLoad(String, String) - Static method in class org.jmol.adapter.smarter.Resolver
Special loading for file directories.
specialLoad(String, String) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
specialLoad(String, String) - Method in class org.jmol.api.JmolAdapter
 
specialposition - Static variable in class org.jmol.script.Token
 
specialTags - Static variable in class org.jmol.adapter.smarter.Resolver
 
specialTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
specular - Static variable in class org.jmol.script.Token
 
specular - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
specularExponent - Static variable in class org.jmol.g3d.Shade3D
 
specularexponent - Static variable in class org.jmol.script.Token
 
specularExponent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
specularFactor - Static variable in class org.jmol.g3d.Shade3D
 
specularOn - Static variable in class org.jmol.g3d.Shade3D
 
specularPercent - Static variable in class org.jmol.g3d.Shade3D
 
specularpercent - Static variable in class org.jmol.script.Token
 
specularPercent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
specularPower - Static variable in class org.jmol.g3d.Shade3D
 
specularpower - Static variable in class org.jmol.script.Token
 
specularPower - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
sphere - Static variable in class org.jmol.script.Token
 
sphere3d - Variable in class org.jmol.g3d.Graphics3D
 
Sphere3D - Class in org.jmol.g3d
Implements high performance rendering of shaded spheres.
Sphere3D(Graphics3D) - Constructor for class org.jmol.g3d.Sphere3D
 
sphere_radiusAngstroms - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
sphereMatrix - Variable in class org.jmol.export.__CartesianExporter
 
sphereMean(Quaternion[], float[], float) - Static method in class org.jmol.util.Quaternion
 
sphereNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
sphereShadeIndexes - Static variable in class org.jmol.g3d.Shade3D
 
sphereShadingCalculated - Static variable in class org.jmol.g3d.Shade3D
 
sphereShapeCache - Static variable in class org.jmol.g3d.Sphere3D
 
sphericalDValues - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
spin - Static variable in class org.jmol.script.Token
 
SPIN_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
SPIN_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
spine - Static variable in class org.jmol.script.Token
 
spinfps - Static variable in class org.jmol.script.Token
 
spinFps - Variable in class org.jmol.viewer.TransformManager
 
spinOn - Variable in class org.jmol.viewer.TransformManager
 
spinOn - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
spinThread - Variable in class org.jmol.viewer.TransformManager
 
spinx - Static variable in class org.jmol.script.Token
 
spinX - Variable in class org.jmol.viewer.TransformManager
 
spinXYBy(int, int, float) - Method in class org.jmol.viewer.TransformManager
 
spinXYBy(int, int, float) - Method in class org.jmol.viewer.Viewer
 
spiny - Static variable in class org.jmol.script.Token
 
spinY - Variable in class org.jmol.viewer.TransformManager
 
spinz - Static variable in class org.jmol.script.Token
 
spinZ - Variable in class org.jmol.viewer.TransformManager
 
splash - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
Splash - Class in org.openscience.jmol.app.jmolpanel
 
Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.jmolpanel.Splash
 
Splash.WindowListener - Class in org.openscience.jmol.app.jmolpanel
 
Splash.WindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
 
splashEnabled - Variable in class org.openscience.jmol.app.JmolApp
 
splashImage - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
SplashInterface - Interface in org.openscience.jmol.app
 
split - Static variable in class org.jmol.script.Token
 
split(String, String) - Static method in class org.jmol.util.TextFormat
proper splitting, even for Java 1.3 -- if the text ends in the run, no new line is appended.
split(String, char) - Static method in class org.jmol.util.TextFormat
 
splitCommandLine(String) - Static method in class org.jmol.script.ScriptCompiler
used by app to separate a command line into three sections: prefix....;cmd ........
sprintf(String, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
 
sprintf(String, ScriptVariable, Object[], int[], float[], double[], boolean, boolean) - Static method in class org.jmol.script.ScriptVariable
 
sprintf(ScriptVariable[]) - Static method in class org.jmol.script.ScriptVariable
sprintf accepts arguments from the format() function First argument is a format string.
sprintf(String, Object[]) - Static method in class org.jmol.util.TextFormat
sprintf emulation uses (almost) c++ standard string formats 's' string 'i' or 'd' integer 'f' float/decimal 'p' point3f 'q' quaternion/plane/axisangle ' with added "i" in addion to the insipid "d" (digits?)
sptContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
sqrt - Static variable in class org.jmol.script.Token
 
sqrt3_2 - Static variable in class org.jmol.modelset.AtomCollection
 
squareCount - Variable in class org.jmol.script.ScriptMathProcessor
 
squared - Static variable in class org.jmol.script.Token
 
sr - Variable in class org.jmol.jvxl.data.VolumeData
 
sRight - Variable in class org.jmol.g3d.Hermite3D
 
Ss - Variable in class org.jmol.util.JpegInfo
 
SSAT - Variable in class org.jmol.util.CompoundDocument
 
ssbond() - Method in class org.jmol.script.ScriptEvaluator
 
ssbond - Static variable in class org.jmol.script.Token
 
ssbondsbackbone - Static variable in class org.jmol.script.Token
 
ssbondsBackbone - Variable in class org.jmol.shape.SticksRenderer
 
ssbondsBackbone - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
stack - Variable in class org.jmol.bspt.CubeIterator
 
STAND_ALONE - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
STANDARD_LABEL - Static variable in class org.jmol.modelset.LabelToken
 
standardLevel - Static variable in class org.jmol.geodesic.Geodesic
3 levels, 0 through 3
star - Static variable in class org.jmol.script.Token
 
Stars - Class in org.jmol.shape
 
Stars() - Constructor for class org.jmol.shape.Stars
 
StarsRenderer - Class in org.jmol.shape
 
StarsRenderer() - Constructor for class org.jmol.shape.StarsRenderer
 
START - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
start() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
startByteArrayReaderThread() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
startChainID - Variable in class org.jmol.adapter.smarter.Structure
 
startCommandWatcher(boolean) - Method in class org.jmol.viewer.ScriptManager
 
startConsoleReaderThread(InputStream) - Method in class org.openscience.jmol.app.jmolpanel.ConsoleTextArea
 
startCoord - Variable in class org.jmol.shapespecial.Dipoles
 
startDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
started - Variable in class org.jmol.export.image.ImageEncoder
 
startedByCommandThread - Variable in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader.MolproHandler
 
startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
startElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
startGestureServer() - Method in interface org.jmol.api.JmolGestureServerInterface
 
startHoverWatcher(boolean) - Method in class org.jmol.viewer.ActionManager
 
startIndexPending - Variable in class org.jmol.shapebio.RocketsRenderer
 
startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
 
startJmol(JmolApp) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
startJsonNioKiosk(int) - Method in class org.openscience.molecularplayground.MPJmolApp
 
startMinimization() - Method in class org.jmol.minimize.Minimizer
 
startMotion(boolean) - Method in class org.jmol.viewer.TransformManager.MotionThread
 
startMotion() - Method in class org.jmol.viewer.TransformManager.MotionThread
 
startPaintClock() - Method in class org.jmol.applet.Jmol
 
startPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
startPixelScale - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
startRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
startRotationRadius - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
startScriptQueue(boolean) - Method in class org.jmol.viewer.ScriptManager
 
startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
 
startServerService() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
startService(int, JsonNioClient, JmolViewer, String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
startSimulator(Object) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
startSparshUIService(boolean) - Method in class org.jmol.multitouch.ActionManagerMT
 
startSpinningAxis(Point3f, Point3f, boolean) - Method in class org.jmol.viewer.Viewer
 
startTime - Variable in class org.jmol.applet.AppletWrapper
 
startTime - Static variable in class org.jmol.util.Logger
 
startTimer() - Static method in class org.jmol.util.Logger
 
startupDimension - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
startupHeight - Variable in class org.openscience.jmol.app.JmolApp
 
startupHeight - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
startupWidth - Variable in class org.openscience.jmol.app.JmolApp
 
startupWidth - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
startViewer(JmolViewer, SplashInterface) - Method in class org.openscience.jmol.app.JmolApp
 
state - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
the current state
state - Variable in class org.jmol.jvxl.readers.Parameters
 
state - Static variable in class org.jmol.script.Token
 
STATE_DATA_COLORED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_DATA_READ - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_INITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_UNINITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_VERSION_STAMP - Static variable in class org.jmol.viewer.Viewer
 
stateButton - Variable in class org.jmol.console.JmolConsole
 
stateButton - Variable in class org.jmol.console.ScriptEditor
 
StateButton - Variable in class org.openscience.jmol.app.webexport.Test
 
stateChanged(ChangeEvent) - Method in class org.jmol.export.dialog.Dialog.QualityListener
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
StateManager - Class in org.jmol.viewer
 
StateManager(Viewer) - Constructor for class org.jmol.viewer.StateManager
 
stateManager - Variable in class org.jmol.viewer.Viewer
 
StateManager.Connection - Class in org.jmol.viewer
 
StateManager.Connection(int, int, short, short, int, float, int) - Constructor for class org.jmol.viewer.StateManager.Connection
 
StateManager.Connections - Class in org.jmol.viewer
 
StateManager.Connections() - Constructor for class org.jmol.viewer.StateManager.Connections
 
StateManager.GlobalSettings - Class in org.jmol.viewer
 
StateManager.GlobalSettings(StateManager.GlobalSettings, boolean) - Constructor for class org.jmol.viewer.StateManager.GlobalSettings
 
StateManager.Orientation - Class in org.jmol.viewer
 
StateManager.Orientation(boolean) - Constructor for class org.jmol.viewer.StateManager.Orientation
 
statement - Variable in class org.jmol.script.ScriptContext
 
statement - Variable in class org.jmol.script.ScriptEvaluator
 
statementAsString(Token[], int, boolean) - Static method in class org.jmol.script.ScriptEvaluator
 
statementLength - Variable in class org.jmol.script.ScriptContext
 
statementLength - Variable in class org.jmol.script.ScriptEvaluator
 
stateScripts - Variable in class org.jmol.modelset.ModelCollection
 
stateScriptVersionInt - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
stateScriptVersionInt - Variable in class org.jmol.viewer.Viewer
 
StaticConstants - Class in org.jmol.constant
 
StaticConstants() - Constructor for class org.jmol.constant.StaticConstants
 
staticFunctions - Static variable in class org.jmol.viewer.StateManager
 
staticGetAtomSetCollectionOrBufferedReaderFromZip(InputStream, String, String[], Map<String, Object>, int, boolean, boolean) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
stats() - Method in class org.jmol.bspt.Bspf
 
stats() - Method in class org.jmol.bspt.Bspt
prints some simple stats to stdout
status - Variable in class org.jmol.viewer.ActionManager.TimeoutThread
 
status - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
status - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
status - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
status - Variable in class org.openscience.jmol.app.jmolpanel.StatusBar
 
StatusBar - Class in org.openscience.jmol.app.jmolpanel
 
StatusBar() - Constructor for class org.openscience.jmol.app.jmolpanel.StatusBar
 
statusForm - Variable in class org.jmol.applet.Jmol
 
statusList - Variable in class org.jmol.viewer.StatusManager
 
statusListener - Variable in class org.jmol.export.JmolFileDropper
 
StatusListener - Class in org.openscience.jmol.app.jmolpanel
 
StatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusListener
 
StatusManager - Class in org.jmol.viewer
The StatusManager class handles all details of status reporting, including: 1) saving the message in a queue that replaces the "callback" mechanism, 2) sending messages off to the console, and 3) delivering messages back to the main Jmol.java class in app or applet to handle differences in capabilities, including true callbacks.
StatusManager(Viewer) - Constructor for class org.jmol.viewer.StatusManager
 
statusManager - Variable in class org.jmol.viewer.Viewer
 
statusPtr - Variable in class org.jmol.viewer.StatusManager
 
statusreporting - Static variable in class org.jmol.script.Token
 
statusReporting - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
STATUSSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
 
statusText - Variable in class org.jmol.applet.Jmol
 
statusText - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
statusTextarea - Variable in class org.jmol.applet.Jmol
 
statusTop - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
STD_ORIENTATION_ATOMIC_NUMBER_OFFSET - Static variable in class org.jmol.adapter.readers.quantum.GaussianReader
Word index of atomic number in line with atom coordinates in an orientation block.
stddev - Static variable in class org.jmol.script.Token
 
stdDev(Quaternion[], Quaternion) - Static method in class org.jmol.util.Quaternion
 
steepestDescentInitialize(int, double) - Method in class org.jmol.minimize.forcefield.ForceField
 
steepestDescentTakeNSteps(int) - Method in class org.jmol.minimize.forcefield.ForceField
 
step - Static variable in class org.jmol.script.Token
 
stepAxisCoordinates() - Method in class org.jmol.shape.SticksRenderer
 
stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
stepButton - Variable in class org.jmol.console.ScriptEditor
 
stepButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
stepMax - Variable in class org.jmol.minimize.forcefield.ForceField
 
stepMinimization() - Method in class org.jmol.minimize.Minimizer
 
stepNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
 
stepPausedExecution() - Method in class org.jmol.script.ScriptEvaluator
 
steps - Variable in class org.jmol.jvxl.readers.Parameters
 
steps - Variable in class org.jmol.minimize.Minimizer
 
stepScriptExecution() - Method in class org.jmol.viewer.Viewer
 
stereo() - Method in class org.jmol.script.ScriptEvaluator
 
stereo - Static variable in class org.jmol.script.Token
 
STEREOCHEMISTRY_ALLENE - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_DEFAULT - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesAtom
 
stereoColors - Variable in class org.jmol.viewer.TransformManager
 
stereodegrees - Static variable in class org.jmol.script.Token
 
stereoDegrees - Variable in class org.jmol.viewer.TransformManager
 
stereoFrame - Variable in class org.jmol.viewer.TransformManager
 
stereoMode - Variable in class org.jmol.viewer.TransformManager
 
stereoRadians - Variable in class org.jmol.viewer.TransformManager
 
stereoState - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
stereoSync - Variable in class org.jmol.viewer.StatusManager
 
Sticks - Class in org.jmol.shape
 
Sticks() - Constructor for class org.jmol.shape.Sticks
 
SticksRenderer - Class in org.jmol.shape
 
SticksRenderer() - Constructor for class org.jmol.shape.SticksRenderer
 
sto_exp - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
stop() - Method in class org.jmol.export.image.ImageEncoder
 
stop - Static variable in class org.jmol.script.Token
 
stop() - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
stopAnimationThreads(String) - Method in class org.jmol.viewer.Viewer
 
stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
 
stopMinimization() - Method in class org.jmol.viewer.Viewer
 
stopMotion() - Method in class org.jmol.viewer.TransformManager
 
stopMotion() - Method in class org.jmol.viewer.Viewer
 
stopPaintClock() - Method in class org.jmol.applet.Jmol
 
stopPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
str - Variable in class org.jmol.util.CifDataReader
 
straightness - Variable in class org.jmol.modelset.Group
 
straightness - Static variable in class org.jmol.script.Token
 
STRAND_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
strandCount - Variable in class org.jmol.adapter.smarter.Structure
 
strandCount - Variable in class org.jmol.modelsetbio.ProteinStructure
 
strandcount - Static variable in class org.jmol.script.Token
 
strandCount - Variable in class org.jmol.shapebio.StrandsRenderer
 
strandcountformeshribbon - Static variable in class org.jmol.script.Token
 
strandCountForMeshRibbon - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
strandcountforstrands - Static variable in class org.jmol.script.Token
 
strandCountForStrands - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
strands - Static variable in class org.jmol.script.Token
 
