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org.jmol.viewer
Class Viewer

java.lang.Object
  extended by org.jmol.api.JmolSimpleViewer
      extended by org.jmol.api.JmolViewer
          extended by org.jmol.viewer.Viewer
All Implemented Interfaces:
AtomDataServer
public class Viewer
extends JmolViewer
implements AtomDataServer

Field Summary
private  ActionManager actionManager
           
private  List<String> actionStates
           
private  List<String> actionStatesRedo
           
private  AnimationManager animationManager
           
private  boolean antialiasDisplay
           
(package private)  JmolAppConsoleInterface appConsole
           
private  String appletCodeBase
           
private  String appletContext
           
private  String appletDocumentBase
           
 boolean autoExit
           
private  boolean axesAreTainted
           
(package private)  BitSet bsFrameOffsets
           
private  BitSet bsRotateBranch
           
private  ColorManager colorManager
           
private  CommandHistory commandHistory
           
 ScriptCompiler compiler
           
private  boolean creatingImage
           
private  int currentCursor
           
private  int currentShapeID
           
private  String currentShapeState
           
private  DataManager dataManager
           
 Map<String,Object> definedAtomSets
           
(package private)  Dimension dimScreen
           
private  Object display
           
(package private)  boolean displayLoadErrors
           
private  String errorMessage
           
private  String errorMessageUntranslated
           
(package private)  ScriptEvaluator eval
           
private  Object executor
           
private  FileManager fileManager
           
(package private)  Point3f[] frameOffsets
           
private  boolean frankOn
           
private  String fullName
           
private  Graphics3D g3d
           
private  StateManager.GlobalSettings global
           
 boolean haveDisplay
           
(package private)  int hoverAtomIndex
           
(package private)  boolean hoverEnabled
           
(package private)  String hoverText
           
private  String htmlName
           
(package private)  Map<String,String[][]> htPdbBondInfo
           
private  float imageFontScaling
           
(package private)  String interruptScript
           
private  boolean isApplet
           
private  boolean isCmdLine_C_Option
           
private  boolean isCmdLine_c_or_C_Option
           
private  boolean isDataOnly
           
private  boolean isKiosk
           
(package private)  boolean isParallel
           
private  boolean isPreviewOnly
           
private  boolean isPrintOnly
           
(package private)  boolean isScriptQueued
           
private  boolean isSignedApplet
           
private  boolean isSignedAppletLocal
           
private  boolean isSilent
           
(package private)  boolean isTainted
           
(package private)  JmolPopupInterface jmolpopup
           
private  String language
           
private  Map<String,Object> ligandModels
           
private  Map<String,Boolean> ligandModelSet
           
private  boolean listCommands
           
private  String logFile
           
private  String logFilePath
           
private static int MAX_ACTION_UNDO
           
private  int maximumSize
           
private  MinimizerInterface minimizer
           
private  JmolAdapter modelAdapter
           
private  JmolModelKitInterface modelkit
           
private  ModelManager modelManager
           
private  ModelSet modelSet
           
(package private)  int motionEventNumber
           
private  boolean mouseEnabled
           
private  boolean movingSelected
           
private  boolean multiTouch
           
private  boolean mustRender
           
private  boolean noneSelected
           
static int nProcessors
           
(package private)  int prevFrame
           
private  double privateKey
           
private  RadiusData rd
           
private  boolean refreshing
           
private  RepaintManager repaintManager
           
private  int rotateBondIndex
           
private  int rotatePrev1
           
private  int rotatePrev2
           
(package private)  JmolScriptEditorInterface scriptEditor
           
private  boolean scriptEditorVisible
           
(package private)  int scriptIndex
           
private  ScriptManager scriptManager
           
private  SelectionManager selectionManager
           
private  ShapeManager shapeManager
           
private  boolean showSelected
           
private  SmilesMatcherInterface smilesMatcher
           
static String STATE_VERSION_STAMP
           
private  StateManager stateManager
           
private  int stateScriptVersionInt
           
private  StatusManager statusManager
           
private  String strJavaVendor
           
private  String strJavaVersion
           
private  String strOSName
           
private  SymmetryInterface symmetry
           
static String SYNC_GRAPHICS_MESSAGE
           
static String SYNC_NO_GRAPHICS_MESSAGE
           
private  String syncId
           
private  TempArray tempManager
           
private  TransformManager transformManager
           
private  boolean undoWorking
           
private  boolean useCommandThread
           
(package private)  boolean wasInMotion
           
 
Fields inherited from class org.jmol.api.JmolViewer
menuStructure
 
Fields inherited from class org.jmol.api.JmolSimpleViewer
apiPlatform
 
Constructor Summary
private Viewer(Object display, JmolAdapter modelAdapter, String commandOptions)
           
 
Method Summary
(package private)  void actionRotateBond(int deltaX, int deltaY, int x, int y)
           
 void addCommand(String command)
          Adds one or more commands to the command history
 void addFunction(ScriptFunction f)
           
 BitSet addHydrogens(BitSet bsAtoms, boolean asScript, boolean isSilent)
           
private  BitSet addHydrogensInline(BitSet bsAtoms, List<Atom> vConnections, Point3f[] pts)
           
 void addSelectionListener(JmolSelectionListener listener)
           
 ModelCollection.StateScript addStateScript(String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)
           
 ModelCollection.StateScript addStateScript(String script, boolean addFrameNumber, boolean postDefinitions)
           
 void addUnitCellOffset(Point3f pt)
           
static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener)
          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.
 EnumStructure[] allocTempEnum(int size)
           
 Point3f[] allocTempPoints(int size)
           
 Point3i[] allocTempScreens(int size)
           
 boolean allowMultiTouch()
           
(package private)  boolean allowRotateSelected()
           
 boolean allowSpecAtom()
           
(package private)  void appendLoadStates(StringBuffer commands)
           
 boolean areAxesTainted()
           
 void assignAromaticBonds()
           
 void assignAtom(int atomIndex, Point3f pt, String type)
           
 void assignBond(int bondIndex, char type)
           
 void assignConnect(int index, int index2)
           
 void autoCalculate(int tokProperty)
           
 int autoHbond(BitSet bsFrom, BitSet bsTo)
           
 void bindAction(String desc, String name, Point3f range1, Point3f range2)
           
 void calcAtomsMinMax(BitSet bs, BoxInfo boxInfo)
           
 void calcBoundBoxDimensions(BitSet bs, float scale)
           
 float calcRotationRadius(BitSet bs)
           
(package private)  float calcRotationRadius(Point3f center)
           
 void calcSelectedGroupsCount()
           
 void calcSelectedMoleculesCount()
           
 void calcSelectedMonomersCount()
           
 Vector3f calculateMolecularDipole()
           
 String calculatePointGroup()
           
 void calculateStraightness()
           
 String calculateStructures(BitSet bsAtoms, boolean asDSSP, boolean setStructure)
           
 int calculateStruts(BitSet bs1, BitSet bs2)
           
 Point3f[] calculateSurface(BitSet bsSelected, float envelopeRadius)
           
 String cd(String dir)
           
(package private)  void centerAt(int x, int y, Point3f pt)
           
 boolean checkAutoBondLegacy()
           
 void checkCoordinatesChanged()
           
private static float checkFloatRange(float value, float min, float max)
           
 boolean checkHalt(String str, boolean isInterrupt)
           
private static int checkIntRange(int value, int min, int max)
           
private  void checkMinimization()
           
(package private)  Map<String,Object> checkObjectClicked(int x, int y, int modifiers)
           
(package private)  void checkObjectDragged(int prevX, int prevY, int x, int y, int action)
           
(package private)  boolean checkObjectHovered(int x, int y)
           
 boolean checkPrivateKey(double privateKey)
          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.
 boolean checkResume(String str)
           
private  String checkScriptExecution(String strScript, boolean isInterrupt)
           
 boolean checkStepping(String str)
           
 void clearAllMeasurements()
           
private  void clearAtomSets()
           
 void clearBfactorRange()
           
(package private)  void clearClickCount()
           
 void clearConsole()
           
 void clearFunctions()
           
 void clearMeasurements()
           
(package private)  void clearMinimization()
           
private  void clearModelDependentObjects()
           
 void clearScriptQueue()
           
 void clearSelection()
           
 void clearShapeRenderers()
           
 void clearTimeout(String name)
           
 String clipImage(String text)
           
 void connect(float[][] connections)
           
 Object createImage(String fileName, String type, Object text_or_bytes, int quality, int width, int height)
           