Strands - Class in org.jmol.shapebio
 
Strands() - Constructor for class org.jmol.shapebio.Strands
 
strandSeparation - Variable in class org.jmol.shapebio.StrandsRenderer
 
StrandsRenderer - Class in org.jmol.shapebio
 
StrandsRenderer() - Constructor for class org.jmol.shapebio.StrandsRenderer
 
strAtomicNumbers - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
strCommand - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ExecuteCommandThread
 
stream - Variable in class org.jmol.util.BinaryDocument
 
streamFileData(String, String, String, int, Object[]) - Method in class org.jmol.viewer.Viewer
 
strFormat - Variable in class org.jmol.modelset.Measurement
 
strFormat - Variable in class org.jmol.modelset.MeasurementData
 
strFormat - Variable in class org.jmol.shape.Measures
 
strFractionTemp - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
strID - Variable in class org.jmol.shapesurface.MolecularOrbital
 
string - Static variable in class org.jmol.script.Token
 
stringClass - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
stringParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
stringParameterSet(int) - Method in class org.jmol.script.ScriptEvaluator
 
stringReaders - Variable in class org.jmol.viewer.FileManager.FilesReader
 
strings - Variable in class org.jmol.shape.Labels
 
stringSetting(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
 
stringsResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
StringtoScriptButton - Variable in class org.openscience.jmol.app.webexport.Test
 
stringWidth(Object, String) - Static method in class org.jmol.awt.Font
 
stringWidth(String) - Method in class org.jmol.g3d.Font3D
 
stringWidth(String) - Method in class org.jmol.shape.Text
 
strJavaVendor - Variable in class org.jmol.viewer.Viewer
 
strJavaVersion - Variable in class org.jmol.viewer.Viewer
 
strMeasurement - Variable in class org.jmol.modelset.Measurement
 
strMenuStructure - Static variable in class org.jmol.popup.JmolPopup
 
strOSName - Variable in class org.jmol.viewer.Viewer
 
strparam - Static variable in class org.jmol.script.Token
 
strPeeked - Variable in class org.jmol.util.CifDataReader
 
strproperty - Static variable in class org.jmol.script.Token
 
strucid - Static variable in class org.jmol.script.Token
 
strucno - Static variable in class org.jmol.script.Token
 
STRUCT_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
structConfFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
structSheetRangeFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
structSiteRangeFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
structure() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
structure - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
Structure - Class in org.jmol.adapter.smarter
 
Structure(EnumStructure) - Constructor for class org.jmol.adapter.smarter.Structure
 
Structure(int, EnumStructure, EnumStructure, String, int, int, char, int, char, char, int, char) - Constructor for class org.jmol.adapter.smarter.Structure
 
structure - Variable in class org.jmol.popup.PopupResource
 
structure() - Method in class org.jmol.script.ScriptEvaluator
 
structure - Static variable in class org.jmol.script.Token
 
structureContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
structureContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
 
structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
structureCount - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
structureID - Variable in class org.jmol.adapter.smarter.Structure
 
structureID - Variable in class org.jmol.modelsetbio.ProteinStructure
 
structureList - Variable in class org.jmol.modelsetbio.AminoPolymer
 
structureList - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
structures - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
structuresDefinedInFile - Variable in class org.jmol.modelset.ModelLoader
 
structureTainted - Variable in class org.jmol.modelset.Model
 
structureType - Variable in class org.jmol.adapter.smarter.Structure
 
structureTypes - Variable in class org.jmol.shapebio.BioShapeRenderer
 
strutdefaultradius - Static variable in class org.jmol.script.Token
 
strutDefaultRadius - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
strutlengthmaximum - Static variable in class org.jmol.script.Token
 
strutLengthMaximum - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
strutPoint(int, int, int) - Static method in class org.jmol.modelsetbio.AlphaPolymer
 
struts() - Method in class org.jmol.script.ScriptEvaluator
 
struts - Static variable in class org.jmol.script.Token
 
strutsmultiple - Static variable in class org.jmol.script.Token
 
strutsMultiple - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
strutspacing - Static variable in class org.jmol.script.Token
 
strutSpacing - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
stub - Variable in class org.jmol.console.JmolConsole.FileChecker
 
sub(double[], double[], Vector3d) - Static method in class org.jmol.minimize.Util
 
sub - Static variable in class org.jmol.script.Token
 
subSearches - Variable in class org.jmol.smiles.SmilesSearch
 
subset() - Method in class org.jmol.script.ScriptEvaluator
 
subset - Static variable in class org.jmol.script.Token
 
substructure - Static variable in class org.jmol.script.Token
 
substructureType - Variable in class org.jmol.adapter.smarter.Structure
 
subtype - Variable in class org.jmol.modelsetbio.ProteinStructure
 
sum - Variable in class org.jmol.quantum.MOCalculation
 
sum - Static variable in class org.jmol.script.Token
 
sum2 - Static variable in class org.jmol.script.Token
 
sumVertexNormals(Point3f[], Vector3f[]) - Method in class org.jmol.shape.Mesh
 
sumVertexNormals(Point3f[], Vector3f[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
supercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
supercell - Static variable in class org.jmol.script.Token
 
SUPPORTED_BASIS_FUNCTIONS - Static variable in class org.jmol.api.JmolAdapter
 
SUPPORTED_BASIS_FUNCTIONS - Static variable in enum org.jmol.constant.EnumQuantumShell
 
supportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
surface - Static variable in class org.jmol.script.Token
 
SURFACE_ATOMICORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_DISTANCE_FOR_CALCULATION - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
SURFACE_DISTANCE_FOR_CALCULATION - Static variable in class org.jmol.shapespecial.Dots
 
SURFACE_ELLIPSOID2 - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_ELLIPSOID3 - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_FUNCTIONXY - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_FUNCTIONXYZ - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_INTERSECT - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_LCAOCARTOON - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_LOBE - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_LONEPAIR - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MEP - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MLP - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MOLECULAR - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MOLECULARORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_NCI - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_NOMAP - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_NONE - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_PROPERTY - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_RADICAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_SASURFACE - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_SOLVENT - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_SPHERE - Static variable in class org.jmol.jvxl.readers.Parameters
 
surfaceDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
surfacedistance - Static variable in class org.jmol.script.Token
 
surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
 
surfaceDistanceMax - Variable in class org.jmol.modelset.AtomCollection
 
SurfaceFileReader - Class in org.jmol.jvxl.readers
 
SurfaceFileReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.SurfaceFileReader
 
SurfaceFileTyper - Class in org.jmol.util
 
SurfaceFileTyper() - Constructor for class org.jmol.util.SurfaceFileTyper
 
SurfaceGenerator - Class in org.jmol.jvxl.readers
 
SurfaceGenerator() - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
 
SurfaceGenerator(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
 
surfaceList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
surfaceNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
surfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
surfaceReader - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
SurfaceReader - Class in org.jmol.jvxl.readers
 
SurfaceReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.SurfaceReader
 
surfaces - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
surfaceScrollPane - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
surfaceSet - Variable in class org.jmol.util.MeshSurface
 
surfacesOnly - Variable in class org.jmol.export._ObjExporter
Flag to cause only surfaces to be output.
SurfaceStatus - Class in org.openscience.jmol.app.surfacetool
Class that holds the surface status information that the surface tool needs.
SurfaceStatus(Mesh, int) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
surfaceTool - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SurfaceTool - Class in org.openscience.jmol.app.surfacetool
 
SurfaceTool(JmolViewer, HistoryFile, String, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceTool
 
SURFACETOOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
surfaceToolAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
surfaceToolActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SurfaceToolGUI - Class in org.openscience.jmol.app.surfacetool
GUI for the Jmol surfaceTool
SurfaceToolGUI(JmolViewer, HistoryFile, String, SurfaceTool) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
Builds and opens a GUI to control slicing.
SurfaceToolGUI(LayoutManager) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SurfaceToolGUI(boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SurfaceToolGUI(LayoutManager, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SurfaceToolGUI.SurfaceListCellRenderer - Class in org.openscience.jmol.app.surfacetool
 
SurfaceToolGUI.SurfaceListCellRenderer() - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
 
surfaceType - Variable in class org.jmol.jvxl.readers.Parameters
 
sVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
sValue(Token) - Static method in class org.jmol.script.ScriptVariable
 
sValueArray(StringBuffer, ScriptVariable, Map<Object, Boolean>, int, boolean) - Static method in class org.jmol.script.ScriptVariable
 
swap(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
 
swapBytes(int) - Static method in class org.jmol.util.BinaryDocument
 
swapBytes(short) - Static method in class org.jmol.util.BinaryDocument
 
swingPopup - Variable in class org.jmol.popup.SimplePopup
 
switchAtoms() - Method in class org.jmol.smiles.SmilesBond
 
switchAtoms() - Method in class org.jmol.util.ContactPair
 
switchCmd(ContextToken, int) - Method in class org.jmol.script.ScriptEvaluator
 
switchcmd - Static variable in class org.jmol.script.Token
 
sym - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
sym - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
SYM_EQUIV_XYZ - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
symbol - Static variable in class org.jmol.script.Token
 
symLine - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
symmetries - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
SYMMETRY - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
symmetry - Static variable in class org.jmol.script.Token
 
Symmetry - Class in org.jmol.symmetry
 
Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
 
symmetry - Variable in class org.jmol.viewer.Viewer
 
symmetryAddAtoms(int, int, int, int, int, int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
symmetryInfo - Variable in class org.jmol.symmetry.Symmetry
 
SymmetryInfo - Class in org.jmol.symmetry
 
SymmetryInfo() - Constructor for class org.jmol.symmetry.SymmetryInfo
 
symmetryInfoString - Variable in class org.jmol.symmetry.SymmetryInfo
 
SymmetryInterface - Interface in org.jmol.api
 
SymmetryOnly - Variable in class org.jmol.popup.SimplePopup
 
SymmetryOperation - Class in org.jmol.symmetry
 
SymmetryOperation() - Constructor for class org.jmol.symmetry.SymmetryOperation
 
SymmetryOperation(boolean, int) - Constructor for class org.jmol.symmetry.SymmetryOperation
 
SymmetryOperation(SymmetryOperation, Point3f[], int, int, boolean) - Constructor for class org.jmol.symmetry.SymmetryOperation
 
symmetryOperations - Variable in class org.jmol.symmetry.SymmetryInfo
 
symmetryOperationsFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
symmetryRange - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
symmetryRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
symop - Static variable in class org.jmol.script.Token
 
SYMOP_XYZ - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
symTemp - Variable in class org.jmol.modelset.ModelCollection
 
sync() - Method in class org.jmol.script.ScriptEvaluator
 
sync - Static variable in class org.jmol.script.Token
 
SYNC_DISABLE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_DRIVER - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_ENABLE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
 
SYNC_NO_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
 
SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_STEREO - Static variable in class org.jmol.viewer.StatusManager
 
syncDisabled - Variable in class org.jmol.viewer.StatusManager
 
syncDone() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
syncId - Variable in class org.jmol.applet.Jmol
 
syncId - Variable in class org.jmol.viewer.Viewer
 
syncingMouse - Variable in class org.jmol.viewer.StatusManager
 
syncingScripts - Variable in class org.jmol.viewer.StatusManager
 
syncLists() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
syncmouse - Static variable in class org.jmol.script.Token
 
syncScript(String, String, int) - Method in class org.jmol.api.JmolViewer
 
syncScript(String) - Method in class org.jmol.applet.Jmol
 
syncScript(String) - Method in interface org.jmol.applet.JmolAppletInterface
 
syncscript - Static variable in class org.jmol.script.Token
 
syncScript(String, String, int) - Method in class org.jmol.viewer.Viewer
 
syncSend(String, String, int) - Method in class org.jmol.viewer.StatusManager
 

T

T1 - Variable in class org.jmol.g3d.Hermite3D
 
T2 - Variable in class org.jmol.g3d.Hermite3D
 
tabPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
tabSwitched() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
tag - Variable in enum org.jmol.constant.EnumQuantumShell
 
tag2 - Variable in enum org.jmol.constant.EnumQuantumShell
 
tags - Static variable in class org.jmol.adapter.readers.xtal.GulpReader
 
taint(BitSet, byte) - Method in class org.jmol.modelset.AtomCollection
 
taint(int, byte) - Method in class org.jmol.modelset.AtomCollection
 
TAINT_ATOMNAME - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ATOMNO - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ATOMTYPE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_COORD - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ELEMENT - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_FORMALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_HYDROPHOBICITY - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_IONICRADIUS - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_MAX - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_OCCUPANCY - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_PARTIALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_TEMPERATURE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VALENCE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VANDERWAALS - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VIBRATION - Static variable in class org.jmol.modelset.AtomCollection
 
tainted - Variable in class org.jmol.modelset.AtomCollection
 
target - Variable in class org.jmol.shape.Object2d
 
targetPixelScale - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
targetRotationRadius - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
targetTime - Variable in class org.jmol.viewer.ActionManager.TimeoutThread
 
targetTime - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
taskNumber - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
The number of the task begin interpreted.
tButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
TEAL - Static variable in class org.jmol.g3d.Graphics3D
 
temp - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
temp3 - Variable in class org.jmol.symmetry.SymmetryOperation
 
tempA - Variable in class org.jmol.export.___Exporter
 
TempArray - Class in org.jmol.util
 
TempArray() - Constructor for class org.jmol.util.TempArray
 
tempDataXml - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
tempDipole - Variable in class org.jmol.shapespecial.Dipoles
 
temperature - Static variable in class org.jmol.script.Token
 
TemperatureOnly - Variable in class org.jmol.popup.SimplePopup
 
templateAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
tempManager - Variable in class org.jmol.viewer.Viewer
 
tempP1 - Variable in class org.jmol.export.___Exporter
 
tempP2 - Variable in class org.jmol.export.___Exporter
 
tempP3 - Variable in class org.jmol.export.___Exporter
 
tempQ1 - Variable in class org.jmol.export._VrmlExporter
 
tempQ2 - Variable in class org.jmol.export._VrmlExporter
 
tempStatement - Variable in class org.jmol.script.ScriptEvaluator
 
tempV1 - Variable in class org.jmol.export.___Exporter
 
tempV2 - Variable in class org.jmol.export.___Exporter
 
tempV3 - Variable in class org.jmol.export.___Exporter
 
tEndcapOpen - Variable in class org.jmol.g3d.Cylinder3D
 
tensScale - Static variable in class org.jmol.util.Parser
 
term - Variable in class org.jmol.export.UseTable
 
terminatorMessage - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
Test - Class in org.openscience.jmol.app.webexport
 
Test(Viewer) - Constructor for class org.openscience.jmol.app.webexport.Test
 
test1 - Variable in class org.jmol.quantum.NciCalculation
 
testData - Static variable in class org.jmol.script.ScriptEvaluator
 
testData2 - Static variable in class org.jmol.script.ScriptEvaluator
 
testflag1 - Static variable in class org.jmol.script.Token
 
testFlag1 - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
testflag2 - Static variable in class org.jmol.script.Token
 
testFlag2 - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
testflag3 - Static variable in class org.jmol.script.Token
 
testFlag3 - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
testflag4 - Static variable in class org.jmol.script.Token
 
testFlag4 - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
testFlags - Variable in class org.jmol.jvxl.readers.Parameters
 
testing - Variable in class org.jmol.quantum.MOCalculation
 
testLinear - Static variable in class org.jmol.jvxl.readers.IsoSolventReader
 
testRadiusAdjust - Variable in class org.jmol.shapespecial.DotsRenderer
 
tEvenDiameter - Variable in class org.jmol.g3d.Cylinder3D
 
text - Variable in class org.jmol.export.image.ImageSelection
 
text - Variable in class org.jmol.modelset.LabelToken
 
text - Variable in class org.jmol.shape.Hover
 
text - Variable in class org.jmol.shape.Labels
 
Text - Class in org.jmol.shape
 
Text(JmolRendererInterface, Font3D, String, short, short, int, int, int, int, int, float) - Constructor for class org.jmol.shape.Text
 