 String createImage(String fileName, String type, Object text_or_bytes, int quality, int width, int height, BitSet bsFrames, String[] fullPath)
          from eval write command only includes option to write set of files
 Object createImage(String fileName, String type, Object text_or_bytes, int quality, int width, int height, String[] fullPath)
          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
private  Object createImage(String fileName, String type, Object text_or_bytes, int quality, int width, int height, String[] fullPath, boolean doCheck)
           
private  String createModelSetAndReturnError(Object atomSetCollection, boolean isAppend, StringBuffer loadScript)
          finally(!) we are ready to create the "model set" from the "atom set collection"
 int deleteAtoms(BitSet bs, boolean fullModels)
           
 void deleteBonds(BitSet bsDeleted)
           
 void deleteMeasurement(int i)
           
 void deleteModelAtoms(int firstAtomIndex, int nAtoms, BitSet bsDeleted)
           
 void deleteSavedState(String saveName)
           
 void deleteShapeAtoms(Object[] value, BitSet bs)
           
(package private)  void depthByPixels(int pixels)
           
 void depthToPercent(int percentDepth)
           
 String dialogAsk(String type, String fileName)
           
 void display(BitSet bs, boolean isDisplay, boolean isGroup, Boolean addRemove, boolean isQuiet)
           
 void displayBonds(Bond.BondSet bs, boolean isDisplay)
           
(package private)  void echoMessage(String msg)
           
 boolean eval(ScriptContext context, ShapeManager shapeManager)
           
 String evalFile(String strFilename)
           
 float evalFunctionFloat(Object func, Object params, float[] values)
           
 String evalString(String strScript)
           
 String evalStringQuiet(String strScript)
           
(package private)  String evalStringQuiet(String strScript, boolean isQuiet, boolean allowSyncScript)
           
 Object evalStringWaitStatus(String returnType, String strScript, String statusList)
           
(package private)  Object evalStringWaitStatus(String returnType, String strScript, String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)
           
 Object evaluateExpression(Object stringOrTokens)
           
 ScriptVariable evaluateExpressionAsVariable(Object stringOrTokens)
           
 void excludeAtoms(BitSet bs, boolean ignoreSubset)
           
 void exitJmol()
           
 void fillAtomData(AtomData atomData, int mode)
           
protected  void finalize()
           
(package private)  void finalizeTransformParameters()
           
(package private)  BitSet findAtomsInRectangle(Rectangle rect)
           
 int findNearestAtomIndex(int x, int y)
           
 int findNearestAtomIndex(int x, int y, boolean mustBeMovable)
           
 String fixInlineString(String strModel, char newLine)
           
 String formatText(String text0)
           
 boolean frankClicked(int x, int y)
           
 boolean frankClickedModelKit(int x, int y)
           
 void freeTempEnum(EnumStructure[] temp)
           
 void freeTempPoints(Point3f[] tempPoints)
           
 void freeTempScreens(Point3i[] tempScreens)
           
 float[][] functionXY(String functionName, int nX, int nY)
          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.
 float[][][] functionXYZ(String functionName, int nX, int nY, int nZ)
           
 String generateOutput(String type, String[] fileName, int width, int height)
           
 Point3f[] getAdditionalHydrogens(BitSet bsAtoms, boolean doAll, boolean justCarbon, List<Atom> vConnections)
           
(package private)  List<Map<String,Object>> getAllAtomInfo(Object atomExpression)
           
(package private)  List<Map<String,Object>> getAllBondInfo(Object atomExpression)
           
 Map<String,List<Map<String,Object>>> getAllChainInfo(Object atomExpression)
           
 boolean getAllowEmbeddedScripts()
           
 boolean getAllowGestures()
           
 Map<String,List<Map<String,Object>>> getAllPolymerInfo(Object atomExpression)
           
 String getAllSettings(String prefix)
           
 String getAltLocListInModel(int modelIndex)
           
(package private)  int getAnimationDirection()
           
 int getAnimationFps()
           
(package private)  Map<String,Object> getAnimationInfo()
           
(package private)  EnumAnimationMode getAnimationReplayMode()
           
 ApiPlatform getApiPlatform()
           
 boolean getAppendNew()
           
 String getAppletContext()
           
(package private)  Map<String,Object> getAppletInfo()
           
 boolean getApplySymmetryToBonds()
           
 int getAtomArgb(int i)
           
 BitSet getAtomBits(int tokType, Object specInfo)
           
 BitSet getAtomBitSet(Object atomExpression)
           
(package private)  BitSet getAtomBitSet(ScriptEvaluator eval, Object atomExpression)
           
(package private)  List<Integer> getAtomBitSetVector(Object atomExpression)
           
(package private)  String getAtomChain(int i)
           
 int getAtomCount()
           
 int getAtomCountInModel(int modelIndex)
           
 Quaternion[] getAtomGroupQuaternions(BitSet bsAtoms, int nMax)
           
 float[] getAtomicCharges()
           
 float[] getAtomicPotentials(boolean isMep, BitSet bsSelected, BitSet bsIgnore, String fileName)
           
(package private)  void getAtomicPropertyState(StringBuffer commands, byte type, BitSet bs, String name, float[] data)
           
 void getAtomIdentityInfo(int atomIndex, Map<String,Object> info)
           
 int getAtomIndexFromAtomNumber(int atomNumber)
           
 int[] getAtomIndices(BitSet bs)
           
 String getAtomInfo(int atomOrPointIndex)
           
 String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
           
 int getAtomModelIndex(int i)
           
 String getAtomName(int i)
           
 int getAtomNumber(int i)
           
private  boolean getAtomPicking()
           
 Point3f getAtomPoint3f(int i)
           
 List<Point3f> getAtomPointVector(BitSet bs)
           
 Quaternion getAtomQuaternion(int i)
           
 float getAtomRadius(int i)
           
 BitSet getAtomsConnected(float min, float max, int intType, BitSet bs)
           
(package private)  String getAtomSequenceCode(int i)
           
 Point3f getAtomSetCenter(BitSet bs)
           
private  Object getAtomSetCollection(String fileName, boolean isAppend, Map<String,Object> htParams, StringBuffer loadScript)
           
 float getAtomShapeValue(int tok, Group group, int atomIndex)
           
 BitSet getAtomsWithin(float distance, BitSet bs, boolean withinAllModels, RadiusData rd)
           
 BitSet getAtomsWithin(float distance, Point3f coord)
           
 BitSet getAtomsWithin(float distance, Point3f[] points, BitSet bsInclude)
           
 BitSet getAtomsWithin(float distance, Point4f plane)
           
 boolean getAutoBond()
           
(package private)  boolean getAutoFps()
           
 Map<String,Object> getAuxiliaryInfo(Object atomExpression)
           
(package private)  Point3f getAverageAtomPoint()
           
 EnumAxesMode getAxesMode()
           
 boolean getAxesOrientationRasmol()
           
 float getAxesScale()
           
 void getAxisAngle(AxisAngle4f axisAngle)
           
 Point3f[] getAxisPoints()
           
 int getBackgroundArgb()
           
 int getBfactor100Hi()
           
 String getBindingInfo(String qualifiers)
           
 BitSet getBitSetTrajectories()
           
 int getBondArgb1(int i)
           
 int getBondArgb2(int i)
           
 int getBondCount()
          For use in setting a for() construct max value
 int getBondCountInModel(int modelIndex)
          from JmolPopup.udateModelSetComputedMenu
 int getBondModelIndex(int i)
           
 int getBondOrder(int i)
           
 boolean getBondPicking()
           
 Point3f getBondPoint3f1(int i)
           
 Point3f getBondPoint3f2(int i)
           
 float getBondRadius(int i)
           
 boolean getBondSelectionModeOr()
           
 BitSet getBondsForSelectedAtoms(BitSet bsAtoms)
           
 float getBondTolerance()
           
 boolean getBooleanProperty(String key)
           
 Point3f getBoundBoxCenter()
           
 int getBoundBoxCenterX()
           
 int getBoundBoxCenterY()
           
 String getBoundBoxCommand(boolean withOptions)
           
 Vector3f getBoundBoxCornerVector()
           
(package private)  Map<String,Object> getBoundBoxInfo()
           
 BitSet getBoundBoxModels()
           
 Point3f[] getBoundBoxVertices()
           
 BoxInfo getBoxInfo(BitSet bs, float scale)
           
 BitSet getBranchBitSet(int atomIndex, int atomIndexNot)
           
 BufferedInputStream getBufferedInputStream(String fullPathName)
           
 Object getBufferedReaderOrErrorMessageFromName(String name, String[] fullPathNameReturn, boolean isBinary)
           
 Point3f[] getCameraFactors()
           
 boolean getCartoonBaseEdgesFlag()
           
 boolean getCartoonRocketFlag()
           