Text(Viewer, Graphics3D, Font3D, String, short, int, int, float) - Constructor for class org.jmol.shape.Text
 
text - Variable in class org.jmol.shape.Text
 
Text3D - Class in org.jmol.g3d
implementation for text rendering
Text3D(String, Font3D) - Constructor for class org.jmol.g3d.Text3D
 
textColor - Variable in class org.jmol.applet.AppletWrapper
 
TEXTCOLOR - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
 
TextFormat - Class in org.jmol.util
 
TextFormat() - Constructor for class org.jmol.util.TextFormat
 
textHeight - Variable in class org.jmol.shape.Text
 
textInfo - Variable in class org.jmol.symmetry.PointGroup
 
TextShape - Class in org.jmol.shape
 
TextShape() - Constructor for class org.jmol.shape.TextShape
 
textUnformatted - Variable in class org.jmol.shape.Text
 
textureCode - Variable in class org.jmol.export._TachyonExporter
 
textureFiles - Variable in class org.jmol.export._ObjExporter
List of texture files created.
textures - Variable in class org.jmol.export._ObjExporter
HashSet for textures.
textures - Variable in class org.jmol.export._TachyonExporter
 
textWidth - Variable in class org.jmol.shape.Text
 
textY - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
tHemisphere - Variable in class org.jmol.bspt.CubeIterator
 
thePlane - Variable in class org.jmol.jvxl.data.VolumeData
 
thePlane - Variable in class org.jmol.jvxl.readers.Parameters
 
thePlane - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
thePlane - Variable in class org.jmol.shape.MeshRenderer
 
thePlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
 
theProperty - Variable in class org.jmol.jvxl.readers.Parameters
 
theta - Variable in class org.jmol.minimize.forcefield.Calculation
 
theta - Variable in class org.jmol.modelset.Group
 
theta - Static variable in class org.jmol.script.Token
 
theTok - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
theTok - Variable in class org.jmol.script.ScriptEvaluator
 
theToken - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
theToken - Variable in class org.jmol.script.ScriptEvaluator
 
theValue - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
theWidgets - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
thickness - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
thickness - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
thicknessMax - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
thicknessSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
thisArgb - Variable in class org.jmol.shapespecial.Dots
 
thisAtom - Variable in class org.jmol.quantum.QuantumCalculation
 
thisAtom - Variable in class org.jmol.shapespecial.Dots
 
thisAtomSet - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
thisCommand - Variable in class org.jmol.script.ScriptEvaluator
 
thisContext - Variable in class org.jmol.script.ScriptEvaluator
 
thisContour - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
thisContour - Variable in class org.jmol.jvxl.readers.Parameters
 
thisDataSetName - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
thisFormula - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
thisFunction - Variable in class org.jmol.script.ScriptCompiler
 
thisID - Variable in class org.jmol.shape.Mesh
 
thisID - Variable in class org.jmol.shape.Object2dShape
 
thisID - Variable in class org.jmol.shapespecial.Dipole
 
thisInside - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
thisMesh - Variable in class org.jmol.shapespecial.Draw
 
thisMesh - Variable in class org.jmol.shapesurface.Isosurface
 
thismodel - Static variable in class org.jmol.script.Token
 
thisModel - Variable in class org.jmol.shapesurface.MolecularOrbital
 
thisName - Variable in class org.jmol.util.ColorEncoder
 
thisPlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
thisPlaneB - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
thisRadius - Variable in class org.jmol.shapespecial.Dots
 
thisScale - Variable in class org.jmol.util.ColorEncoder
 
thisSet - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
thisSet - Variable in class org.jmol.shapesurface.LcaoCartoon
 
thisStateModel - Variable in class org.jmol.modelset.ModelCollection
 
thisStructuralFormula - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
thisType - Variable in class org.jmol.export.dialog.Dialog.TypeFilter
 
thisType - Variable in class org.jmol.shapesurface.LcaoCartoon
 
thisX - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
thisx - Variable in class org.jmol.popup.SimplePopup
 
thisy - Variable in class org.jmol.popup.SimplePopup
 
thread - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
threadSafe - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
tickEdges - Variable in class org.jmol.shape.CageRenderer
 
TickerThread - Class in org.jmol.applet
 
TickerThread(AppletWrapper) - Constructor for class org.jmol.applet.TickerThread
 
tickInfo - Variable in class org.jmol.modelset.Measurement
 
tickInfo - Variable in class org.jmol.modelset.MeasurementData
 
TickInfo - Class in org.jmol.modelset
 
TickInfo(Point3f) - Constructor for class org.jmol.modelset.TickInfo
 
tickInfo - Variable in class org.jmol.shape.FontLineShapeRenderer
 
tickInfo - Variable in class org.jmol.shape.Measures
 
tickInfos - Variable in class org.jmol.shape.FontLineShape
 
tickLabelFormats - Variable in class org.jmol.modelset.TickInfo
 
ticks - Variable in class org.jmol.modelset.TickInfo
 
ticks - Static variable in class org.jmol.script.Token
 
time - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
time - Variable in class org.jmol.viewer.ActionManager.MotionPoint
 
time - Variable in class org.jmol.viewer.ActionManager.Mouse
 
time0 - Variable in class org.jmol.viewer.ActionManager.Gesture
 
timeBegin - Variable in class org.jmol.applet.Jmol
 
timeBegin - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeBegin - Variable in class org.openscience.jvxl.MonitorInputStream
 
timeBeginExecution - Variable in class org.jmol.script.ScriptEvaluator
 
timeCount - Variable in class org.jmol.applet.Jmol
 
timeCount - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeEndExecution - Variable in class org.jmol.script.ScriptEvaluator
 
timeLast - Variable in class org.jmol.applet.Jmol
 
timeLast - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeout(int) - Method in class org.jmol.script.ScriptEvaluator
 
timeout - Static variable in class org.jmol.script.Token
 
timeouts - Variable in class org.jmol.viewer.ActionManager
 
times - Static variable in class org.jmol.script.Token
 
TimeStamp_WebLink() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
timestimes - Static variable in class org.jmol.script.Token
 
timeTotal - Variable in class org.jmol.applet.Jmol
 
timeTotal - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
TIMINGS - Static variable in class org.jmol.g3d.Normix3D
 
title() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
title - Variable in class org.jmol.adapter.readers.quantum.DgridReader
 
title - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
title - Variable in class org.jmol.console.ScriptEditor
 
title - Variable in class org.jmol.jvxl.data.JvxlData
 
title - Variable in class org.jmol.jvxl.readers.Parameters
 
title - Static variable in class org.jmol.script.Token
 
title - Variable in class org.jmol.shape.Mesh
 
title - Variable in class org.jmol.shape.MeshCollection
 
title - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
 
title - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
 
title - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
TITLE_MAX_WIDTH - Static variable in class org.jmol.popup.JmolPopup
 
titleformat - Static variable in class org.jmol.script.Token
 
titles - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
to - Static variable in class org.jmol.script.Token
 
toArray() - Method in class org.jmol.script.ScriptVariable
 
toAxisAngle4f() - Method in class org.jmol.util.Quaternion
 
toBitSet() - Method in class org.jmol.util.FastBitSet
 
toBytes(StringBuffer) - Static method in class org.jmol.util.Base64
 
toCanonical - Static variable in class org.jmol.util.BoxInfo
 
toCartesian(SymmetryInterface) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
toCartesian(Point3f, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
toCartesian(Point3f, boolean) - Method in class org.jmol.symmetry.Symmetry
 
toCartesian(Point3f, boolean) - Method in class org.jmol.util.SimpleUnitCell
 
toCartesian(Point3f, boolean) - Method in class org.jmol.viewer.Viewer
absolute or relative to origin of UNITCELL {x y z}
toFloat(String) - Static method in class org.jmol.script.ScriptVariable
 
toFractional(Point3f, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
toFractional(Point3f, boolean) - Method in class org.jmol.symmetry.Symmetry
 
toFractional(float) - Static method in class org.jmol.symmetry.UnitCell
 
toFractional(Point3f, boolean) - Method in class org.jmol.util.SimpleUnitCell
 
toFractional(Point3f, boolean) - Method in class org.jmol.viewer.Viewer
absolute or relative to origin of UNITCELL {x y z}
toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
Brings the surfaceTool to the front and updates sliders, etc...
toFrontOrGotFocus() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
toggle(Measurement) - Method in class org.jmol.shape.Measures
 
toggleInPlace(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
togglelabel - Static variable in class org.jmol.script.Token
 
toggleMeasurement() - Method in class org.jmol.viewer.ActionManager
 
toggleMode() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
toggleOn(int[]) - Method in class org.jmol.shape.Measures
 
togglePickingLabel(BitSet) - Method in class org.jmol.viewer.Viewer
 
toJSON(String, Object) - Static method in class org.jmol.util.Escape
 
tok - Variable in class org.jmol.modelset.LabelToken
 
tok - Variable in class org.jmol.script.ScriptFunction
 
tok - Variable in class org.jmol.script.Token
 
tokAction - Variable in class org.jmol.modelset.MeasurementData
 
tokAction - Variable in class org.jmol.shape.Measures
 
tokAt(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
tokAt(int) - Method in class org.jmol.script.ScriptCompiler
 
tokAt(int) - Method in class org.jmol.script.ScriptEvaluator
 
tokAt(int, Token[]) - Method in class org.jmol.script.ScriptEvaluator
 
tokAttr(int, int) - Static method in class org.jmol.script.Token
 
tokAttrOr(int, int, int) - Static method in class org.jmol.script.Token
 
tokCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
token - Variable in class org.jmol.script.ScriptContext
 
token - Variable in class org.jmol.script.ScriptFlowContext
 
Token - Class in org.jmol.script
 
Token() - Constructor for class org.jmol.script.Token
 
Token(int, int, Object) - Constructor for class org.jmol.script.Token
 
Token(int) - Constructor for class org.jmol.script.Token
 
Token(int, int) - Constructor for class org.jmol.script.Token
 
Token(int, Object) - Constructor for class org.jmol.script.Token
 
TOKEN_AROMATIC - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_ALLYLIC - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_CHARGED - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_CONNECTED - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_ONLY - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_SP - Static variable in class org.jmol.minimize.Minimizer
 
tokenAll - Static variable in class org.jmol.script.Token
 
tokenAnd - Static variable in class org.jmol.script.Token
 
tokenAND - Static variable in class org.jmol.script.Token
 
tokenAndEquals - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
tokenAndFALSE - Static variable in class org.jmol.script.Token
 
tokenArraySelector - Static variable in class org.jmol.script.Token
 
tokenArraySquare - Static variable in class org.jmol.script.Token
 
tokenAt(int) - Method in class org.jmol.script.ScriptCompiler
 
tokenAt(int, Token[]) - Method in class org.jmol.script.ScriptEvaluator
 
tokenAttr(Token, int) - Static method in class org.jmol.script.ScriptCompilationTokenParser
 
tokenColon - Static variable in class org.jmol.script.Token
 
tokenComma - Static variable in class org.jmol.script.Token
 
tokenCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
tokenConnected - Static variable in class org.jmol.script.Token
 
tokenCoordinateBegin - Static variable in class org.jmol.script.Token
 
tokenCoordinateEnd - Static variable in class org.jmol.script.Token
 
tokenCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
tokenDefineString - Static variable in class org.jmol.script.Token
 
tokenDivide - Static variable in class org.jmol.script.Token
 
tokenEquals - Static variable in class org.jmol.script.Token
 
tokenExpressionBegin - Static variable in class org.jmol.script.Token
 
tokenExpressionEnd - Static variable in class org.jmol.script.Token
 
tokenIf - Static variable in class org.jmol.script.Token
 
tokenize(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Take the given string and chop it up into a series of strings on whitespace boundries.
tokenizeCastepCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
tokenizePlusPlus(int, boolean) - Method in class org.jmol.script.ScriptCompiler
 
tokenizer - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
tokenLeftParen - Static variable in class org.jmol.script.Token
 
tokenMap - Static variable in class org.jmol.script.Token
 
tokenMinus - Static variable in class org.jmol.script.Token
 
tokenNext() - Method in class org.jmol.script.ScriptCompilationTokenParser
increments the pointer; does NOT set theToken or theValue
tokenNext(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
tokenOff - Static variable in class org.jmol.script.Token
 
tokenOn - Static variable in class org.jmol.script.Token
 
tokenOpIf - Static variable in class org.jmol.script.Token
 
tokenOr - Static variable in class org.jmol.script.Token
 
tokenOrTRUE - Static variable in class org.jmol.script.Token
 
tokenPlus - Static variable in class org.jmol.script.Token
 
tokenRightBrace - Static variable in class org.jmol.script.Token
 
tokenRightParen - Static variable in class org.jmol.script.Token
 
tokens - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
tokens - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
tokens - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
tokens - Variable in class org.jmol.jvxl.readers.PmeshReader
 
tokenScript - Static variable in class org.jmol.script.Token
 
tokenSet - Static variable in class org.jmol.script.Token
 
tokenSetArray - Static variable in class org.jmol.script.Token
 
tokenSetCmd - Static variable in class org.jmol.script.Token
 
tokenSetProperty - Static variable in class org.jmol.script.Token
 
tokenSetVar - Static variable in class org.jmol.script.Token
 
tokenSpaceBeforeSquare - Static variable in class org.jmol.script.Token
 
tokenSwitch - Static variable in class org.jmol.script.Token
 
tokenTimes - Static variable in class org.jmol.script.Token
 
tokenTypes - Static variable in class org.jmol.minimize.Minimizer
 
tokInitialPlusPlus - Variable in class org.jmol.script.ScriptCompiler
 
tokLastMath - Variable in class org.jmol.script.ScriptCompiler
 
tokPeek() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
tokPeek(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
 
toolbar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
toolbarButtonGroup - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
top - Static variable in class org.jmol.script.Token
 
topAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
topButton - Variable in class org.jmol.console.ScriptEditor
 
topButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
toPoint4f() - Method in class org.jmol.util.Quaternion
 
topPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
toRadians - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
toRadians - Static variable in class org.jmol.util.SimpleUnitCell
 
toReadable(Object) - Static method in class org.jmol.util.Escape
 
toReadable(String, Object) - Static method in class org.jmol.util.Escape
 
torsion - Static variable in class org.jmol.script.Token
 
torsionCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
torsions - Variable in class org.jmol.minimize.forcefield.Calculations
 
torsions - Variable in class org.jmol.minimize.Minimizer
 
toString() - Method in class org.jmol.atomdata.RadiusData
 
toString() - Method in class org.jmol.bspt.Leaf
 
toString() - Method in class org.jmol.bspt.Node
 
toString() - Method in class org.jmol.g3d.Rgb16
 
toString() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
toString() - Method in class org.jmol.minimize.MinAtom
 
toString() - Method in class org.jmol.modelset.Atom
 
toString() - Method in class org.jmol.modelset.Bond
 
toString() - Method in class org.jmol.modelset.Group
 
toString() - Method in class org.jmol.modelset.ModelCollection.StateScript
 
toString() - Method in class org.jmol.modelsetbio.AminoPolymer.Bridge
 
toString() - Method in exception org.jmol.script.ScriptEvaluator.ScriptException
 
toString() - Method in class org.jmol.script.ScriptEvaluator
 
toString() - Method in class org.jmol.script.ScriptFlowContext
 
toString() - Method in class org.jmol.script.ScriptFunction
 
toString() - Method in class org.jmol.script.ScriptVariable
 
toString() - Method in class org.jmol.script.Token
 
toString() - Method in class org.jmol.smiles.SmilesAtom
 
toString() - Method in class org.jmol.smiles.SmilesBond
 
toString() - Method in class org.jmol.smiles.SmilesMeasure
 
toString() - Method in class org.jmol.smiles.SmilesSearch
 
toString() - Method in class org.jmol.util.ContactPair
 
toString() - Method in class org.jmol.util.FastBitSet
 
toString() - Method in class org.jmol.util.OutputStringBuffer
 
toString() - Method in class org.jmol.util.Quaternion
Java axisAngle / plane / Point4f format all have the format {x y z w} so we go with that here as well
toString() - Method in class org.jmol.viewer.ActionManager.Gesture
 
toString() - Method in class org.jmol.viewer.ActionManager.MotionPoint
 
toString() - Method in class org.jmol.viewer.ActionManager.TimeoutThread
 
toString() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
 
toTag(String) - Method in class org.jmol.util.XmlReader
 
totalSteps - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
totE - Variable in class org.jmol.adapter.readers.xtal.DmolReader
 
totEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
totEnergy - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
 
totEnergy - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
TOUCH_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
TOUCH_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
toUnitCell(Point3f, Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
toUnitCell(Point3f, Point3f) - Method in class org.jmol.symmetry.Symmetry
 
toUnitCell(Point3f, Point3f) - Method in class org.jmol.symmetry.UnitCell
when offset is null,
toUnitCell(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
relative to origin without regard to UNITCELL {x y z}
toVector(boolean) - Method in class org.jmol.modelset.Measurement
 
toWebAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
toWebActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
toXml(StringBuffer, String, List<Object[]>) - Static method in class org.jmol.util.XmlUtil
 
tPending - Variable in class org.jmol.shapebio.RocketsRenderer
 
tql2() - Method in class org.jmol.util.Eigen
 
tQuiet - Variable in class org.jmol.script.ScriptEvaluator
 
trace - Static variable in class org.jmol.script.Token
 
Trace - Class in org.jmol.shapebio
 
Trace() - Constructor for class org.jmol.shapebio.Trace
 
tracealpha - Static variable in class org.jmol.script.Token
 
traceAlpha - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
TraceRenderer - Class in org.jmol.shapebio
 
TraceRenderer() - Constructor for class org.jmol.shapebio.TraceRenderer
 
traceX - Variable in class org.jmol.modelset.Measurement
 
traceY - Variable in class org.jmol.modelset.Measurement
 
trajectory - Static variable in class org.jmol.script.Token
 
trajectoryBaseIndex - Variable in class org.jmol.modelset.Model
 
trajectoryNames - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
trajectoryStepCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
trajectorySteps - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
trajectorySteps - Variable in class org.jmol.adapter.readers.more.MdCrdReader
 
trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
trajectorySteps - Variable in class org.jmol.modelset.ModelCollection
 
trans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
transferResource(File, String, File, String) - Method in class org.openscience.chimetojmol.ChimePanel
 
transform(Vector3f, Vector3f) - Method in interface org.jmol.api.VolumeDataInterface
 
transform(Vector3f, Vector3f) - Method in class org.jmol.jvxl.data.VolumeData
 
transform - Static variable in class org.jmol.script.Token
 
transform(Dipole) - Method in class org.jmol.shapespecial.DipolesRenderer
 
transform(short, Atom, Vector3f) - Method in class org.jmol.shapespecial.VectorsRenderer
 
transform(Point3f) - Method in class org.jmol.util.Quaternion
 
transform(Point3f, Point3f) - Method in class org.jmol.util.Quaternion
 
transform(Vector3f) - Method in class org.jmol.util.Quaternion
 
transformAtoms() - Method in class org.jmol.viewer.ShapeManager
 
transformCartesian(UnitCell, Point3f) - Method in class org.jmol.symmetry.SymmetryOperation
 
transformedVectors - Variable in class org.jmol.g3d.Normix3D
 
transformedVectors - Variable in class org.jmol.shape.MeshRenderer
 
TransformFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
TransformManager - Class in org.jmol.viewer
 
TransformManager() - Constructor for class org.jmol.viewer.TransformManager
 
TransformManager(Viewer) - Constructor for class org.jmol.viewer.TransformManager
 
TransformManager(Viewer, int, int) - Constructor for class org.jmol.viewer.TransformManager
 
transformManager - Variable in class org.jmol.viewer.Viewer
 
TransformManager.MotionThread - Class in org.jmol.viewer
 
TransformManager.MotionThread() - Constructor for class org.jmol.viewer.TransformManager.MotionThread
 
TransformManager.SpinThread - Class in org.jmol.viewer
 
TransformManager.SpinThread(float, List<Point3f>, BitSet, boolean, boolean) - Constructor for class org.jmol.viewer.TransformManager.SpinThread
 
TransformManager.VibrationThread - Class in org.jmol.viewer
 
TransformManager.VibrationThread() - Constructor for class org.jmol.viewer.TransformManager.VibrationThread
 
TransformManager10 - Class in org.jmol.viewer
 
TransformManager10(Viewer) - Constructor for class org.jmol.viewer.TransformManager10
 
TransformManager10(Viewer, int, int) - Constructor for class org.jmol.viewer.TransformManager10
 
TransformManager11 - Class in org.jmol.viewer
 
TransformManager11() - Constructor for class org.jmol.viewer.TransformManager11
 
TransformManager11(Viewer) - Constructor for class org.jmol.viewer.TransformManager11
 
TransformManager11(Viewer, int, int) - Constructor for class org.jmol.viewer.TransformManager11
 
TRANSFORMMAT - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
transformPoint(Point3f, Point3i) - Method in class org.jmol.viewer.TransformManager
 
transformPoint(Point3f) - Method in class org.jmol.viewer.TransformManager
CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
transformPoint(Point3f, Vector3f) - Method in class org.jmol.viewer.TransformManager
 
transformPoint(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
transformPoint(Point3f) - Method in class org.jmol.viewer.Viewer
 
transformPoint(Point3f, Vector3f) - Method in class org.jmol.viewer.Viewer
 
transformPoint(Point3f, Point3i) - Method in class org.jmol.viewer.Viewer
 
transformPoint(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
transformPointNoClip(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
transformPointNoClip(Point3f) - Method in class org.jmol.viewer.TransformManager
CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
transformPointNoClip(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
transformPoints(List<Point3f>, Matrix4f, Point3f) - Static method in class org.jmol.util.Measure
 
transformPoints(int, Point3f[], Point3i[]) - Method in class org.jmol.viewer.TransformManager
 
transformPoints(Point3f[], Point3i[]) - Method in class org.jmol.viewer.Viewer
 
transformScreenPoint(Point3f) - Method in class org.jmol.viewer.TransformManager
 
transformVector(Vector3f, Vector3f) - Method in class org.jmol.viewer.TransformManager
 
transformVector(Vector3f, Vector3f) - Method in class org.jmol.viewer.Viewer
 
transitionDipole - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
translate(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
translate - Static variable in class org.jmol.script.Token
 
translate(char, float, char, BitSet) - Method in class org.jmol.viewer.Viewer
 
translate(String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
translateSelected - Static variable in class org.jmol.script.Token
 
translateSelected() - Method in class org.jmol.viewer.RepaintManager
 
translateToPercent(char, float) - Method in class org.jmol.viewer.TransformManager
 
translateXYBy(int, int) - Method in class org.jmol.viewer.TransformManager
 
translateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
 
translateZBy(int) - Method in class org.jmol.viewer.TransformManager
 
translation - Static variable in class org.jmol.script.Token
 
translation - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
Translation - Class in org.jmol.symmetry
 
Translation() - Constructor for class org.jmol.symmetry.Translation
 
Translation(char, int) - Constructor for class org.jmol.symmetry.Translation
 
Translation(char, Point3i) - Constructor for class org.jmol.symmetry.Translation
 
Translation(char, int, int) - Constructor for class org.jmol.symmetry.Translation
 
translationCode - Variable in class org.jmol.symmetry.Translation
 
translationResources - Variable in class org.jmol.i18n.GT
 
translationResourcesCount - Variable in class org.jmol.i18n.GT
 
translations - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
translationString - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
translucency - Variable in class org.jmol.jvxl.data.JvxlData
 
translucency - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
translucencyFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
 
translucencyMask - Variable in class org.jmol.g3d.Graphics3D
 
translucent - Static variable in class org.jmol.script.Token
 
TRANSLUCENT_50 - Static variable in class org.jmol.g3d.Graphics3D
 
TRANSLUCENT_MASK - Static variable in class org.jmol.g3d.Graphics3D
 
TRANSLUCENT_SCREENED - Static variable in class org.jmol.g3d.Graphics3D
 
TRANSLUCENT_SHIFT - Static variable in class org.jmol.g3d.Graphics3D
 
translucentAllowed - Variable in class org.jmol.shape.Shape
 
translucentCoverOnly - Variable in class org.jmol.g3d.Graphics3D
 
translucentLevel - Variable in class org.jmol.shape.Shape
 
translucentLevel - Variable in class org.jmol.shapesurface.LcaoCartoon
 
TRANSPARENT - Static variable in class org.jmol.g3d.Graphics3D
 
transparentBackground - Variable in class org.openscience.jmol.app.JmolApp
 
transparentColor - Variable in class org.jmol.export.image.PngEncoder
 
tRaster - Variable in class org.jmol.g3d.Cylinder3D
 
tred2() - Method in class org.jmol.util.Eigen
 
tree - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
treeDepth - Variable in class org.jmol.bspt.Bspt
 
treeModel - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
triad(Tuple3f) - Method in class org.jmol.export._PovrayExporter
 
triad(int[]) - Method in class org.jmol.export._PovrayExporter
 
triad(float, float, float) - Method in class org.jmol.export._TachyonExporter
 
triad(Tuple3f) - Method in class org.jmol.export._TachyonExporter
 
triangle3d - Variable in class org.jmol.g3d.Graphics3D
 
Triangle3D - Class in org.jmol.g3d
renders triangles
Triangle3D(Graphics3D) - Constructor for class org.jmol.g3d.Triangle3D
 
triangleCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
TriangleData - Class in org.jmol.util
 
TriangleData() - Constructor for class org.jmol.util.TriangleData
 
triangleFace - Variable in class org.jmol.export._IdtfExporter
 
triangleNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
triangles - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
triangles - Static variable in class org.jmol.script.Token
 
triangleTable2 - Static variable in class org.jmol.util.TriangleData
 
trigger() - Method in class org.jmol.viewer.ActionManager.TimeoutThread
 
triggered - Variable in class org.jmol.viewer.ActionManager.TimeoutThread
 
triggerTimeout(String) - Method in class org.jmol.viewer.ActionManager
 
triggerTimeout(String) - Method in class org.jmol.viewer.Viewer
 
trim - Static variable in class org.jmol.script.Token
 
trim(String, String) - Static method in class org.jmol.util.TextFormat
 
TRUE - Static variable in class org.jmol.viewer.SelectionManager
 
truncate0(StringBuffer, float) - Static method in class org.jmol.viewer.TransformManager
 
truncate2(StringBuffer, float) - Static method in class org.jmol.viewer.TransformManager
 
trycmd - Static variable in class org.jmol.script.Token
 
tScreened - Variable in class org.jmol.g3d.Sphere3D
 
tuples - Variable in class org.jmol.bspt.Leaf
 
Turn - Class in org.jmol.modelsetbio
 
Turn(AlphaPolymer, int, int, int) - Constructor for class org.jmol.modelsetbio.Turn
 
twelfths - Static variable in class org.jmol.symmetry.SymmetryOperation
 
twelfthsOf(float) - Static method in class org.jmol.symmetry.SymmetryOperation
 
TWO_PI - Static variable in class org.jmol.minimize.forcefield.Calculations
 
TWO_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
twoChar - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
twoCharLabelTokenIds - Static variable in class org.jmol.modelset.LabelToken
 
twoCharLabelTokenParams - Static variable in class org.jmol.modelset.LabelToken
 
twodots - Static variable in class org.jmol.shape.SticksRenderer
 
twoP2 - Static variable in class org.jmol.symmetry.UnitCell
 
twoPass - Variable in class org.jmol.g3d.Graphics3D
 
TWOPI - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
 
twoPI - Static variable in class org.jmol.viewer.TransformManager
 
TwoPointGesture - Class in org.jmol.multitouch.sparshui
TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.
TwoPointGesture() - Constructor for class org.jmol.multitouch.sparshui.TwoPointGesture
 
txRaster - Variable in class org.jmol.g3d.Cylinder3D
 
type - Variable in enum org.jmol.constant.EnumVdw
 
type - Variable in class org.jmol.jvxl.readers.IsoMepReader
 
type - Variable in class org.jmol.jvxl.readers.PmeshReader
 
type - Variable in class org.jmol.minimize.MinAtom
 
type - Variable in class org.jmol.modelset.Polymer
 
type - Variable in class org.jmol.modelset.TickInfo
 
type - Variable in class org.jmol.modelsetbio.ProteinStructure
 
type - Variable in class org.jmol.quantum.NciCalculation
 
type - Static variable in class org.jmol.script.Token
 
type - Variable in class org.jmol.shapespecial.Dipole
 
type - Variable in class org.jmol.smiles.SmilesMeasure
 
type - Variable in class org.jmol.symmetry.PointGroup.Operation
 
type2 - Variable in enum org.jmol.constant.EnumVdw
 
TYPE_ALL - Static variable in class org.jmol.quantum.NciCalculation
 
TYPE_AMINO - Static variable in class org.jmol.modelset.Polymer
 
TYPE_ANY - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_ATROPISOMER_1 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_ATROPISOMER_2 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_BIO_PAIR - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_BIO_SEQUENCE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_CARBOHYDRATE - Static variable in class org.jmol.modelset.Polymer
 
TYPE_DIFF - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_DIFF_PAIR - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_DIRECTIONAL_1 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_DIRECTIONAL_2 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_DOUBLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_FUNCTION - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_INTER - Static variable in class org.jmol.quantum.NciCalculation
 
TYPE_INTRA - Static variable in class org.jmol.quantum.NciCalculation
 
TYPE_LIGAND - Static variable in class org.jmol.quantum.NciCalculation
 
TYPE_MAX - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_MULTIPLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_NOBONDING - Static variable in class org.jmol.modelset.Polymer
 
TYPE_NONE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_NUCLEIC - Static variable in class org.jmol.modelset.Polymer
 
TYPE_RING - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_SINGLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_SUM - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
TYPE_TRIPLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_UNKNOWN - Static variable in class org.jmol.smiles.SmilesBond
 
typeName - Variable in class org.jmol.script.ScriptFunction
 
typeNames - Static variable in class org.jmol.symmetry.PointGroup
 
typeOf(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
 
TYPES - Static variable in class org.jmol.smiles.SmilesMeasure
 
tyRaster - Variable in class org.jmol.g3d.Cylinder3D
 
tzRaster - Variable in class org.jmol.g3d.Cylinder3D
 

U

U_ISO_OR_EQUIV - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
Uccage - Class in org.jmol.shape
 