 Point3f[][] getCenterAndPoints(List<BitSet[]> atomSets, boolean addCenter)
           
 boolean getChainCaseSensitive()
           
 int getChainCount()
           
 int getChainCountInModel(int modelIndex)
           
 int getChainCountInModel(int modelIndex, boolean countWater)
           
 String getChemicalInfo(String smiles, char type)
           
 String getChimeInfo(int tok)
           
 Map<String,Object> getCifData(int modelIndex)
           
 BitSet getClickableSet()
           
(package private)  short getColix(Object object)
           
 short getColixAtomPalette(Atom atom, byte pid)
           
 short getColixBackgroundContrast()
           
 short getColixBondPalette(Bond bond, int pid)
           
 short getColixForPropertyValue(float val)
           
 short getColixRubberband()
           
 int getColorArgbOrGray(short colix)
           
 ColorEncoder getColorEncoder(String colorScheme)
           
 Point3f getColorPointForPropertyValue(float val)
           
 String getColorSchemeList(String colorScheme)
           
 BitSet getConformation(int iModel, int conformationIndex, boolean doSet)
           
 Map<String,ScriptVariable> getContextVariables()
           
 String getCoordinateState(BitSet bsSelected)
           
 boolean getCreatingImage()
           
 int[] getCrossHairMinMax()
           
 float[] getCurrentColorRange()
           
 String getCurrentFileAsString()
           
 int getCurrentModelIndex()
           
 float getCurrentSolventProbeRadius()
           
 SymmetryInterface getCurrentUnitCell()
           
 int getCursor()
           
 int getCursorX()
           
 int getCursorY()
           
 Object[] getData(String type)
           
 String getData(String atomExpression, String type)
           
 float[] getDataFloat(String label)
           
 float getDataFloat(String label, int atomIndex)
           
 float[][] getDataFloat2D(String label)
           
 float[][][] getDataFloat3D(String label)
           
(package private)  String getDataSeparator()
           
 boolean getDebugScript()
           
(package private)  String getDefaultDirectory()
           
 float getDefaultDrawArrowScale()
           
 Point3f getDefaultLattice()
           
 String getDefaultLoadFilter()
           
 String getDefaultLoadScript()
           
 String getDefaultMeasurementLabel(int nPoints)
           
 RadiusData getDefaultRadiusData()
           
 String getDefaultStructure(BitSet bsAtoms, BitSet bsAllAtoms)
           
 boolean getDefaultStructureDSSP()
           
 float getDefaultTranslucent()
           
 String getDefaultVdwTypeNameOrData(int iMode, EnumVdw vType)
           
 int getDelayMaximum()
           
 BitSet getDeletedAtoms()
           
 float getDipoleScale()
           
(package private)  boolean getDisablePopupMenu()
           
 Object getDisplay()
           
 boolean getDisplayCellParameters()
           
 int getDisplayModelIndex()
           
 int getDotDensity()
           
 int getDotScale()
           
 boolean getDotsSelectedOnlyFlag()
           
 boolean getDotSurfaceFlag()
           
 boolean getDragSelected()
           
 boolean getDrawHover()
           
 boolean getDrawPicking()
           
 boolean getDynamicMeasurements()
           
 boolean getEchoStateActive()
           
 String[] getElectronDensityLoadInfo()
           
(package private)  int getElementNumber(int i)
           
 BitSet getElementsPresentBitSet(int modelIndex)
           
(package private)  String getElementSymbol(int i)
           
 String getErrorMessage()
           
 String getErrorMessageUntranslated()
           
 Object getExecutor()
           
 String getExportDriverList()
           
 Object getFileAsBytes(String pathName, OutputStream os)
           
 Object getFileAsImage(String pathName, String[] retFileNameOrError)
           
 String getFileAsString(String name)
           
 boolean getFileAsString(String[] data, int nBytesMax, boolean doSpecialLoad)
           
 String getFileAsString(String name, int nBytesMax, boolean doSpecialLoad)
           
(package private)  Object getFileData()
           
(package private)  String getFileHeader()
           
 String[] getFileInfo()
           
 String getFileName()
           
private  String getFileNameFromDialog(String fileName, int quality)
           
 String getFilePath(String name, boolean asShortName)
           
 Font3D getFont3D(String fontFace, String fontStyle, float fontSize)
           
 boolean getFontCaching()
           
 boolean getFontScaling()
           
 boolean getForceAutoBond()
           
 boolean getFractionalRelative()
           
 BitSet getFrameOffsets()
           
 String getFrameTitle()
           
 int getFrontPlane()
           
 String getFullPathName()
           
 String[] getFullPathNameOrError(String filename)
           
 ScriptFunction getFunction(String name)
           
 String getFunctionCalls(String selectedFunction)
           
(package private)  StateManager.GlobalSettings getGlobalSettings()
           
 Graphics3D getGraphics3D()
           
(package private)  boolean getGreyscaleRendering()
           
 int getGroupCount()
           
 int getGroupCountInModel(int modelIndex)
           
 BitSet getGroupsWithin(int nResidues, BitSet bs)
           
 float getHbondsAngleMin()
           
 boolean getHbondsBackbone()
           
 float getHbondsDistanceMax()
           
 boolean getHbondsRasmol()
           
 boolean getHbondsSolid()
           
 Object getHelixData(BitSet bs, int tokType)
           
 int getHelixStep()
           
 void getHelp(String what)
           
 int getHermiteLevel()
           
 Map<String,String> getHeteroList(int modelIndex)
           
 BitSet getHiddenSet()
           
(package private)  boolean getHideNameInPopup()
           
 boolean getHighResolution()
           
(package private)  int getHoverDelay()
           
(package private)  String getHtmlName()
           
 String getHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x, String lcaoType)
           
private  Object getImage(boolean isDouble)
           
 Object getImageAs(String type, int quality, int width, int height, String fileName, OutputStream os)
           
(package private)  Object getImageAs(String type, int quality, int width, int height, String fileName, OutputStream os, String comment)
           
 float getImageFontScaling()
           
 char getInlineChar()
           
static void getInlineData(StringBuffer loadScript, String strModel, boolean isAppend)
           
 boolean getInMotion()
           
 String getInterruptScript()
           
 boolean getIsosurfaceKey()
           
 int getIsosurfacePropertySmoothing(boolean asPower)
           
 String getJavaVendor()
           
 String getJavaVersion()
           
 int getJmolDataFrameIndex(int modelIndex, String type)
           
 int getJmolDataSourceFrame(int modelIndex)
           
(package private)  String getJmolFrameType(int modelIndex)
           
static String getJmolVersion()
           
 boolean getJustifyMeasurements()
           
 String getLanguage()
           
 Map<String,Object> getLigandInfo(Object atomExpression)
           
 Object getLigandModel(String id)
          obtain CIF data for a ligand for purposes of adding hydrogens
 float getLoadAtomDataTolerance()
           
(package private)  String getLoadState(Map<String,Object> htParams)
           
 String getLogFile()
           
 boolean getLogGestures()
           
 short getMadBond()
           
 short getMarBond()
           
(package private)  Matrix3f getMatrixRotate()
           
 Matrix4f getMatrixtransform()
           
 float getMaxZoomPercent()
           
 boolean getMeasureAllModelsFlag()
           
 String getMeasureDistanceUnits()
           
 int getMeasurementCount()
           
 int[] getMeasurementCountPlusIndices(int i)
           
(package private)  List<Map<String,Object>> getMeasurementInfo()
           
 String getMeasurementInfoAsString()
           
 String getMeasurementStringValue(int i)
           
 String getMenu(String type)
           
(package private)  String getMenuName(int i)
           
 Map<String,List<List<Object>>> getMessageQueue()
           
 boolean getMessageStyleChime()
           
 float getMinBondDistance()
           
 String getMinimizationInfo()
           
 MinimizerInterface getMinimizer(boolean createNew)
           
 int getMinPixelSelRadius()
           
 JmolAdapter getModelAdapter()
           
 String getModelAtomProperty(Atom atom, String text)
           
 Map<String,Object> getModelAuxiliaryInfo(int modelIndex)
           
 Object getModelAuxiliaryInfo(int modelIndex, String keyName)
           
 BitSet getModelBitSet(BitSet atomList, boolean allTrajectories)
           
 String getModelCml(BitSet bs, int nAtomsMax, boolean addBonds)
           
 int getModelCount()
           
 Vector3f getModelDipole()
           
 String getModelExtract(Object atomExpression, boolean doTransform, String type)
           
 String getModelFileInfo()
           
 String getModelFileInfoAll()
           
 String getModelFileName(int modelIndex)
           
 int getModelFileNumber(int modelIndex)
           