Uccage() - Constructor for class org.jmol.shape.Uccage
 
UccageRenderer - Class in org.jmol.shape
 
UccageRenderer() - Constructor for class org.jmol.shape.UccageRenderer
 
uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
 
uguideAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
uicrcifContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
unaryMinus - Static variable in class org.jmol.script.Token
 
unbind() - Method in class org.jmol.script.ScriptEvaluator
 
unbind - Static variable in class org.jmol.script.Token
 
unbind(int, int) - Method in class org.jmol.viewer.binding.Binding
 
unbind(int, String) - Method in class org.jmol.viewer.binding.Binding
 
unbindAction(String, String) - Method in class org.jmol.viewer.ActionManager
 
unBindAction(String, String) - Method in class org.jmol.viewer.Viewer
 
unbindJmolAction(int) - Method in class org.jmol.viewer.binding.Binding
 
unbindMouseAction(int) - Method in class org.jmol.viewer.binding.Binding
 
unbindUserAction(String) - Method in class org.jmol.viewer.binding.Binding
 
UNBRACKETED_SET - Static variable in class org.jmol.smiles.SmilesAtom
 
undeleteAtom(int) - Method in class org.jmol.modelset.ModelLoader
called from org.jmol.modelsetbio.resolver when adding hydrogens.
undo - Variable in class org.jmol.console.ScriptEditor.EditorDocument
 
undo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
undo - Static variable in class org.jmol.script.Token
 
undoableEditHappened(UndoableEditEvent) - Method in class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
 
undoButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
undoClear() - Method in class org.jmol.viewer.Viewer
 
undoClear() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
undomove - Static variable in class org.jmol.script.Token
 
undoMoveAction(int, int) - Method in class org.jmol.viewer.Viewer
 
undoMoveAction(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
undoPointer - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
undoRedo(boolean) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
undoRedoMove() - Method in class org.jmol.script.ScriptEvaluator
 
undoSave(boolean) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
undoSaved - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
undoSetEnabled() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
undoStack - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
undoWorking - Variable in class org.jmol.viewer.Viewer
 
unescapeBitset(String) - Static method in class org.jmol.util.Escape
 
unEscapeBitSetArray(BitSet) - Method in class org.jmol.script.ScriptVariable
 
unEscapeBitSetArray(ArrayList<ScriptVariable>, boolean) - Static method in class org.jmol.script.ScriptVariable
 
unescapeMatrix(String) - Static method in class org.jmol.util.Escape
 
unescapePoint(String) - Static method in class org.jmol.util.Escape
 
unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.ScriptVariable
 
unescapePointOrBitsetOrMatrixOrArray(String) - Static method in class org.jmol.util.Escape
 
unescapeStringArray(String) - Static method in class org.jmol.util.Escape
 
unescapeUnicode(String) - Static method in class org.jmol.util.Escape
 
unicode(char) - Static method in class org.jmol.util.Escape
 
unicodeName - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
uniqueAtomMap - Variable in class org.jmol.adapter.readers.quantum.PsiReader
 
uniqueAxis - Variable in class org.jmol.symmetry.SpaceGroup
 
uniqueID - Variable in class org.jmol.modelsetbio.ProteinStructure
 
uniqueID - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
uniqueID - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
unitAxisVectors - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
unitAxisVectors - Static variable in class org.jmol.viewer.JmolConstants
 
unitBboxPoints - Static variable in class org.jmol.util.BoxInfo
 
unitcell(int) - Method in class org.jmol.script.ScriptEvaluator
 
unitcell - Static variable in class org.jmol.script.Token
 
unitCell - Variable in class org.jmol.symmetry.Symmetry
 
UnitCell - Class in org.jmol.symmetry
a class private to the org.jmol.symmetry package to be accessed only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.
UnitCell(float[]) - Constructor for class org.jmol.symmetry.UnitCell
 
UnitCell.Esort - Class in org.jmol.symmetry
 
UnitCell.Esort() - Constructor for class org.jmol.symmetry.UnitCell.Esort
 
unitcellcolor - Static variable in class org.jmol.script.Token
 
unitCellData - Variable in class org.jmol.adapter.readers.xtal.DmolReader
 
unitCellData - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
 
unitCellData - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
unitCellMultiplier - Variable in class org.jmol.symmetry.UnitCell
 
unitCellOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
unitCellOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
unitCellOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
UnitcellOnly - Variable in class org.jmol.popup.SimplePopup
 
unitCells - Variable in class org.jmol.modelset.ModelCollection
 
unitCellTranslations - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
unitCubePoints - Static variable in class org.jmol.util.BoxInfo
 
unitFactor - Variable in class org.jmol.quantum.QuantumCalculation
 
units - Variable in class org.jmol.modelset.MeasurementData
 
UNITS_PI - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
unitVectors - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
unitVectorX - Variable in class org.jmol.modelsetbio.BioPolymer
 
unitVolumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
unitx - Static variable in class org.jmol.script.Token
 
unitxyz - Static variable in class org.jmol.script.Token
 
unity - Static variable in class org.jmol.script.Token
 
unitz - Static variable in class org.jmol.script.Token
 
UNKNOWN - Static variable in class org.jmol.viewer.SelectionManager
 
UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.g3d.Graphics3D
 
unreportedProperties - Static variable in class org.jmol.viewer.StateManager
 
unscaleToScreen(float, float) - Method in class org.jmol.viewer.TransformManager
 
unscaleToScreen(float, float) - Method in class org.jmol.viewer.Viewer
 
UNSET - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
unsetProperty(String) - Method in class org.jmol.viewer.Viewer
 
unsetUserVariable(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
unsetVariables(Map<String, ScriptVariable>, List<ScriptVariable>) - Method in class org.jmol.script.ScriptFunction
 
unsetVoxelData() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
unsetVoxelData() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
unsupportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
untaint(int, byte) - Method in class org.jmol.modelset.AtomCollection
 
unTaintAtoms(BitSet, byte) - Method in class org.jmol.modelset.AtomCollection
 
untransformedPoint - Variable in class org.jmol.viewer.TransformManager
 
unTransformPoint(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
unTransformPoint(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
untranslated - Variable in exception org.jmol.script.ScriptEvaluator.ScriptException
 
unused - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
unused - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
unused2 - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
unwrapCdata(String) - Static method in class org.jmol.util.XmlUtil
 
update(Graphics) - Method in class org.jmol.applet.AppletWrapper
 
update(Graphics) - Method in class org.jmol.applet.Jmol
 
update(Graphics, String) - Method in class org.jmol.applet.Jmol
 
update(Graphics) - Method in interface org.jmol.applet.WrappedApplet
 
UPDATE_ALL - Static variable in class org.jmol.popup.SimplePopup
 
UPDATE_CONFIG - Static variable in class org.jmol.popup.SimplePopup
 
UPDATE_SHOW - Static variable in class org.jmol.popup.SimplePopup
 
updateAboutSubmenu() - Method in class org.jmol.popup.JmolPopup
 
updateAngleSliders() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
updateAtomXYZ() - Method in class org.jmol.minimize.Minimizer
 
updateButton(AbstractButton, String, String) - Method in class org.jmol.popup.SimplePopup
 
updateCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
updateComponents() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
updateComputedMenus() - Method in interface org.jmol.api.JmolPopupInterface
 
updateComputedMenus() - Method in class org.jmol.popup.JmolPopup
 
updateConfigurationComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateCoordinates(Matrix4f, BitSet) - Method in class org.jmol.shape.Mesh
 
updateElementsComputedMenu(BitSet) - Method in class org.jmol.popup.JmolPopup
 
updateEquation(Ellipsoids.Ellipsoid) - Method in class org.jmol.shapespecial.Ellipsoids
 
updateExisting(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
updateFileMenu() - Method in class org.jmol.popup.JmolPopup
 
updateFileTypeDependentMenus() - Method in class org.jmol.popup.SimplePopup
 
updateForShow() - Method in class org.jmol.popup.JmolPopup
 
updateForShow() - Method in class org.jmol.popup.SimplePopup
 
updateFRAMESbyModelComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateGroup3List(Object, String) - Method in class org.jmol.popup.JmolPopup
 
updateHeteroComputedMenu(Map<String, String>) - Method in class org.jmol.popup.JmolPopup
 
updateInvalidatedVertices(BitSet) - Method in class org.jmol.jvxl.data.MeshData
 
updateLabel(JCheckBox, String, char) - Static method in class org.jmol.console.KeyJCheckBox
 
updateLabels() - Method in class org.jmol.console.JmolConsole
 
updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
updateLanguageSubmenu() - Method in class org.jmol.popup.JmolPopup
 
updateLocations(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
updateMeasurementTableData() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
updateMeshInfo(Shape[], int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
updateMode - Variable in class org.jmol.popup.SimplePopup
 
updateModelSetComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateOffsetsForAlternativeLocations(Atom[], BitSet) - Method in class org.jmol.modelsetbio.Monomer
 
updateParameters() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
updatePDBComputedMenus() - Method in class org.jmol.popup.JmolPopup
 
updatePositionSlider() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
updatePreview(File) - Method in class org.jmol.export.dialog.FilePreview
Update preview
updateScreen() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Update screen informations
updateSelectMenu() - Method in class org.jmol.popup.JmolPopup
 
updateSize(boolean) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
updateSlices() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
updateSurfaceData(String, float[], int, int, char) - Static method in class org.jmol.jvxl.data.JvxlData
 
updateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
updateSurfaceInfo() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
updateSurfaceList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
updateSurfMoComputedMenu(Map<String, Object>) - Method in class org.jmol.popup.JmolPopup
 
updateSYMMETRYComputedMenus() - Method in class org.jmol.popup.JmolPopup
 
updateSYMMETRYSelectComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateSYMMETRYShowComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateTables() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
updateThicknessSlider() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
updateTriangles() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
updateUI() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
updateVars() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
upperNeighborIsHelixOrSheet() - Method in class org.jmol.modelsetbio.ProteinStructure
 
url - Static variable in class org.jmol.script.Token
 
url - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog.PageLoader
 
url - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
 
url - Variable in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog.PageLoader
 
URL_LOCAL - Static variable in class org.jmol.viewer.FileManager
 
urlPrefixes - Static variable in class org.jmol.viewer.FileManager
 
urlPrefixPairs - Static variable in class org.jmol.viewer.FileManager
 
urlTypeIndex(String) - Static method in class org.jmol.viewer.FileManager
 
USE_PALETTE - Static variable in class org.jmol.g3d.Graphics3D
 
useAbsolute - Variable in class org.jmol.quantum.NciCalculation
 
useAltNames - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
useAppletJS - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
usearcball - Static variable in class org.jmol.script.Token
 
useArcBall - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
useArcBall() - Method in class org.jmol.viewer.Viewer
 
useAutoBond - Static variable in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
useClearingThread - Variable in class org.jmol.g3d.Platform3D
 
useCommandThread - Variable in class org.jmol.viewer.Viewer
 
useCommandWatcherThread - Variable in class org.jmol.viewer.ScriptManager
 
useGUI - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
useIndependentCommandThread - Variable in class org.openscience.jmol.app.JmolApp
 
useminimizationthread - Static variable in class org.jmol.script.Token
 
useMinimizationThread - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
useMinimizationThread() - Method in class org.jmol.viewer.Viewer
 
useMolecular - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
usenumberlocalization - Static variable in class org.jmol.script.Token
 
useNumberLocalization - Static variable in class org.jmol.util.TextFormat
 
useNumberLocalization - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
useOriginStepsPoints - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
usePercent - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
usePhongExponent - Static variable in class org.jmol.g3d.Shade3D
 
usePropertyForColorRange - Variable in class org.jmol.jvxl.readers.Parameters
 
user - Static variable in class org.jmol.script.Token
 
USER - Static variable in class org.jmol.util.ColorEncoder
 
userAtomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
usercolorscheme - Static variable in class org.jmol.script.Token
 
userDefinedVanDerWaalRadius - Variable in class org.jmol.modelset.Atom
 
userflags - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
userPropsFile - Variable in class org.openscience.jmol.app.JmolApp
 
userScale - Variable in class org.jmol.util.ColorEncoder
 
userSettableValues - Static variable in class org.jmol.modelset.AtomCollection
 
userVdwMars - Variable in class org.jmol.viewer.DataManager
 
userVdws - Variable in class org.jmol.viewer.DataManager
 
useScriptQueue - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
useTable - Variable in class org.jmol.export._VrmlExporter
 
UseTable - Class in org.jmol.export
 
UseTable(String) - Constructor for class org.jmol.export.UseTable
 
useZoomLarge - Variable in class org.jmol.viewer.TransformManager
 
usingScriptQueue() - Method in class org.jmol.viewer.Viewer
 
Util - Class in org.jmol.minimize
 
Util() - Constructor for class org.jmol.minimize.Util
 

V

v - Variable in class org.jmol.console.JmolConsole.FileChecker
 
v - Variable in class org.jmol.smiles.SmilesSearch
 
V - Variable in class org.jmol.util.Eigen
Array for internal storage of eigenvectors.
v1 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v1 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
v2 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v2 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
v3 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v3 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
vA - Variable in class org.jmol.smiles.SmilesSearch.VTemp
 
vAB - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
vAB - Variable in class org.jmol.modelsetbio.Resolver
 
vAB - Variable in class org.jmol.shape.Mesh
 
vAB - Variable in class org.jmol.shapespecial.Draw
 
vAB - Variable in class org.jmol.shapespecial.Polyhedra
 
vAB - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
vAC - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
vAC - Variable in class org.jmol.modelsetbio.Resolver
 
vAC - Variable in class org.jmol.shape.Mesh
 
vAC - Variable in class org.jmol.shapespecial.Draw
 
vAC - Variable in class org.jmol.shapespecial.Polyhedra
 
vAC - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
val - Static variable in class org.jmol.script.Token
 
valACchrominance - Static variable in class org.jmol.util.Huffman
 
valACluminance - Static variable in class org.jmol.util.Huffman
 
valDCchrominance - Static variable in class org.jmol.util.Huffman
 
valDCluminance - Static variable in class org.jmol.util.Huffman
 
valence - Variable in class org.jmol.modelset.Atom
 
valence - Static variable in class org.jmol.script.Token
 
valence - Variable in class org.jmol.smiles.SmilesAtom
 
validate(boolean) - Method in class org.jmol.bspt.Bspf
 
validate(int, boolean) - Method in class org.jmol.bspt.Bspf
 
VALIDATE - Static variable in class org.jmol.geodesic.Geodesic
 
validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.AlphaMonomer
 
validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
validateAndAllocate(Chain, String, int, int, int) - Static method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
 
validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.PhosphorusMonomer
 
validateBspf(boolean) - Method in class org.jmol.modelset.AtomCollection
 
validateBspf(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
validateFace(IsoSolventReader.Face) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
validatePolyhedronNew(Atom, int, Point3f[]) - Method in class org.jmol.shapespecial.Polyhedra
 
validSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
valign - Variable in class org.jmol.shape.Object2d
 
VALIGN_BOTTOM - Static variable in class org.jmol.shape.Object2d
 
VALIGN_MIDDLE - Static variable in class org.jmol.shape.Object2d
 
VALIGN_TOP - Static variable in class org.jmol.shape.Object2d
 
VALIGN_XY - Static variable in class org.jmol.shape.Object2d
 
VALIGN_XYZ - Static variable in class org.jmol.shape.Object2d
 
vAlignNames - Static variable in class org.jmol.shape.Object2d
 
vAll - Static variable in class org.jmol.script.ScriptVariable
 
value - Variable in class org.jmol.atomdata.RadiusData
 
value - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
value - Variable in class org.jmol.modelset.Measurement
 
value - Variable in class org.jmol.script.Token
 
value - Variable in class org.jmol.util.Int2IntHash.Entry
 
valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
valueCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
valueExtended - Variable in class org.jmol.atomdata.RadiusData
 
valueFor(float, float, int) - Method in interface org.jmol.api.MepCalculationInterface
 
valueFor(float, float, int) - Method in class org.jmol.quantum.MepCalculation
 
valueMappedToBlue - Variable in class org.jmol.jvxl.data.JvxlData
 
valueMappedToBlue - Variable in class org.jmol.jvxl.readers.Parameters
 
valueMappedToRed - Variable in class org.jmol.jvxl.data.JvxlData
 
valueMappedToRed - Variable in class org.jmol.jvxl.readers.Parameters
 
valueMax - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
valueMin - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
valueMin - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
valueOf(String) - Static method in enum org.jmol.atomdata.RadiusData.EnumType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumAnimationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumAxesMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumCallback
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumHBondType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumPalette
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumQuantumShell
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumStereoMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumStructure
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumVdw
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.viewer.FileManager.Encoding
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.viewer.FileManager.EnumFileStatus
Returns the enum constant of this type with the specified name.
valuePeek() - Method in class org.jmol.script.ScriptCompilationTokenParser
 
valueRange - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
values() - Static method in enum org.jmol.atomdata.RadiusData.EnumType
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.jmol.atomdata.RadiusData
 
values() - Static method in enum org.jmol.constant.EnumAnimationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumAxesMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumCallback
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumHBondType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumPalette
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumQuantumShell
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumStereoMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumStructure
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumVdw
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
values - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
values() - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.viewer.FileManager.Encoding
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.viewer.FileManager.EnumFileStatus
Returns an array containing the constants of this enum type, in the order they are declared.
vanderwaals - Static variable in class org.jmol.script.Token
 