 Map<String,Object> getModelInfo(Object atomExpression)
           
 String getModelInfoAsString()
           
 boolean getModelkitMode()
           
(package private)  BitSet getModelKitStateBitSet(BitSet bs, BitSet bsDeleted)
           
 String getModelName(int modelIndex)
           
 int getModelNumber(int modelIndex)
           
 String getModelNumberDotted(int modelIndex)
           
 int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
           
 Properties getModelProperties(int modelIndex)
           
 String getModelProperty(int modelIndex, String propertyName)
           
 ModelSet getModelSet()
           
 Map<String,Object> getModelSetAuxiliaryInfo()
           
 Object getModelSetAuxiliaryInfo(String strKey)
           
 String getModelSetFileName()
           
 String getModelSetName()
           
 String getModelSetPathName()
           
 Properties getModelSetProperties()
           
 String getModelSetProperty(String strProp)
           
 String getModelSetTypeName()
           
private  String getModelTitle(int modelIndex)
           
 BitSet getModelUndeletedAtomsBitSet(BitSet bsModels)
           
 BitSet getModelUndeletedAtomsBitSet(int modelIndex)
           
 SymmetryInterface getModelUnitCell(int modelIndex)
           
 byte getModeMultipleBond()
           
 String getMoInfo(int modelIndex)
           
 BitSet getMoleculeBitSet(int atomIndex)
           
(package private)  List<Map<String,Object>> getMoleculeInfo(Object atomExpression)
           
 int getMotionEventNumber()
           
 BitSet getMotionFixedAtoms()
           
 boolean getMouseEnabled()
           
 Object getMouseInfo()
           
(package private)  String getMoveToText(float timespan)
           
 float getMultipleBondRadiusFactor()
           
 float getMultipleBondSpacing()
           
 boolean getNavigateSurface()
           
 Point3f getNavigationCenter()
           
 float getNavigationDepthPercent()
           
 boolean getNavigationMode()
           
 Point3f getNavigationOffset()
           
(package private)  float getNavigationOffsetPercent(char XorY)
           
 boolean getNavigationPeriodic()
           
(package private)  float getNavigationSpeed()
           
(package private)  boolean getNavOn()
           
 Boolean getNoneSelected()
           
(package private)  int getObjectArgb(int objId)
           
 short getObjectColix(int objId)
           
 int getObjectMad(int objId)
           
 void getObjectMap(Map<String,Token> map, boolean withDollar)
          retrieves list of draw/isosurface objects
 String getObjectState(String name)
           
 String getOperatingSystemName()
           
 StateManager.Orientation getOrientation()
           
(package private)  Map<String,Object> getOrientationInfo()
           
 String getOrientationText(int type, String name)
           
 ScriptVariable getOrSetNewVariable(String key, boolean doSet)
           
 OutputStream getOutputStream(String localName, String[] fullPath)
           
 Object getParameter(String key)
           
 Object getParameterEscaped(String key)
           
 float[] getPartialCharges()
           
 boolean getPartialDots()
           
 String[][] getPdbBondInfo(String group3)
           
 String getPdbData(BitSet bs, OutputStringBuffer sb)
           
 String getPdbData(int modelIndex, String type, Object[] parameters)
           
 String getPDBHeader()
           
(package private)  MeasurementPending getPendingMeasurement()
           
 int getPercentVdwAtom()
           
 boolean getPerspectiveDepth()
           
 int getPickingMode()
           
(package private)  int getPickingSpinRate()
           
 List<Object> getPlaneIntersection(int type, Point4f plane, float scale, int flags)
           
 String getPointGroupAsString(boolean asDraw, String type, int index, float scale)
           
 Map<String,Object> getPointGroupInfo(Object atomExpression)
           
 float getPointGroupTolerance(int type)
           
 int getPolymerCount()
           
 int getPolymerCountInModel(int modelIndex)
           
 Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
           
 void getPolymerPointsAndVectors(BitSet bs, List<Point3f[]> vList)
           
private  Object getPopupMenu()
           
 boolean getPreserveState()
          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.
 Object getProperty(String returnType, String infoType, Object paramInfo)
           
 Object getProperty(String returnType, String infoType, String paramInfo)
           
 String getPropertyColorScheme()
           
 String getProteinStructureState()
           
 char getQuaternionFrame()
           
 boolean getRasmolSetting(int tok)
           
 boolean getRefreshing()
           
 BitSet getRenderableBitSet()
           
 int getRepaintWait()
           
 int getRibbonAspectRatio()
           
 boolean getRibbonBorder()
           
 boolean getRocketBarrelFlag()
           
(package private)  int getRotateBondIndex()
           
(package private)  void getRotation(Matrix3f matrixRotation)
           
 Point3f getRotationCenter()
           
 Quaternion getRotationQuaternion()
           
 float getRotationRadius()
           
(package private)  Rectangle getRubberBandSelection()
           
 String getSavedCoordinates(String saveName)
           
 String getSavedOrienationText(String name)
           
 String getSavedState(String saveName)
           
 String getSavedStructure(String saveName)
           
 float getScalePixelsPerAngstrom(boolean asAntialiased)
           
 int getScreenDim()
           
 int getScreenHeight()
           
 Object getScreenImage(Object g)
           
 int getScreenWidth()
           
 int getScriptDelay()
           
(package private)  boolean getSelectAllModels()
           
 AtomIndexIterator getSelectedAtomIterator(BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel)
           
 int getSelectionCount()
           
 boolean getSelectionHaloEnabled(boolean isRenderer)
           
 BitSet getSelectionSet(boolean includeDeleted)
           
 BitSet getSelectionSubset()
           
 BitSet getSequenceBits(String specInfo, BitSet bs)
           
 String getSetHistory(int howFarBack)
          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;
 String getShapeErrorState()
           
 Map<String,Object> getShapeInfo()
           
 ShapeManager getShapeManager()
           
 Object getShapeProperty(int shapeType, String propertyName)
           
 Object getShapeProperty(int shapeType, String propertyName, int index)
           
 boolean getShapeProperty(int shapeType, String propertyName, Object[] data)
           
private  int getShapePropertyAsInt(int shapeID, String propertyName)
           
 void getShapeState(StringBuffer commands, boolean isAll)
           
 float getSheetSmoothing()
           
 boolean getShowAxes()
           
 boolean getShowBbcage()
           
 boolean getShowFrank()
           
 boolean getShowHiddenSelectionHalos()
           
 boolean getShowHydrogens()
           
 boolean getShowMeasurementLabels()
           
 boolean getShowMeasurements()
           
 boolean getShowMultipleBonds()
           
 boolean getShowNavigationPoint()
           
 boolean getShowUnitCell()
           
 boolean getSlabByAtom()
           
 boolean getSlabByMolecule()
           
 boolean getSlabEnabled()
           
 int getSmallMoleculeMaxAtoms()
           
 boolean getSmartAromatic()
           
 BitSet getSmartsMatch(String smarts, BitSet bsSelected)
           
 String getSmiles(int index1, int index2, BitSet bsSelected, boolean isBioSmiles, boolean allowUnmatchedRings, boolean addCrossLinks, boolean addComment)
          returns the SMILES string for a sequence or atom set does not include attached protons on groups
 SmilesMatcherInterface getSmilesMatcher()
           
(package private)  boolean getSolventOn()
           
 float getSolventProbeRadius()
           
 Map<String,Object> getSpaceGroupInfo(String spaceGroup)
           
 String getSpecularState()
           
(package private)  boolean getSpinOn()
           
 String getSpinState()
           
 boolean getSsbondsBackbone()
           
 String getStandardLabelFormat(int type)
           
 String getStateInfo()
           
 String getStateInfo(String type, int width, int height)
           
(package private)  List<List<List<Object>>> getStatusChanged(String statusNameList)
           
(package private)  StatusManager getStatusManager()
           
private  Object getStereoImage(EnumStereoMode stereoMode)
           
 int getStrandCount(int type)
           
 Map<EnumStructure,float[]> getStructureList()
           
 String getStructureState()
           
 float getStrutDefaultRadius()
           
 float getStrutLengthMaximum()
           
 boolean getStrutsMultiple()
           
 int getStrutSpacingMinimum()
           
(package private)  int getSurfaceDistanceMax()
           
 SymmetryInterface getSymmetry()
           
 Object getSymmetryInfo(BitSet bsAtoms, String xyz, int op, Point3f pt, Point3f pt2, String id, int type)
           
 String getSymmetryInfoAsString()
           
 String getSymmetryOperation(String spaceGroup, int symop, Point3f pt1, Point3f pt2, boolean labelOnly)
           