vanderwaalsMars - Static variable in class org.jmol.util.Elements
Default table of van der Waals Radii.
var - Variable in class org.jmol.script.ScriptFlowContext
 
var - Static variable in class org.jmol.script.Token
 
varButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
 
varClip(String, String, int) - Static method in class org.jmol.viewer.StateManager
 
variable - Static variable in class org.jmol.script.Token
 
variables - Variable in class org.jmol.script.ScriptFunction
 
variables - Static variable in class org.jmol.script.Token
 
varray - Static variable in class org.jmol.script.Token
 
vaspImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
vaspOutcarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
VaspOutcarReader - Class in org.jmol.adapter.readers.xtal
http://cms.mpi.univie.ac.at/vasp/
VaspOutcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
vB - Variable in class org.jmol.smiles.SmilesSearch.VTemp
 
vBraces - Variable in class org.jmol.script.ScriptCompiler
 
vButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
vCompnds - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
vConnect - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
vContours - Variable in class org.jmol.jvxl.data.JvxlData
 
vd - Variable in class org.jmol.quantum.QuantumCalculation
 
vData - Variable in class org.jmol.shapespecial.Draw
 
vdc - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
vdc - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
vDist - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
vdw1 - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
vdwPercentSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
VdwPROBE - Static variable in class org.jmol.viewer.JmolConstants
 
vdws - Variable in class org.jmol.util.ContactPair
 
vdwType - Variable in class org.jmol.atomdata.RadiusData
 
vdwVolume - Variable in class org.jmol.util.ContactPair
 
vector() - Method in class org.jmol.script.ScriptEvaluator
 
vector - Static variable in class org.jmol.script.Token
 
vector - Variable in class org.jmol.shapespecial.Dipole
 
VECTOR - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
String for prefix/resource identifier for the vector area.
vector12ths - Variable in class org.jmol.symmetry.HallInfo
 
vectorAB - Variable in class org.jmol.g3d.Graphics3D
 
vectorAC - Variable in class org.jmol.g3d.Graphics3D
 
vectorAngleRadians(Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
vectorCode - Variable in class org.jmol.symmetry.HallInfo
 
vectorNormal - Variable in class org.jmol.g3d.Graphics3D
 
vectorProjection - Variable in class org.jmol.modelsetbio.ProteinStructure
 
vectors - Variable in class org.jmol.jvxl.readers.MapFileReader
 
Vectors - Class in org.jmol.shapespecial
 
Vectors() - Constructor for class org.jmol.shapespecial.Vectors
 
vectorscale - Static variable in class org.jmol.script.Token
 
vectorScale - Variable in class org.jmol.shapespecial.VectorsRenderer
 
vectorScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
vectorShift12ths - Variable in class org.jmol.symmetry.Translation
 
VectorsRenderer - Class in org.jmol.shapespecial
 
VectorsRenderer() - Constructor for class org.jmol.shapespecial.VectorsRenderer
 
vectorT - Variable in class org.jmol.shape.FontLineShapeRenderer
 
vectorT - Variable in class org.jmol.viewer.TransformManager
 
vectorT2 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
vectorT2 - Variable in class org.jmol.viewer.TransformManager
 
vectorT3 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
vectorTemp - Variable in class org.jmol.viewer.TransformManager
 
vectorX - Variable in class org.jmol.adapter.smarter.Atom
 
vectorY - Variable in class org.jmol.adapter.smarter.Atom
 
vectorZ - Variable in class org.jmol.adapter.smarter.Atom
 
vEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
VERIFY - Static variable in class org.jmol.g3d.Triangle3D
 
verNumber - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
version - Variable in class org.jmol.jvxl.data.JvxlData
 
version - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
version - Static variable in class org.jmol.viewer.JmolConstants
 
VERSION - Static variable in class org.openscience.jvxl.Jvxl
 
VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
vertexBase - Variable in class org.jmol.jvxl.readers.PmeshReader
 
vertexColixes - Variable in class org.jmol.util.MeshSurface
 
vertexColorMap - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexColorMap - Variable in class org.jmol.shape.Mesh
 
vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexCount - Variable in class org.jmol.shape.MeshRenderer
 
vertexCount - Variable in class org.jmol.util.MeshSurface
 
vertexCount0 - Variable in class org.jmol.util.MeshSurface
 
vertexCounts - Static variable in class org.jmol.geodesic.Geodesic
 
vertexDataOnly - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexDataOnly - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
VertexDataServer - Interface in org.jmol.jvxl.api
 
vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
 
vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
vertexMap - Variable in class org.jmol.jvxl.readers.PmeshReader
 
vertexNext - Static variable in class org.jmol.geodesic.Geodesic
 
vertexPoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
vertexSets - Variable in class org.jmol.util.MeshSurface
 
vertexSource - Variable in class org.jmol.jvxl.readers.Parameters
 
vertexSource - Variable in class org.jmol.util.MeshSurface
 
vertexTest - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
vertexValues - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
vertexValues - Variable in class org.jmol.util.MeshSurface
 
vertexValues - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
vertexVectors - Static variable in class org.jmol.g3d.Normix3D
 
vertexVectors - Static variable in class org.jmol.geodesic.Geodesic
 
vertices - Static variable in class org.jmol.script.Token
 
vertices - Variable in class org.jmol.shape.MeshRenderer
 
vertices - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
vertices - Variable in class org.jmol.symmetry.UnitCell
 
vertices - Variable in class org.jmol.util.MeshSurface
 
verticesT - Variable in class org.jmol.shape.UccageRenderer
 
verticesTransformed - Variable in class org.jmol.shapespecial.DotsRenderer
 
vF - Static variable in class org.jmol.script.ScriptVariable
 
vFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
vFunctionStack - Variable in class org.jmol.script.ScriptCompiler
 
vibEnergy - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
vibFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
vibFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
vibOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
vibration() - Method in class org.jmol.script.ScriptEvaluator
 
vibration - Static variable in class org.jmol.script.Token
 
VIBRATION_VECTOR_FLAG - Static variable in class org.jmol.modelset.Atom
 
vibrationAmplitude - Variable in class org.jmol.viewer.TransformManager
 
vibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
vibrationOn - Variable in class org.jmol.viewer.TransformManager
 
VibrationOnly - Variable in class org.jmol.popup.SimplePopup
 
vibrationperiod - Static variable in class org.jmol.script.Token
 
vibrationPeriod - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
vibrationPeriod - Variable in class org.jmol.viewer.TransformManager
 
vibrationPeriodMs - Variable in class org.jmol.viewer.TransformManager
 
vibrationRadians - Variable in class org.jmol.viewer.TransformManager
 
vibrationscale - Static variable in class org.jmol.script.Token
 
vibrationScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
vibrationScale - Variable in class org.jmol.viewer.TransformManager
 
vibrationSteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
vibrationSteps - Variable in class org.jmol.modelset.ModelCollection
 
vibrationThread - Variable in class org.jmol.viewer.TransformManager
 
vibrationVectors - Variable in class org.jmol.modelset.AtomCollection
 
vibx - Static variable in class org.jmol.script.Token
 
vibxyz - Static variable in class org.jmol.script.Token
 
viby - Static variable in class org.jmol.script.Token
 
vibz - Static variable in class org.jmol.script.Token
 
viewCenterButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
viewer - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
viewer - Variable in class org.jmol.applet.Jmol
 
viewer - Variable in class org.jmol.awt.Mouse
 
viewer - Variable in class org.jmol.console.JmolConsole
 
viewer - Variable in class org.jmol.console.ScriptEditor
 
viewer - Variable in class org.jmol.export.___Exporter
 
viewer - Variable in class org.jmol.export.dialog.Dialog
 
viewer - Variable in class org.jmol.export.dialog.FilePreview.FPPanel
 
viewer - Variable in class org.jmol.export.image.ImageCreator
 
viewer - Variable in class org.jmol.export.JmolFileDropper
 
viewer - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
viewer - Variable in class org.jmol.minimize.Minimizer
 
viewer - Variable in class org.jmol.modelkit.ModelKit
 
viewer - Variable in class org.jmol.modelset.AtomCollection
 
viewer - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
viewer - Variable in class org.jmol.modelset.Measurement
 
viewer - Variable in class org.jmol.modelset.MeasurementData
 
viewer - Variable in class org.jmol.modelset.ModelLoader
 
viewer - Variable in class org.jmol.popup.SimplePopup
 
viewer - Variable in class org.jmol.script.ParallelProcessor
 
viewer - Variable in class org.jmol.script.ScriptCompilationTokenParser
 
viewer - Variable in class org.jmol.script.ScriptEvaluator
 
viewer - Variable in class org.jmol.script.ScriptMathProcessor
 
viewer - Variable in class org.jmol.shape.Object2d
 
viewer - Variable in class org.jmol.shape.Shape
 
viewer - Variable in class org.jmol.shape.ShapeRenderer
 
viewer - Variable in class org.jmol.viewer.ActionManager
 
viewer - Variable in class org.jmol.viewer.AnimationManager
 
viewer - Variable in class org.jmol.viewer.ColorManager
 
viewer - Variable in class org.jmol.viewer.DataManager
 
viewer - Variable in class org.jmol.viewer.FileManager
 
viewer - Variable in class org.jmol.viewer.ModelManager
 
viewer - Variable in class org.jmol.viewer.RepaintManager
 
viewer - Variable in class org.jmol.viewer.ScriptManager
 
viewer - Variable in class org.jmol.viewer.SelectionManager
 
viewer - Variable in class org.jmol.viewer.ShapeManager
 
viewer - Variable in class org.jmol.viewer.StateManager
 
viewer - Variable in class org.jmol.viewer.StatusManager
 
viewer - Variable in class org.jmol.viewer.TransformManager
 
Viewer - Class in org.jmol.viewer
 
Viewer(Object, JmolAdapter, String) - Constructor for class org.jmol.viewer.Viewer
 
viewer - Variable in class org.openscience.jmol.app.JmolApp
 
viewer - Variable in class org.openscience.jmol.app.JmolData
 
viewer - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
viewer - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
viewer - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
viewer - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
viewer - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
viewer - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
viewer - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
viewer - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
viewer - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
viewer - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
viewer - Variable in class org.openscience.jmol.app.webexport.Test
 
viewer - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
viewerFrame - Variable in class org.jmol.console.JmolConsole
 
viewMeasurementTableAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
viewpoint - Variable in class org.jmol.export.__CartesianExporter
 
vInputCoords - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
VISIBILITY_CLIPPED - Static variable in class org.jmol.g3d.Line3D
 
VISIBILITY_OFFSCREEN - Static variable in class org.jmol.g3d.Line3D
 
VISIBILITY_UNCLIPPED - Static variable in class org.jmol.g3d.Line3D
 
visibilityFlags - Variable in class org.jmol.shape.Mesh
 
visibilityFlags - Variable in class org.jmol.shapespecial.Dipole
 
visibilityFlags - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
visible - Static variable in class org.jmol.script.Token
 
visible - Variable in class org.jmol.shape.Mesh
 
visible - Variable in class org.jmol.shape.Object2d
 
visible - Variable in class org.jmol.shapespecial.Dipole
 
visible - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
visible - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
visualrange - Static variable in class org.jmol.script.Token
 
visualRange - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
visualRange - Variable in class org.jmol.viewer.TransformManager
 
VK_ALT - Static variable in class org.jmol.api.Event
 
VK_CONTROL - Static variable in class org.jmol.api.Event
 
VK_DOWN - Static variable in class org.jmol.api.Event
 
VK_LEFT - Static variable in class org.jmol.api.Event
 
VK_PERIOD - Static variable in class org.jmol.api.Event
 
VK_RIGHT - Static variable in class org.jmol.api.Event
 
VK_SHIFT - Static variable in class org.jmol.api.Event
 
VK_SPACE - Static variable in class org.jmol.api.Event
 
VK_UP - Static variable in class org.jmol.api.Event
 
vMax - Variable in class org.jmol.jvxl.readers.KinemageReader
 
vMin - Variable in class org.jmol.jvxl.readers.KinemageReader
 
vNorm - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
vNorm - Variable in class org.jmol.modelsetbio.Resolver
 
vNorm1 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
 
vNorm2 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
 
vNorm3 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
 
volume - Variable in class org.jmol.quantum.QuantumCalculation
 
volume - Static variable in class org.jmol.script.Token
 
volume - Variable in class org.jmol.util.ContactPair
 
volume - Variable in class org.jmol.util.SimpleUnitCell
 
volumeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
volumeData - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
VolumeData - Class in org.jmol.jvxl.data
 
VolumeData() - Constructor for class org.jmol.jvxl.data.VolumeData
 
volumeData - Variable in class org.jmol.jvxl.readers.Parameters
 
volumeData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
volumeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
volumeData - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
volumeData - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
VolumeDataInterface - Interface in org.jmol.api
 
VolumeDataReader - Class in org.jmol.jvxl.readers
 
VolumeDataReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.VolumeDataReader
 
VolumeFileReader - Class in org.jmol.jvxl.readers
 
VolumeFileReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.VolumeFileReader
 
volumeRender(boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
volumeRender(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
volumeRender(boolean) - Method in class org.jmol.export.Export3D
 
volumeRender(int, int, int, int) - Method in class org.jmol.export.Export3D
 
volumeRender(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
 
volumeRender - Variable in class org.jmol.shape.MeshRenderer
 
volumeRenderPointSize - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
volumetricMatrix - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricOrigin - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricOrigin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricVectors - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelCounts - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
voxelData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
voxelData - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
voxelData - Variable in class org.jmol.quantum.QuantumCalculation
 
VoxelDataCreator - Class in org.openscience.jvxl.simplewriter
 
VoxelDataCreator(VolumeData) - Constructor for class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
voxelDataTemp - Variable in class org.jmol.quantum.MOCalculation
 
voxelIsInTrough(float, float, float, float, float) - Static method in class org.jmol.jvxl.readers.IsoSolventReader
 
voxelMap - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelPtToXYZ(int, int, int, Point3f) - Method in interface org.jmol.api.VolumeDataInterface
 
voxelPtToXYZ(int, int, int, Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
voxelSource - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
voxelVolume - Variable in class org.jmol.jvxl.data.JvxlData
 
voxelVolume - Variable in class org.jmol.jvxl.data.VolumeData
 
vProcess - Variable in class org.jmol.script.ScriptEvaluator
 
vpt0 - Variable in class org.jmol.shapespecial.DrawRenderer
 
vpt1 - Variable in class org.jmol.shapespecial.DrawRenderer
 
vpt2 - Variable in class org.jmol.shapespecial.DrawRenderer
 
vPush - Variable in class org.jmol.script.ScriptCompiler
 
vRef - Static variable in class org.jmol.modelset.AtomCollection
 
vReturn - Variable in class org.jmol.smiles.SmilesSearch
 
VsampFactor - Variable in class org.jmol.util.JpegInfo
 
vStereo - Variable in class org.jmol.modelset.ModelLoader
 
vSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
vT - Static variable in class org.jmol.script.ScriptVariable
 
vTemp - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
vTemp - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
vTemp - Variable in class org.jmol.modelset.ModelSet
 
vTemp - Variable in class org.jmol.shape.Mesh
 
vTemp - Variable in class org.jmol.shapespecial.DrawRenderer
 
vTemp - Variable in class org.jmol.smiles.SmilesGenerator
 
vTemp - Variable in class org.jmol.smiles.SmilesSearch.VTemp
 
vTemp - Variable in class org.jmol.symmetry.PointGroup
 
vTemp - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
vTemp1 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
 
vTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
vTemp2 - Variable in class org.jmol.shapespecial.DrawRenderer
 
vTemp2 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
 
vTemp3 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
vX - Variable in class org.jmol.shapesurface.Contact
 
vY - Variable in class org.jmol.shapesurface.Contact
 
vZ - Variable in class org.jmol.shapesurface.Contact
 

W

w - Static variable in class org.jmol.script.Token
 
waitForClientRelease() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
waitForDisplay(Object, Object) - Method in interface org.jmol.api.ApiPlatform
can be ignored (return false) if platform cannot save images
waitForDisplay(Object, Object) - Static method in class org.jmol.awt.Image
 
waitForDisplay(Object, Object) - Method in class org.jmol.awt.Platform
 
waitformoveto - Static variable in class org.jmol.script.Token
 
waitForMoveTo - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
waitForMoveTo() - Method in class org.jmol.viewer.Viewer
 
waitForQueue() - Method in class org.jmol.viewer.ScriptManager
 
walkDOMTree(JSObject) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
warn(String) - Method in class org.jmol.util.DefaultLogger
 
warn(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
warn(String) - Static method in class org.jmol.util.Logger
Writes a log at WARN level.
warn(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at WARN level with detail on exception.
warn(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at WARN level.
warn(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at WARN level with detail on exception.
warning(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
warning(int, String, String) - Method in class org.jmol.script.ScriptEvaluator
 
wasClicked(int, int) - Method in class org.jmol.shape.Frank
 
wasClicked(int, int) - Method in class org.jmol.shape.Shape
 
wasCubic - Variable in class org.jmol.jvxl.data.JvxlData
 
wasInMotion - Variable in class org.jmol.viewer.Viewer
 
wasJvxl - Variable in class org.jmol.jvxl.data.JvxlData
 
wasPerspectiveDepth - Variable in class org.jmol.export._TachyonExporter
 
wasSpinOn - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
 
wasSyntaxCheck - Variable in class org.jmol.script.ScriptMathProcessor
 
wasUnQuoted - Variable in class org.jmol.util.CifDataReader
 
wasX - Variable in class org.jmol.script.ScriptMathProcessor
 
WB - Static variable in class org.jmol.util.ColorEncoder
 
WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
webExport - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
WebExport - Class in org.openscience.jmol.app.webexport
 
WebExport(JmolViewer, HistoryFile) - Constructor for class org.openscience.jmol.app.webexport.WebExport
 
webExport - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
webFrame - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
webmoFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
WebMOReader - Class in org.jmol.adapter.readers.quantum
A molecular orbital reader for WebMO files.
WebMOReader() - Constructor for class org.jmol.adapter.readers.quantum.WebMOReader
 
webPageTitle - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
webPanel - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
WebPanel - Class in org.openscience.jmol.app.webexport
 
WebPanel(JmolViewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.WebPanel
 
WebPanel.InstanceCellRenderer - Class in org.openscience.jmol.app.webexport
 
WebPanel.InstanceCellRenderer() - Constructor for class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
 
webPanels - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
webPanels - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
whatsnewAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
WhatsNewDialog - Class in org.openscience.jmol.app.jmolpanel
 
WhatsNewDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
 
WhatsNewDialog.PageLoader - Class in org.openscience.jmol.app.jmolpanel
temporary class that loads synchronously (although later than the request so that a cursor change can be done).
WhatsNewDialog.PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.jmolpanel.WhatsNewDialog.PageLoader
 
WHEEL - Static variable in class org.jmol.viewer.binding.Binding
 
WHEELED - Static variable in class org.jmol.viewer.binding.Binding
 
whichOrigin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
whichWidgets - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
whilecmd - Static variable in class org.jmol.script.Token
 
WHITE - Static variable in class org.jmol.g3d.Graphics3D
 
widgetCheckboxes - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
widgetList - Variable in class org.openscience.jmol.app.webexport.Widgets
 
Widgets - Class in org.openscience.jmol.app.webexport
 
Widgets() - Constructor for class org.openscience.jmol.app.webexport.Widgets
 
Widgets.AnimationWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.AnimationWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
 
Widgets.BackgroundColorWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.BackgroundColorWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
 
Widgets.ConsoleWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.ConsoleWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
 
Widgets.DownLoadWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.DownLoadWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
 
Widgets.SpinOnWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.SpinOnWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
 
Widgets.StereoViewWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.StereoViewWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
 
Widgets.Widget - Class in org.openscience.jmol.app.webexport
 
Widgets.Widget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.Widget
 
width - Variable in class org.jmol.export.Export3D
 
width - Variable in class org.jmol.export.image.GifEncoder
 
Width - Variable in class org.jmol.export.image.GifEncoder
 
width - Variable in class org.jmol.export.image.ImageEncoder
 
width - Variable in class org.jmol.export.image.PngEncoder
 
width - Variable in class org.jmol.g3d.Graphics3D
 
width - Variable in class org.jmol.g3d.Sphere3D
 
width - Variable in class org.jmol.g3d.Text3D
 
width - Variable in class org.jmol.modelset.LabelToken
 
width - Static variable in class org.jmol.script.Token
 
width - Variable in class org.jmol.shape.Mesh
 
width - Variable in class org.jmol.shape.MeshRenderer
 
width - Variable in class org.jmol.shape.SticksRenderer
 
width - Variable in class org.jmol.shapespecial.Draw
 
width - Variable in class org.jmol.util.Dimension
 
width - Variable in class org.jmol.util.Rectangle
 
width - Variable in class org.jmol.viewer.TransformManager
 
width - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
widthOffscreen - Variable in class org.jmol.g3d.Platform3D
 
widths - Variable in class org.jmol.shape.Text
 
widthUnitVector - Variable in class org.jmol.modelsetbio.Sheet
 
Wien2kReader - Class in org.jmol.adapter.readers.xtal
A reader for Wein2k DFT files.
Wien2kReader() - Constructor for class org.jmol.adapter.readers.xtal.Wien2kReader
 
wildID - Variable in class org.jmol.shapespecial.Dipoles
 
windowActivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowcentered - Static variable in class org.jmol.script.Token
 
windowCentered - Variable in class org.jmol.viewer.TransformManager
 
windowCenteredFlag - Variable in class org.jmol.viewer.StateManager.Orientation
 
windowClosed(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowClosing(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowClosing(WindowEvent) - Method in class org.openscience.chimetojmol.ChimeToJmol.ApplicationCloser
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementListWindowListener
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
Closes the dialog when window closing event occurs.
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowDeactivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowDeiconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowHeight - Variable in class org.jmol.g3d.Graphics3D
 
windowHeight - Variable in class org.jmol.g3d.Platform3D
 
windowHeight - Variable in class org.jmol.shape.Object2d
 
windowIconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowName - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
windowOpened(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowSize - Variable in class org.jmol.g3d.Platform3D
 
windowStateChanged(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowWidth - Variable in class org.jmol.g3d.Graphics3D
 
windowWidth - Variable in class org.jmol.g3d.Platform3D
 
windowWidth - Variable in class org.jmol.shape.Object2d
 
wing - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wing0 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wing1 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wingHermites - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wingT - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wingVectors - Variable in class org.jmol.modelset.Polymer
 
wingVectors - Variable in class org.jmol.shapebio.BioShape
 
wingVectors - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wireframe() - Method in class org.jmol.script.ScriptEvaluator
 
wireframe - Static variable in class org.jmol.script.Token
 
Wireframe - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
Wireframe - Static variable in class org.openscience.jmol.app.webexport.Orbitals
 
wireframeOnly - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
wireframerotation - Static variable in class org.jmol.script.Token
 
wireframeRotation - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
within - Static variable in class org.jmol.script.Token
 
withinDistance2 - Variable in class org.jmol.shapesurface.Isosurface
 
withinPoints - Variable in class org.jmol.shapesurface.Isosurface
 
words - Variable in class org.jmol.popup.PopupResource
 
working - Static variable in class org.jmol.g3d.Text3D
 
wrapCdata(Object) - Static method in class org.jmol.util.XmlUtil
wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination
wrappedApplet - Variable in class org.jmol.applet.AppletWrapper
 
WrappedApplet - Interface in org.jmol.applet
 
wrappedAppletClassName - Variable in class org.jmol.applet.AppletWrapper
 
wrappedAppletClassName - Variable in class org.jmol.applet.WrappedAppletLoader
 
WrappedAppletLoader - Class in org.jmol.applet
 
WrappedAppletLoader(AppletWrapper, String) - Constructor for class org.jmol.applet.WrappedAppletLoader
 
write(Image, OutputStream) - Static method in class org.jmol.export.image.GifEncoder
 
write(Image, int, OutputStream) - Static method in class org.jmol.export.image.PngEncoder
 
write(Image, int, OutputStream, int) - Static method in class org.jmol.export.image.PngEncoder
 
write(Image, OutputStream) - Static method in class org.jmol.export.image.PpmEncoder
 
write(Token[]) - Method in class org.jmol.script.ScriptEvaluator
 
write - Static variable in class org.jmol.script.Token
 
write(byte[], OutputStream) - Static method in class org.jmol.util.Base64
 
write(ApiPlatform, Object, int, OutputStream, String) - Static method in class org.jmol.util.JpegEncoder
 
writeAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
writeActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
writeArray(byte[], BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeByte(int, int) - Method in class org.jmol.export.image.PngEncoder
Write a single byte into the pngBytes array at a given position.
writeBytes(byte[], int) - Method in class org.jmol.export.image.PngEncoder
Write an array of bytes into the pngBytes array.
writeBytes(byte[], int, int) - Method in class org.jmol.export.image.PngEncoder
Write an array of bytes into the pngBytes array, specifying number of bytes to write.
writeBytes(byte[]) - Method in class org.jmol.util.BinaryDocument
 
writeBytes(byte[], int, int) - Method in class org.jmol.util.BinaryDocument
 
WriteCompressedData(BufferedOutputStream, JpegInfo, DCT, Huffman) - Static method in class org.jmol.util.JpegEncoder
 
writeCurrentFile(OutputStream) - Method in class org.jmol.viewer.Viewer
 
WriteDHTHeader(int[], int[], BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeEnd() - Method in class org.jmol.export.image.PngEncoder
Write a PNG "IEND" chunk into the pngBytes array.
WriteEOI(BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeFile(String, String) - Static method in class org.openscience.jvxl.Jvxl
 
writeFile(String, String) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
writeFileZipped(String[], byte[], int) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
writeHeader() - Method in class org.jmol.export.image.PngEncoder
Write a PNG "IHDR" chunk into the pngBytes array.
WriteHeaders(BufferedOutputStream, JpegInfo, DCT) - Static method in class org.jmol.util.JpegEncoder
 
writeImageData() - Method in class org.jmol.export.image.PngEncoder
Write the image data into the pngBytes array.
writeInt(int) - Method in class org.jmol.util.BinaryDocument
 
writeInt2(int, int) - Method in class org.jmol.export.image.PngEncoder
Write a two-byte integer into the pngBytes array at a given position.
writeInt4(int, int) - Method in class org.jmol.export.image.PngEncoder
Write a four-byte integer into the pngBytes array at a given position.
writeLong(long) - Method in class org.jmol.util.BinaryDocument
 
writeMacros() - Method in class org.jmol.export._PovrayExporter
 
writeMacros2() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosAtom() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosBond() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosFinish() - Method in class org.jmol.export._PovrayExporter
 
WriteMarker(byte[], BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeShort(short) - Method in class org.jmol.util.BinaryDocument
 
writeString(OutputStream, String) - Static method in class org.jmol.export.image.GifEncoder
 
writeString(String, int) - Method in class org.jmol.export.image.PngEncoder
Write a string into the pngBytes array at a given position.
writeString(OutputStream, String) - Static method in class org.jmol.export.image.PpmEncoder
 
writeString(String, byte, BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeTag(int, byte, BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeTextFile(String, String) - Method in class org.jmol.api.JmolViewer
 
writeTextFile(String, String) - Method in class org.jmol.viewer.Viewer
 
writeTransparentColor(int) - Method in class org.jmol.export.image.PngEncoder
Write a PNG "tRNS" chunk into the pngBytes array.
writeZipFile(String, List<Object>, boolean, String) - Static method in class org.jmol.viewer.FileManager
generic method to create a zip file based on http://www.exampledepot.com/egs/java.util.zip/CreateZip.html

X

x - Variable in class org.jmol.g3d.Sphere3D
 
X - Variable in class org.jmol.quantum.QuantumCalculation
 
x - Variable in class org.jmol.quantum.SlaterData
 
x - Static variable in class org.jmol.script.Token
 
x - Variable in class org.jmol.shape.Frank
 
x - Variable in class org.jmol.shape.SticksRenderer
 
x - Variable in class org.jmol.util.Rectangle
 
x - Variable in class org.jmol.viewer.ActionManager.MotionPoint
 
x - Variable in class org.jmol.viewer.ActionManager.Mouse
 
x1t - Variable in class org.jmol.g3d.Line3D
 
X2 - Variable in class org.jmol.quantum.QuantumCalculation
 
x2t - Variable in class org.jmol.g3d.Line3D
 
xA - Variable in class org.jmol.g3d.Cylinder3D
 
xA - Variable in class org.jmol.shape.SticksRenderer
 
xAf - Variable in class org.jmol.g3d.Cylinder3D
 
xAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
xAxis1 - Variable in class org.jmol.shape.SticksRenderer
 
xAxis2 - Variable in class org.jmol.shape.SticksRenderer
 
xB - Variable in class org.jmol.shape.SticksRenderer
 
xBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
xCenter - Variable in class org.jmol.g3d.Circle3D
 
xEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
xGT - Static variable in class org.jmol.g3d.Graphics3D
 
xLast - Variable in class org.jmol.g3d.Graphics3D
 
xlateAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
xLight - Static variable in class org.jmol.g3d.Shade3D
 
xLightsource - Static variable in class org.jmol.g3d.Shade3D
 
xLT - Static variable in class org.jmol.g3d.Graphics3D
 
xMax - Variable in class org.jmol.g3d.Cylinder3D
 
xMax - Variable in class org.jmol.quantum.QuantumCalculation
 
xMin - Variable in class org.jmol.g3d.Cylinder3D
 
xMin - Variable in class org.jmol.quantum.QuantumCalculation
 
XmlArgusReader - Class in org.jmol.adapter.readers.xml
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
XmlArgusReader() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
 
XmlArgusReader.ArgusHandler - Class in org.jmol.adapter.readers.xml
 
XmlArgusReader.ArgusHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader.ArgusHandler
 
XmlArgusReader.ArgusHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader.ArgusHandler
 
XmlChem3dReader - Class in org.jmol.adapter.readers.xml
An chem3d c3xml reader
XmlChem3dReader() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
 
XmlChem3dReader.Chem3dHandler - Class in org.jmol.adapter.readers.xml
 
XmlChem3dReader.Chem3dHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader.Chem3dHandler
 
XmlChem3dReader.Chem3dHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader.Chem3dHandler
 
XmlCmlReader - Class in org.jmol.adapter.readers.xml
A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.
XmlCmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
 
XmlCmlReader.CmlHandler - Class in org.jmol.adapter.readers.xml
 
XmlCmlReader.CmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader.CmlHandler
 
XmlCmlReader.CmlHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader.CmlHandler
 
xmlContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
xmlData - Variable in class org.jmol.jvxl.data.VolumeData
 
XmlMolproReader - Class in org.jmol.adapter.readers.xml
A Molpro 2005 reader
XmlMolproReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
 
XmlMolproReader.MolproHandler - Class in org.jmol.adapter.readers.xml
 
XmlMolproReader.MolproHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader.MolproHandler
 
XmlMolproReader.MolproHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader.MolproHandler
 
XmlOdysseyReader - Class in org.jmol.adapter.readers.xml
An Odyssey xodydata reader
XmlOdysseyReader() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
XmlOdysseyReader.OdysseyHandler - Class in org.jmol.adapter.readers.xml
 
XmlOdysseyReader.OdysseyHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader.OdysseyHandler
 
XmlOdysseyReader.OdysseyHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader.OdysseyHandler
 
xmlProperties - Variable in class org.jmol.shape.Mesh
 
xmlProperties - Variable in class org.jmol.shape.Shape
 
XmlQEReader - Class in org.jmol.adapter.readers.xml
QuantumEspresso XML reader
XmlQEReader() - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader
 