 BitSet getTaintedAtoms(byte type)
           
 boolean getTestFlag(int i)
           
 boolean getTraceAlpha()
           
 String getTrajectoryInfo()
           
 String getTransformText()
           
 String getTranslationScript()
           
 float getTranslationXPercent()
           
 float getTranslationYPercent()
           
(package private)  float getTranslationZPercent()
           
private  BitSet getUndeletedGroupAtomBits(BitSet bs)
           
 float getUnitCellInfo(int infoType)
           
 String getUnitCellInfoText()
           
 Matrix4f getUnscaledTransformMatrix()
           
 boolean getUseNumberLocalization()
           
 int getVanderwaalsMar(int i)
           
 int getVanderwaalsMar(int i, EnumVdw type)
           
 String getVariableList()
           
 float getVectorScale()
           
 float getVibrationPeriod()
           
(package private)  float getVibrationScale()
           
 Vector3f getVibrationVector(int atomIndex)
           
 BitSet getVisibleFramesBitSet()
           
 BitSet getVisibleSet()
           
 float getVolume(BitSet bs, String type)
           
 boolean getWireframeRotation()
           
 String getWrappedState(boolean isImage, int width, int height)
           
 String getZapName()
           
 boolean getZeroBasedXyzRasmol()
           
 boolean getZoomEnabled()
           
(package private)  boolean getZoomLarge()
           
 int getZoomPercent()
           
 float getZoomPercentFloat()
           
 float getZoomSetting()
           
 void haltScriptExecution()
           
 void handleError(Error er, boolean doClear)
           
 boolean handleOldJvm10Event(int id, int x, int y, int modifiers, long time)
           
 boolean hasCalculatedHBonds(BitSet bsAtoms)
           
 boolean hasFocus()
           
 boolean haveFileSet()
           
 boolean haveFrame()
           
(package private)  boolean haveModelKit()
           
(package private)  boolean haveModelSet()
           
 boolean havePartialCharges()
           
 void highlight(BitSet bs)
           
 void highlightBond(int index, boolean isHover)
           
 void homePosition()
           
(package private)  void hoverOff()
           
(package private)  void hoverOn(int atomIndex, int action)
           
 void hoverOn(int x, int y, String text)
           
 void initialize(boolean clearUserVariables)
           
(package private)  boolean initializeExporter(JmolRendererInterface g3dExport, String type, Object output)
           
private  void initializeModel(boolean isAppend)
           
 void invertAtomCoord(Point3f pt, BitSet bs)
           
 void invertAtomCoord(Point4f plane, BitSet bs)
           
 void invertSelected(Point3f pt, Point4f plane, int iAtom, BitSet invAtoms)
           
 void invertSelection()
           
(package private)  boolean isAnimationOn()
           
(package private)  boolean isAntialiased()
           
 boolean isApplet()
           
(package private)  boolean isAtomAssignable(int i)
           
 boolean isAtomPDB(int i)
           
 boolean isAtomSelected(int atomIndex)
           
 boolean isBound(int action, int gesture)
           
 boolean isDataOnly()
           
 boolean isFunction(String name)
           
 boolean isHoverEnabled()
           
 boolean isInPosition(Vector3f axis, float degrees)
           
(package private)  boolean isInSelectionSubset(int atomIndex)
           
 boolean isJmolDataFrame()
           
 boolean isJmolDataFrame(int modelIndex)
           
 boolean isJmolVariable(String key)
           
(package private)  boolean isKiosk()
           
 boolean isModelKitMode()
           
 boolean isModelPDB(int i)
           
 boolean isNavigating()
           
 boolean isParallel()
           
 boolean isPdbSequential()
           
 boolean isPreviewOnly()
           
 boolean isRangeSelected()
           
(package private)  boolean isRepaintPending()
           
 boolean isScriptEditorVisible()
           
 boolean isScriptExecuting()
           
 boolean isSelected(int atomIndex)
           
 boolean isSignedApplet()
           
(package private)  boolean isStereoDouble()
           
 boolean isTrajectory(int modelIndex)
           
 boolean isVibrationOn()
           
 boolean isWindowCentered()
           
private  void jmolTest()
           
 String jsEval(String strEval)
           
 String listSavedStates()
           
private  String loadAtomDataAndReturnError(Object atomSetCollection, int tokType)
          or just apply the data to the current model set
 String loadInline(List<Object> arrayData, boolean isAppend)
          does not preserver state, intentionally!
 String loadInline(String strModel)
           
 String loadInline(String[] arrayModels)
           
 String loadInline(String[] arrayModels, boolean isAppend)
           
 String loadInline(String strModel, boolean isAppend)
           
 String loadInline(String strModel, char newLine)
           
 String loadInline(String strModel, char newLine, boolean isAppend, Map<String,Object> htParams)
           
 String loadModelFromFile(String fullPathName, String fileName, String[] fileNames, Object reader, boolean isAppend, Map<String,Object> htParams, StringBuffer loadScript, int tokType)
          Used by the ScriptEvaluator LOAD command to open one or more files.
 void loadShape(int shapeID)
           
 void log(String data)
           
 boolean logCommands()
           
 int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds, boolean addGroup, float energy)
           
 boolean menuEnabled()
           
 void mergeShapes(Shape[] newShapes)
           
 void minimize(int steps, float crit, BitSet bsSelected, BitSet bsFixed, float rangeFixed, boolean addHydrogen, boolean isSilent, boolean asScript)
           
 boolean modelHasVibrationVectors(int modelIndex)
           
(package private)  boolean modelSetHasVibrationVectors()
           
 void move(Vector3f dRot, float dZoom, Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)
           
(package private)  void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate, Vector3f translation, Point3f center, boolean isInternal, BitSet bsAtoms)
           
protected  void moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, int deltaZ, BitSet bsAtoms)
           
 void moveSelected(int deltaX, int deltaY, int deltaZ, int x, int y, BitSet bsSelected, boolean isTranslation, boolean asAtoms)
           
 void moveTo(float floatSecondsTotal, Point3f center, Vector3f rotAxis, float degrees, Matrix3f rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)
           
private  void moveUpdate(float floatSecondsTotal)
           
(package private)  boolean mustRenderFlag()
           
 void navigate(float timeSeconds, Point3f center)
           
 void navigate(float timeSeconds, Point3f[][] pathGuide)
           
 void navigate(float timeSeconds, Point3f[] path, float[] theta, int indexStart, int indexEnd)
           
 void navigate(float timeSeconds, Vector3f rotAxis, float degrees)
           
(package private)  void navigate(int keyWhere, int modifiers)
           
 void navigateSurface(float timeSeconds, String name)
           
 void navTranslate(float timeSeconds, Point3f center)
           
 void navTranslatePercent(float timeSeconds, float x, float y)
           
 void notifyError(String errType, String errMsg, String errMsgUntranslated)
           
 void notifyMinimizationStatus()
           
 int notifyMouseClicked(int x, int y, int action, int mode)
           
 void notifyViewerRepaintDone()
           
 String openDOM(Object DOMNode)
          applet DOM method -- does not preserve state
 String openFile(String fileName)
          for JmolSimpleViewer -- external applications only
 void openFileAsynchronously(String fileName)
          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
 String openFiles(String[] fileNames)
          for JmolSimpleViewer -- external applications only
 String openReader(String fullPathName, String fileName, Reader reader)
          Opens the file, given an already-created reader.
 String openStringInline(String strModel)
           
private  String openStringInline(String strModel, Map<String,Object> htParams, boolean isAppend)
           
private  String openStringsInline(String[] arrayModels, Map<String,Object> htParams, boolean isAppend)
           
 void pauseScriptExecution()
           
 void popHoldRepaint()
           
 void popHoldRepaint(String why)
           
(package private)  void popupMenu(int x, int y, char type)
           
 void processEvent(int groupID, int eventType, int touchID, int iData, Point3f pt, long time)
           
 String prompt(String label, String data, String[] list, boolean asButtons)
           
 void pushHoldRepaint()
           
 void pushHoldRepaint(String why)
           
 void rebond()
           
 void rebond(boolean isStateScript)
           
 void refresh(int mode, String strWhy)
          initiate a repaint/update sequence if it has not already been requested.
 void refreshMeasures(boolean andStopMinimization)
           
 void releaseScreenImage()
           
 String removeCommand()
          Removes one command from the command history
 void removeSelectionListener(JmolSelectionListener listener)
           
 void removeUserVariable(String key)
           
private  void render()
           
private  void render1(Object g, Object img, int x, int y)
           
 void renderScreenImage(Object g, int width, int height)
           
 void renderScreenImage(Object gLeft, Object gRight, int width, int height)
          an added class for rendering stereo in two independent applets
(package private)  void repaint()
           