XmlQEReader.Handler - Class in org.jmol.adapter.readers.xml
 
XmlQEReader.Handler() - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader.Handler
 
XmlQEReader.Handler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader.Handler
 
XmlReader - Class in org.jmol.adapter.readers.xml
A generic XML reader template -- by itself, does nothing.
XmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlReader
 
XmlReader - Class in org.jmol.util
 
XmlReader(BufferedReader) - Constructor for class org.jmol.util.XmlReader
 
XmlReader.DummyResolver - Class in org.jmol.adapter.readers.xml
 
XmlReader.DummyResolver() - Constructor for class org.jmol.adapter.readers.xml.XmlReader.DummyResolver
 
XmlReader.JmolXmlHandler - Class in org.jmol.adapter.readers.xml
 
XmlReader.JmolXmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
XmlReader.JmolXmlHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
XmlUtil - Class in org.jmol.util
 
XmlUtil() - Constructor for class org.jmol.util.XmlUtil
 
XmlVaspReader - Class in org.jmol.adapter.readers.xml
Vasp vasprun.xml reader
XmlVaspReader() - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader
 
XmlVaspReader.VaspHandler - Class in org.jmol.adapter.readers.xml
 
XmlVaspReader.VaspHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader.VaspHandler
 
XmlVaspReader.VaspHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader.VaspHandler
 
XmlXsdReader - Class in org.jmol.adapter.readers.xml
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09
XmlXsdReader() - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader
 
XmlXsdReader.XsdHandler - Class in org.jmol.adapter.readers.xml
 
XmlXsdReader.XsdHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader.XsdHandler
 
XmlXsdReader.XsdHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader.XsdHandler
 
xNav - Variable in class org.jmol.viewer.StateManager.Orientation
 
xNav - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
xNavTransDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
xNavTransStart - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
xor(FastBitSet) - Method in class org.jmol.util.FastBitSet
 
XplorReader - Class in org.jmol.jvxl.readers
 
XplorReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.XplorReader
 
xPt - Variable in class org.jmol.script.ScriptMathProcessor
 
xr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
xRaster - Variable in class org.jmol.g3d.Cylinder3D
 
xsdImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
xStack - Variable in class org.jmol.script.ScriptMathProcessor
 
xTip - Variable in class org.jmol.g3d.Cylinder3D
 
xTrans - Variable in class org.jmol.viewer.StateManager.Orientation
 
xTrans - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
xTransDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
xTranslationFraction - Variable in class org.jmol.viewer.TransformManager
 
xTransStart - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
xVdwClash - Variable in class org.jmol.util.ContactPair
 
xWhenPressed - Variable in class org.jmol.awt.Mouse
 
xy - Variable in class org.jmol.shape.Hover
 
XY_ZTOP - Static variable in class org.jmol.viewer.JmolConstants
 
xyCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
xyPlanePts - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
xypParameter(int) - Method in class org.jmol.script.ScriptEvaluator
 
xyRange - Variable in class org.jmol.viewer.ActionManager
 
xyTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
xyz - Static variable in class org.jmol.script.Token
 
xyz - Variable in class org.jmol.shape.Object2d
 
xyz - Variable in class org.jmol.symmetry.SymmetryOperation
 
xyz_coordinates - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
xyzFraction(float, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
xyzList - Variable in class org.jmol.symmetry.SpaceGroup
 
xyzMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
xyzMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
xyzOriginal - Variable in class org.jmol.symmetry.SymmetryOperation
 
XyzReader - Class in org.jmol.adapter.readers.molxyz
Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c
XyzReader() - Constructor for class org.jmol.adapter.readers.molxyz.XyzReader
 
xyzToVoxelPt(float, float, float, Point3i) - Method in interface org.jmol.api.VolumeDataInterface
 
xyzToVoxelPt(float, float, float, Point3i) - Method in class org.jmol.jvxl.data.VolumeData
 

Y

y - Variable in class org.jmol.g3d.Sphere3D
 
Y - Variable in class org.jmol.quantum.QuantumCalculation
 
y - Variable in class org.jmol.quantum.SlaterData
 
y - Static variable in class org.jmol.script.Token
 
y - Variable in class org.jmol.shape.Frank
 
y - Variable in class org.jmol.shape.SticksRenderer
 
y - Variable in class org.jmol.util.Rectangle
 
y - Variable in class org.jmol.viewer.ActionManager.MotionPoint
 
y - Variable in class org.jmol.viewer.ActionManager.Mouse
 
y1t - Variable in class org.jmol.g3d.Line3D
 
Y2 - Variable in class org.jmol.quantum.QuantumCalculation
 
y2t - Variable in class org.jmol.g3d.Line3D
 
yA - Variable in class org.jmol.g3d.Cylinder3D
 
yA - Variable in class org.jmol.shape.SticksRenderer
 
yAf - Variable in class org.jmol.g3d.Cylinder3D
 
yAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
yAxis1 - Variable in class org.jmol.shape.SticksRenderer
 
yAxis2 - Variable in class org.jmol.shape.SticksRenderer
 
yB - Variable in class org.jmol.shape.SticksRenderer
 
yBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
yCenter - Variable in class org.jmol.g3d.Circle3D
 
YELLOW - Static variable in class org.jmol.g3d.Graphics3D
 
yEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
yGT - Static variable in class org.jmol.g3d.Graphics3D
 
yLast - Variable in class org.jmol.g3d.Graphics3D
 
yLight - Static variable in class org.jmol.g3d.Shade3D
 
yLightsource - Static variable in class org.jmol.g3d.Shade3D
 
yLT - Static variable in class org.jmol.g3d.Graphics3D
 
yMax - Variable in class org.jmol.g3d.Cylinder3D
 
yMax - Variable in class org.jmol.quantum.QuantumCalculation
 
yMin - Variable in class org.jmol.g3d.Cylinder3D
 
yMin - Variable in class org.jmol.quantum.QuantumCalculation
 
yNav - Variable in class org.jmol.viewer.StateManager.Orientation
 
yNav - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
yNavTransDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
yNavTransStart - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
yRaster - Variable in class org.jmol.g3d.Cylinder3D
 
yTip - Variable in class org.jmol.g3d.Cylinder3D
 
yTrans - Variable in class org.jmol.viewer.StateManager.Orientation
 
yTrans - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
yTransDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
yTranslationFraction - Variable in class org.jmol.viewer.TransformManager
 
yTransStart - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
yWhenPressed - Variable in class org.jmol.awt.Mouse
 
yzCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzCount - Variable in class org.jmol.jvxl.data.VolumeData
 
yzCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
yzCount - Variable in class org.jmol.quantum.NciCalculation
 
yzCount - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
yzPlanePts - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzPlanes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
yzPlanesRaw - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
yzPlanesRaw - Variable in class org.jmol.quantum.NciCalculation
 
yzPlanesRho - Variable in class org.jmol.quantum.NciCalculation
 

Z

z - Variable in class org.jmol.g3d.Sphere3D
 
Z - Variable in class org.jmol.quantum.QuantumCalculation
 
z - Variable in class org.jmol.quantum.SlaterData
 
z - Static variable in class org.jmol.script.Token
 
z - Variable in class org.jmol.shape.Object2d
 
z - Variable in class org.jmol.shape.SticksRenderer
 
Z - Variable in class org.jmol.shapebio.BioShapeRenderer
 
z1t - Variable in class org.jmol.g3d.Line3D
 
Z2 - Variable in class org.jmol.quantum.QuantumCalculation
 
z2t - Variable in class org.jmol.g3d.Line3D
 
zA - Variable in class org.jmol.g3d.Cylinder3D
 
zA - Variable in class org.jmol.shape.SticksRenderer
 
zAf - Variable in class org.jmol.g3d.Cylinder3D
 
zAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
zap() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
zap() - Method in class org.jmol.console.AppletConsole
 
zap(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
zap - Static variable in class org.jmol.script.Token
 
zap() - Method in class org.jmol.viewer.ModelManager
 
zap(boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
zap(String) - Method in class org.jmol.viewer.Viewer
 
zap() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
 
zB - Variable in class org.jmol.shape.SticksRenderer
 
zBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
zbuf - Variable in class org.jmol.g3d.Graphics3D
 
zbuf - Variable in class org.jmol.g3d.Sphere3D
 
zBuffer - Variable in class org.jmol.g3d.Platform3D
 
zBufferT - Variable in class org.jmol.g3d.Platform3D
 
zbufT - Variable in class org.jmol.g3d.Graphics3D
 
zCenter - Variable in class org.jmol.g3d.Circle3D
 
zDepth - Variable in class org.jmol.g3d.Graphics3D
 
zdepth - Static variable in class org.jmol.script.Token
 
zDepth - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
zDepthPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
zDepthToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
zDepthValue - Variable in class org.jmol.viewer.TransformManager
 
zEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
zeroBase - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
zerobasedxyzrasmol - Static variable in class org.jmol.script.Token
 
zeroBasedXyzRasmol - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
zeroFontId - Variable in class org.jmol.shape.Labels
 
zeroOffset - Static variable in class org.jmol.shape.Labels
 
zeroPad - Variable in class org.jmol.modelset.LabelToken
 
zeta - Variable in class org.jmol.quantum.SlaterData
 
zeta1 - Static variable in class org.jmol.quantum.NciCalculation
 
zeta2 - Static variable in class org.jmol.quantum.NciCalculation
 
zeta3 - Static variable in class org.jmol.quantum.NciCalculation
 
zGT - Static variable in class org.jmol.g3d.Graphics3D
 
ZipUtil - Class in org.jmol.util
 
ZipUtil() - Constructor for class org.jmol.util.ZipUtil
 
ZipUtil.GZipData - Class in org.jmol.util
 
ZipUtil.GZipData(int) - Constructor for class org.jmol.util.ZipUtil.GZipData
 
zLight - Static variable in class org.jmol.g3d.Shade3D
 
zLightsource - Static variable in class org.jmol.g3d.Shade3D
 
zLT - Static variable in class org.jmol.g3d.Graphics3D
 
zMargin - Variable in class org.jmol.g3d.Graphics3D
 
zMax - Variable in class org.jmol.quantum.QuantumCalculation
 
zMin - Variable in class org.jmol.quantum.QuantumCalculation
 
znuc - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
 
zoom(boolean) - Method in class org.jmol.script.ScriptEvaluator
 
zoom - Static variable in class org.jmol.script.Token
 
zoom - Variable in class org.jmol.viewer.StateManager.Orientation
 
zoom - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
ZOOM_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
ZOOM_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
zoomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
zoomBy(int) - Method in class org.jmol.viewer.TransformManager
standard response to user mouse vertical shift-drag
zoomBy(int) - Method in class org.jmol.viewer.Viewer
 
zoomByFactor(int, int, int) - Method in class org.jmol.viewer.ActionManager
 
zoomByFactor(float, int, int) - Method in class org.jmol.viewer.TransformManager
 
zoomByFactor(float, int, int) - Method in class org.jmol.viewer.TransformManager11
 
zoomByFactor(float, int, int) - Method in class org.jmol.viewer.Viewer
 
zoomByPercent(float) - Method in class org.jmol.viewer.TransformManager
 
zoomDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
zoomenabled - Static variable in class org.jmol.script.Token
 
zoomEnabled - Variable in class org.jmol.viewer.TransformManager
 
zoomFactor - Variable in class org.jmol.viewer.TransformManager11
 
zoomlarge - Static variable in class org.jmol.script.Token
 
zoomLarge - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
zoomPercent - Variable in class org.jmol.viewer.TransformManager
 
zoomPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
zoomRatio - Variable in class org.jmol.viewer.TransformManager
 
zoomStart - Variable in class org.jmol.viewer.TransformManager.MotionThread
 
zoomTo - Static variable in class org.jmol.script.Token
 
zoomToPercent(float) - Method in class org.jmol.viewer.TransformManager
 
ZPOS_FLAGS - Static variable in class org.jmol.shape.Labels
 
zPower - Static variable in class org.jmol.g3d.Shade3D
 
zRaster - Variable in class org.jmol.g3d.Cylinder3D
 
zroot - Variable in class org.jmol.g3d.Sphere3D
 
zShade - Variable in class org.jmol.g3d.Graphics3D
 
zshade - Static variable in class org.jmol.script.Token
 
zShadeB - Variable in class org.jmol.g3d.Graphics3D
 
zShadeEnabled - Variable in class org.jmol.viewer.TransformManager
 
zShadeG - Variable in class org.jmol.g3d.Graphics3D
 
zshadepower - Static variable in class org.jmol.script.Token
 
zShadePower - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
zShadeR - Variable in class org.jmol.g3d.Graphics3D
 
zSlab - Variable in class org.jmol.g3d.Graphics3D
 
zslab - Static variable in class org.jmol.script.Token
 
zSlab - Variable in class org.jmol.shape.Object2d
 
zSlab - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
zSlabPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
zSlabPoint - Variable in class org.jmol.viewer.TransformManager
 
zSlabToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
zSlabValue - Variable in class org.jmol.viewer.TransformManager
 
zTip - Variable in class org.jmol.g3d.Cylinder3D
 
zValueFromPercent(int) - Method in class org.jmol.viewer.TransformManager
 
zValueFromPercent(int) - Method in class org.jmol.viewer.Viewer
 
zXMax - Variable in class org.jmol.g3d.Cylinder3D
 
zXMin - Variable in class org.jmol.g3d.Cylinder3D
 

_

_(String) - Static method in class org.jmol.i18n.GT
 
_(String, String) - Static method in class org.jmol.i18n.GT
 
_(String, int) - Static method in class org.jmol.i18n.GT
 
_(String, Object[]) - Static method in class org.jmol.i18n.GT
 
_(String, boolean) - Static method in class org.jmol.i18n.GT
 
_(String, String, boolean) - Static method in class org.jmol.i18n.GT
 
_(String, int, boolean) - Static method in class org.jmol.i18n.GT
 
_(String, Object[], boolean) - Static method in class org.jmol.i18n.GT
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
___Exporter - Class in org.jmol.export
 
___Exporter() - Constructor for class org.jmol.export.___Exporter
 
__CartesianExporter - Class in org.jmol.export
 
__CartesianExporter() - Constructor for class org.jmol.export.__CartesianExporter
 
__RayTracerExporter - Class in org.jmol.export
 
__RayTracerExporter() - Constructor for class org.jmol.export.__RayTracerExporter
 
_activeLevels - Static variable in class org.jmol.util.Logger
 
_birth - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
_id1 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_id2 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_IdtfExporter - Class in org.jmol.export
 
_IdtfExporter() - Constructor for class org.jmol.export._IdtfExporter
 
_logger - Static variable in class org.jmol.util.Logger
 
_logLevel - Static variable in class org.jmol.util.Logger
 
_MayaExporter - Class in org.jmol.export
 
_MayaExporter() - Constructor for class org.jmol.export._MayaExporter
 
_myId - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
_myType - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_nCurrent - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
_nMoves - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
_nTraces - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_ObjExporter - Class in org.jmol.export
Class to export Wavefront OBJ files.
_ObjExporter() - Constructor for class org.jmol.export._ObjExporter
 
_offset - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_offsetCentroid - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_PovrayExporter - Class in org.jmol.export
 
_PovrayExporter() - Constructor for class org.jmol.export._PovrayExporter
 
_rotation - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_scale - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_TachyonExporter - Class in org.jmol.export
 
_TachyonExporter() - Constructor for class org.jmol.export._TachyonExporter
 
_traces1 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_traces2 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_VrmlExporter - Class in org.jmol.export
 
_VrmlExporter() - Constructor for class org.jmol.export._VrmlExporter
 
_X3dExporter - Class in org.jmol.export
 
_X3dExporter() - Constructor for class org.jmol.export._X3dExporter
 
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