(package private)  void reportSelection(String msg)
           
 void requestRepaintAndWait()
           
 void reset(boolean includingSpin)
           
 void resetAromatic()
           
 void resetBioshapes(BitSet bsAllAtoms)
           
 void resetError()
           
 void resetShapes()
           
private  void resizeImage(int width, int height, boolean isImageWrite, boolean isExport, boolean isReset)
           
 boolean restoreBonds(String saveName)
           
(package private)  void restoreModelOrientation(int modelIndex)
           
(package private)  void restoreModelRotation(int modelIndex)
           
 boolean restoreOrientation(String saveName, float timeSeconds)
           
 void restoreRotation(String saveName, float timeSeconds)
           
 boolean restoreSelection(String saveName)
           
 void resumeScriptExecution()
           
 void rotateAboutPointsInternal(Point3f point1, Point3f point2, float degreesPerSecond, float endDegrees, boolean isSpin, BitSet bsSelected, Vector3f translation, List<Point3f> finalPoints)
           
(package private)  void rotateArcBall(int x, int y, float factor)
           
 void rotateAxisAngleAtCenter(Point3f rotCenter, Vector3f rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BitSet bsSelected)
           
 void rotateFront()
           
 void rotatePoint(Point3f pt, Point3f ptRot)
           
(package private)  void rotateSelected(float deltaX, float deltaY, BitSet bsSelected)
           
 void rotateX(float angleRadians)
           
 void rotateX(int angleDegrees)
           
(package private)  void rotateXYBy(float xDelta, float yDelta)
           
 void rotateY(float angleRadians)
           
 void rotateY(int angleDegrees)
           
 void rotateZ(float angleRadians)
           
 void rotateZBy(int zDelta, int x, int y)
           
 boolean runScriptImmediately(String script)
           
 void saveBonds(String saveName)
           
 void saveCoordinates(String saveName, BitSet bsSelected)
           
(package private)  void saveModelOrientation()
           
 void saveOrientation(String saveName)
           
 void saveSelection(String saveName)
           
 void saveState(String saveName)
           
 void saveStructure(String saveName)
           
 float scaleToPerspective(int z, float sizeAngstroms)
           
 short scaleToScreen(int z, int milliAngstroms)
           
 String script(String strScript)
           
 Object scriptCheck(String strScript)
           
private  Object scriptCheck(String strScript, boolean returnContext)
           
 void scriptEcho(String strEcho)
           
 void scriptStatus(String strStatus)
           
 void scriptStatus(String strStatus, String statusMessage)
           
 void scriptStatus(String strStatus, String statusMessage, int msWalltime, String strErrorMessageUntranslated)
           
 String scriptWait(String strScript)
           
 Object scriptWaitStatus(String strScript, String statusList)
           
 void select(BitSet bs, boolean isGroup, Boolean addRemove, boolean isQuiet)
           
 void selectAll()
           
 void selectBonds(BitSet bs)
           
 void setAnimation(int tok)
           
 void setAnimationDirection(int direction)
           
 void setAnimationFps(int fps)
           
 void setAnimationOn(boolean animationOn)
           
 void setAnimationRange(int modelIndex1, int modelIndex2)
           
 void setAnimationReplayMode(EnumAnimationMode replayMode, float firstFrameDelay, float lastFrameDelay)
           
private  void setAntialias(int mode, boolean TF)
           
 void setAppendNew(boolean value)
           
 void setAppletContext(String fullName, URL documentBase, URL codeBase, String commandOptions)
           
(package private)  void setApplySymmetryToBonds(boolean TF)
           
 void setAtomCoord(BitSet bs, int tokType, Object xyzValues)
           
 void setAtomCoord(int atomIndex, float x, float y, float z)
           
 void setAtomCoordRelative(int atomIndex, float x, float y, float z)
           
 void setAtomCoordRelative(Tuple3f offset, BitSet bs)
           
 void setAtomData(int type, String name, String coordinateData, boolean isDefault)
           
 void setAtomLabel(String value, int i)
           
private  void setAtomPickingOption(String option)
           
 void setAtomProperty(BitSet bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)
           
 void setAutoBond(boolean TF)
           
private  void setAxesModeMolecular(boolean TF)
           
(package private)  void setAxesModeUnitCell(boolean TF)
           
 void setAxesOrientationRasmol(boolean TF)
           
(package private)  void setAxesScale(float scale)
           
 void setBackgroundImage(String fileName, Object image)
           
 void setBackgroundModelIndex(int modelIndex)
           
private  void setBondPickingOption(String option)
           
 void setBondTolerance(float bondTolerance)
           
 void setBooleanProperty(String key, boolean value)
           
private  void setBooleanProperty(String key, int tok, boolean value)
           
 void setBoundBox(Point3f pt1, Point3f pt2, boolean byCorner, float scale)
           
 void setCenterAt(String relativeTo, Point3f pt)
           
 void setCenterBitSet(BitSet bsCenter, boolean doScale)
           
 void setCenterSelected()
           
 void setColorBackground(String colorName)
           
 BitSet setConformation()
           
 void setCurrentColorRange(float[] data, BitSet bs)
           
 void setCurrentColorRange(float min, float max)
           
 void setCurrentColorRange(String label)
           
 void setCurrentModelIndex(int modelIndex)
           
 void setCurrentModelIndex(int modelIndex, boolean clearBackground)
           
 void setCurrentUnitCellOffset(int ijk)
           
 void setCurrentUnitCellOffset(Point3f pt)
           
 void setCursor(int cursor)
           
 void setData(String type, Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
           
 void setDebugScript(boolean debugScript)
           
private  void setDefaultColors(boolean isRasmol)
           
 void setDefaultLattice(Point3f ptLattice)
           
private  void setDefaults()
           
private  void setDefaults(String type)
           
(package private)  void setDefaultVdw(String type)
           
(package private)  void setDynamicMeasurements(boolean TF)
           
 void setEchoStateActive(boolean TF)
           
 void setElementArgb(int elementNumber, int argb)
           
private  String setErrorMessage(String errMsg)
           
private  String setErrorMessage(String errMsg, String errMsgUntranslated)
           
 void setFileInfo(String[] fileInfo)
           
private  void setFileLoadStatus(FileManager.EnumFileStatus ptLoad, String fullPathName, String fileName, String modelName, String strError)
           
 void setFloatProperty(String key, float value)
           
private  void setFloatProperty(String key, int tok, float value)
           
 void setFocus()
           
 void setFormalCharges(int formalCharge)
           
(package private)  void setFrameOffset(int modelIndex)
           
 void setFrameOffsets(BitSet bsAtoms)
           
 void setFrameTitle(int modelIndex, String title)
           
 void setFrameTitle(Object title)
           
(package private)  void setFrameVariables(int firstModelIndex, int lastModelIndex)
           
 void setFrankOn(boolean TF)
           
 void setHoverLabel(String strLabel)
           
(package private)  void setInMotion(boolean inMotion)
           
 void setIntProperty(String key, int value)
           
private  void setIntProperty(String key, int tok, int value)
           
 void setIteratorForAtom(AtomIndexIterator iterator, int atomIndex, float distance)
           
 void setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, Point3f pt, float distance)
           
 void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
           
 void setJmolDataFrame(String type, int modelIndex, int dataIndex)
           
 void setJmolDefaults()
           
 void setJmolStatusListener(JmolStatusListener jmolStatusListener)
           
 void setLigandModel(String id, String data)
           
 Object setLoadFormat(String name, char type, boolean withPrefix)
           
private  Map<String,Object> setLoadParameters(Map<String,Object> htParams, boolean isAppend)
           
private  String setLogFile(String value)
           
 void setMarBond(short marBond)
           
private  void setMaximumSize(int x)
           
 void setMeasureDistanceUnits(String units)
           
 void setMenu(String fileOrText, boolean isFile)
           
 void setMeshCreator(Object meshCreator)
          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.
 void setMinBondDistance(float minBondDistance)
           
private  void setModelKitMode(boolean value)
           
 void setModelVisibility()
           
 void setModeMouse(int modeMouse)
           
 void setMotionFixedAtoms(BitSet bs)
           
 void setMouseEnabled(boolean TF)
           
private  BitSet setMovableBitSet(BitSet bsSelected, boolean checkMolecule)
           
 void setNavigationDepthPercent(float timeSec, float percent)
           
private  void setNavigationMode(boolean TF)
           
 void setNavOn(boolean navOn)
           
 void setNavXYZ(float x, float y, float z)
           
 void setNewRotationCenter(Point3f center)
           
 void setNoneSelected(boolean noneSelected)
           
 void setObjectArgb(String name, int argb)
           
(package private)  void setObjectColor(String name, String colorName)
           
 void setObjectMad(int iShape, String name, int mad)
           
 boolean setParallel(boolean TF)
           
 void setPdbConectBonding(boolean isAuto, boolean isStateScript)
           
(package private)  void setPendingMeasurement(MeasurementPending measurementPending)
           
 void setPercentVdwAtom(int value)
           
 void setPerspectiveDepth(boolean perspectiveDepth)
           
private  void setPerspectiveModel(int mode)
           
 void setPicked(int iAtom)
           
(package private)  void setPickingMode(String strMode, int pickingMode)
           
(package private)  void setPickingStyle(String style, int pickingStyle)
           
 void setPrivateKeyForShape(int iShape)
           
 void setPropertyColorScheme(String scheme, boolean isTranslucent, boolean isOverloaded)
           
 void setProteinType(EnumStructure type, BitSet bs)
           
 void setRasmolDefaults()
           
private  void setRefreshing(boolean TF)
           
(package private)  void setRotateBondIndex(int index)
           
(package private)  void setRotationMatrix(Matrix3f rotationMatrix)
           
 void setRotationRadius(float angstroms, boolean doAll)
           
 void setRubberbandArgb(int argb)
           
 void setScreenDimension(int width, int height)
           
private  void setScriptQueue(boolean TF)
           
 void setSelectedAtom(int atomIndex, boolean TF)
           
 void setSelectionHalos(boolean TF)
           
 void setSelectionSet(BitSet set)
           
 void setSelectionSubset(BitSet subset)
           
 void setShapeErrorState(int shapeID, String state)
           
 void setShapeProperty(int shapeID, String propertyName, Object value)
           
 void setShapeSize(int shapeID, int mad, BitSet bsSelected)
           
 void setShapeSize(int shapeID, RadiusData rd, BitSet bsAtoms)
           
 void setShowAxes(boolean value)
           
 void setShowBbcage(boolean value)
           
 void setShowHydrogens(boolean TF)
           
 void setShowMeasurements(boolean TF)
           
 void setShowUnitCell(boolean value)
           
 void setSlabDepthInternal(boolean isDepth)
           
 void setSmilesString(String s)
           
 void setSpin(String key, int value)
           
 void setSpinOn(boolean spinOn)
           
 void setStateScriptVersion(String version)
           
 void setStatusAtomHovered(int atomIndex, String info)
           
 void setStatusAtomPicked(int atomIndex, String info)
           
(package private)  void setStatusFrameChanged(int frameNo)
           
 void setStatusMeasuring(String status, int intInfo, String strMeasure, float value)
           
 void setStatusResized(int width, int height)
           
 void setStereoMode(int[] twoColors, EnumStereoMode stereoMode, float degrees)
           
private  void setStrandCount(int type, int value)
           
private  void setStringProperty(String key, int tok, String value)
           
 void setStringProperty(String key, String value)
           
 void setStructureList(float[] list, EnumStructure type)
           
private  void setSync()
           
(package private)  void setSyncDriver(int mode)
           
private  void setSyncTarget(int mode, boolean TF)
           
 void setTainted(boolean TF)
           
 void setTaintedAtoms(BitSet bs, byte type)
           
 void setTimeout(String name, int mSec, String script)
           
 void setTrajectory(BitSet bsModels)
           
(package private)  void setTrajectory(int modelIndex)
           
 void setTransformManager(TransformManager transformManager)
          for an external application
private  void setTransformManagerDefaults()
           
 void setUserScale(int[] scale)
           
 ScriptVariable setUserVariable(String name, ScriptVariable value)
           
 void setVectorScale(float scale)
           
 void setVibrationOff()
           
 void setVibrationPeriod(float period)
           
 void setVibrationScale(float scale)
           
 void setZslabPoint(Point3f pt)
           
 void show2D(String smiles)
           
 void showConsole(boolean showConsole)
           
(package private)  void showEditor(String[] file_text)
           
 void showMessage(String s)
           
 boolean showModelSetDownload()
           
 void showParameter(String key, boolean ifNotSet, int nMax)
           
 void showString(String str, boolean isPrint)
           
 String showTimeout(String name)
           
 void showUrl(String urlString)
           
(package private)  void slabByPixels(int pixels)
           
(package private)  void slabDepthByPixels(int pixels)
           
 void slabInternal(Point4f plane, boolean isDepth)
           
 void slabReset()
           
 void slabToPercent(int percentSlab)
           
 void spinXYBy(int xDelta, int yDelta, float speed)
           
 void startSpinningAxis(Point3f pt1, Point3f pt2, boolean isClockwise)
           
 void stepScriptExecution()
           
private  void stopAnimationThreads(String fromWhere)
           
(package private)  void stopMinimization()
           
 void stopMotion()
           
 String streamFileData(String fileName, String type, String type2, int modelIndex, Object[] parameters)
           
 void syncScript(String script, String applet, int port)
           
 void toCartesian(Point3f pt, boolean asAbsolute)
          absolute or relative to origin of UNITCELL {x y z}
 void toFractional(Point3f pt, boolean asAbsolute)
          absolute or relative to origin of UNITCELL {x y z}
 void togglePickingLabel(BitSet bs)
           
 void toUnitCell(Point3f pt, Point3f offset)
          relative to origin without regard to UNITCELL {x y z}
 Point3i transformPoint(Point3f pointAngstroms)
           
 void transformPoint(Point3f pointAngstroms, Point3f pointScreen)
           
 void transformPoint(Point3f pointAngstroms, Point3i pointScreen)
           
 Point3i transformPoint(Point3f pointAngstroms, Vector3f vibrationVector)
           
 void transformPointNoClip(Point3f pointAngstroms, Point3f pt)
           
 void transformPoints(Point3f[] pointsAngstroms, Point3i[] pointsScreens)
           
 void transformVector(Vector3f vectorAngstroms, Vector3f vectorTransformed)
           
 void translate(char xyz, float x, char type, BitSet bsAtoms)
           
 void translateXYBy(int xDelta, int yDelta)
           
 void triggerTimeout(String name)
           
 void unBindAction(String desc, String name)
           
(package private)  void undoClear()
           
 void undoMoveAction(int action, int n)
           
(package private)  void undoMoveAction(int taintedAtom, int type, boolean clearRedo)
           
 float unscaleToScreen(float z, float screenDistance)
           
 void unsetProperty(String name)
           
 void unTransformPoint(Point3f pointScreen, Point3f pointAngstroms)
           
(package private)  boolean useArcBall()
           
 boolean useMinimizationThread()
           
 boolean usingScriptQueue()
           
 boolean waitForMoveTo()
           
 String writeCurrentFile(OutputStream os)
           
 void writeTextFile(String fileName, String data)
           
 void zap(boolean notify, boolean resetUndo, boolean zapModelKit)
           
private  void zap(String msg)
           
(package private)  void zoomBy(int pixels)
           
(package private)  void zoomByFactor(float factor, int x, int y)
           
 int zValueFromPercent(int zPercent)
           
 
Methods inherited from class org.jmol.api.JmolViewer
allocateViewer, checkOption, getBooleanProperty, renderScreenImage, setConsole
 
Methods inherited from class org.jmol.api.JmolSimpleViewer
allocateSimpleViewer
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

display

private Object display

g3d

private Graphics3D g3d

modelAdapter

private JmolAdapter modelAdapter

commandHistory

private CommandHistory commandHistory

colorManager

private ColorManager colorManager

compiler

public ScriptCompiler compiler

definedAtomSets

public Map<String,Object> definedAtomSets

symmetry

private SymmetryInterface symmetry

smilesMatcher

private SmilesMatcherInterface smilesMatcher

eval

ScriptEvaluator eval

animationManager

private AnimationManager animationManager

dataManager

private DataManager dataManager

fileManager

private FileManager fileManager

actionManager

private ActionManager actionManager

shapeManager

private ShapeManager shapeManager

modelManager

private ModelManager modelManager

modelSet

private ModelSet modelSet

repaintManager

private RepaintManager repaintManager

scriptManager

private ScriptManager scriptManager

selectionManager

private SelectionManager selectionManager

stateManager

private StateManager stateManager

global

private StateManager.GlobalSettings global

statusManager

private StatusManager statusManager

tempManager

private TempArray tempManager

transformManager

private TransformManager transformManager

strJavaVendor

private String strJavaVendor

strJavaVersion

private String strJavaVersion

strOSName

private String strOSName

htmlName

private String htmlName

fullName

private String fullName

syncId

private String syncId

appletDocumentBase

private String appletDocumentBase

appletCodeBase

private String appletCodeBase

logFilePath

private String logFilePath

multiTouch

private boolean multiTouch

isSilent

private boolean isSilent

isApplet

private boolean isApplet

isPreviewOnly

private boolean isPreviewOnly

haveDisplay

public boolean haveDisplay

autoExit

public boolean autoExit

mustRender

private boolean mustRender

isPrintOnly

private boolean isPrintOnly

isCmdLine_C_Option

private boolean isCmdLine_C_Option

isCmdLine_c_or_C_Option

private boolean isCmdLine_c_or_C_Option

listCommands

private boolean listCommands

useCommandThread

private boolean useCommandThread

isSignedApplet

private boolean isSignedApplet

isSignedAppletLocal

private boolean isSignedAppletLocal

isDataOnly

private boolean isDataOnly

appletContext

private String appletContext

mouseEnabled

private boolean mouseEnabled

noneSelected

private boolean noneSelected

ligandModels

private Map<String,Object> ligandModels

ligandModelSet

private Map<String,Boolean> ligandModelSet

STATE_VERSION_STAMP

public static final String STATE_VERSION_STAMP
See Also:
Constant Field Values

bsFrameOffsets

BitSet bsFrameOffsets

frameOffsets

Point3f[] frameOffsets

wasInMotion

boolean wasInMotion

motionEventNumber

int motionEventNumber

refreshing

private boolean refreshing

axesAreTainted

private boolean axesAreTainted

dimScreen

final Dimension dimScreen

maximumSize

private int maximumSize

imageFontScaling

private float imageFontScaling

antialiasDisplay

private boolean antialiasDisplay

interruptScript

String interruptScript

scriptIndex

int scriptIndex

isScriptQueued

boolean isScriptQueued

hoverAtomIndex

int hoverAtomIndex

hoverText

String hoverText

hoverEnabled

boolean hoverEnabled

currentCursor

private int currentCursor

prevFrame

int prevFrame

language

private String language

rd

private RadiusData rd

frankOn

private boolean frankOn

scriptEditorVisible

private boolean scriptEditorVisible

appConsole

JmolAppConsoleInterface appConsole

scriptEditor

JmolScriptEditorInterface scriptEditor

jmolpopup

JmolPopupInterface jmolpopup

modelkit

private JmolModelKitInterface modelkit

isTainted

boolean isTainted

movingSelected

private boolean movingSelected

showSelected

private boolean showSelected

rotateBondIndex

private int rotateBondIndex

rotatePrev1

private int rotatePrev1

rotatePrev2

private int rotatePrev2

bsRotateBranch

private BitSet bsRotateBranch

creatingImage

private boolean creatingImage

SYNC_GRAPHICS_MESSAGE

public static final String SYNC_GRAPHICS_MESSAGE
See Also:
Constant Field Values

SYNC_NO_GRAPHICS_MESSAGE

public static final String SYNC_NO_GRAPHICS_MESSAGE
See Also:
Constant Field Values

errorMessage

private String errorMessage

errorMessageUntranslated

private String errorMessageUntranslated

currentShapeID

private int currentShapeID

currentShapeState

private String currentShapeState

privateKey

private double privateKey

logFile

private String logFile

isKiosk

private boolean isKiosk

minimizer

private MinimizerInterface minimizer

executor

private Object executor

nProcessors

public static int nProcessors

displayLoadErrors

boolean displayLoadErrors

isParallel

boolean isParallel

MAX_ACTION_UNDO

private static final int MAX_ACTION_UNDO
See Also:
Constant Field Values

actionStates

private final List<String> actionStates

actionStatesRedo

private final List<String> actionStatesRedo

undoWorking

private boolean undoWorking

stateScriptVersionInt

private int stateScriptVersionInt

htPdbBondInfo

Map<String,String[][]> htPdbBondInfo
Constructor Detail

Viewer

private Viewer(Object display,
               JmolAdapter modelAdapter,
               String commandOptions)
Method Detail

finalize

protected void finalize()
                 throws Throwable
Overrides:
finalize in class Object
Throws:
Throwable

getModelAdapter

public JmolAdapter getModelAdapter()
Specified by:
getModelAdapter in class JmolViewer

getSymmetry

public SymmetryInterface getSymmetry()

getSymmetryInfo

public Object getSymmetryInfo(BitSet bsAtoms,
                              String xyz,
                              int op,
                              Point3f pt,
                              Point3f pt2,
                              String id,
                              int type)

clearModelDependentObjects

private void clearModelDependentObjects()

getSmilesMatcher

public SmilesMatcherInterface getSmilesMatcher()

getSmartsMatch

public BitSet getSmartsMatch(String smarts,
                             BitSet bsSelected)
Specified by:
getSmartsMatch in class JmolViewer

getGlobalSettings

StateManager.GlobalSettings getGlobalSettings()

getStatusManager

StatusManager getStatusManager()

getApiPlatform

public ApiPlatform getApiPlatform()

allocateViewer

public static JmolViewer allocateViewer(Object display,
                                        JmolAdapter modelAdapter,
                                        String fullName,
                                        URL documentBase,
                                        URL codeBase,
                                        String commandOptions,
                                        JmolStatusListener statusListener)
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.

Parameters:
display - either DisplayPanel or WrappedApplet
modelAdapter - the model reader
fullName - or null
documentBase - or null
codeBase - or null
commandOptions - or null
statusListener - or null
Returns:
a viewer instance

isApplet

public boolean isApplet()
Specified by:
isApplet in class JmolViewer

isPreviewOnly

public boolean isPreviewOnly()

getAppletContext

public String getAppletContext()

setAppletContext

public void setAppletContext(String fullName,
                             URL documentBase,
                             URL codeBase,
                             String commandOptions)
Specified by:
setAppletContext in class JmolViewer

isDataOnly

public boolean isDataOnly()

getJmolVersion

public static String getJmolVersion()

getExportDriverList

public String getExportDriverList()

getHtmlName

String getHtmlName()

mustRenderFlag

boolean mustRenderFlag()

getDisplay

public Object getDisplay()
Specified by:
getDisplay in class JmolViewer

handleOldJvm10Event

public boolean handleOldJvm10Event(int id,
                                   int x,
                                   int y,
                                   int modifiers,
                                   long time)
Specified by:
handleOldJvm10Event in class JmolViewer

reset

public void reset(boolean includingSpin)

homePosition

public void homePosition()
Specified by:
homePosition in class JmolViewer

getAppletInfo

Map<String,Object> getAppletInfo()

initialize

public void initialize(boolean clearUserVariables)

listSavedStates

public String listSavedStates()

saveOrientation

public void saveOrientation(String saveName)

restoreOrientation

public boolean restoreOrientation(String saveName,
                                  float timeSeconds)

restoreRotation

public void restoreRotation(String saveName,
                            float timeSeconds)

saveModelOrientation

void saveModelOrientation()

getOrientation

public StateManager.Orientation getOrientation()

getSavedOrienationText

public String getSavedOrienationText(String name)

restoreModelOrientation

void restoreModelOrientation(int modelIndex)

restoreModelRotation

void restoreModelRotation(int modelIndex)

saveBonds

public void saveBonds(String saveName)

restoreBonds

public boolean restoreBonds(String saveName)

saveState

public void saveState(String saveName)

deleteSavedState

public void deleteSavedState(String saveName)

getSavedState

public String getSavedState(String saveName)

saveStructure

public void saveStructure(String saveName)

getSavedStructure

public String getSavedStructure(String saveName)

saveCoordinates

public void saveCoordinates(String saveName,
                            BitSet bsSelected)

getSavedCoordinates

public String getSavedCoordinates(String saveName)

saveSelection

public void saveSelection(String saveName)

restoreSelection

public boolean restoreSelection(String saveName)

getMatrixtransform

public Matrix4f getMatrixtransform()

getRotationQuaternion

public Quaternion getRotationQuaternion()

getRotationRadius

public float getRotationRadius()
Specified by:
getRotationRadius in class JmolViewer

setRotationRadius

public void setRotationRadius(float angstroms,
                              boolean doAll)

getRotationCenter

public Point3f getRotationCenter()

setCenterAt

public void setCenterAt(String relativeTo,
                        Point3f pt)

setCenterBitSet

public void setCenterBitSet(BitSet bsCenter,
                            boolean doScale)

setNewRotationCenter

public void setNewRotationCenter(Point3f center)

getNavigationCenter

public Point3f getNavigationCenter()

getNavigationDepthPercent

public float getNavigationDepthPercent()

navigate

void navigate(int keyWhere,
              int modifiers)

getNavigationOffset

public Point3f getNavigationOffset()

getNavigationOffsetPercent

float getNavigationOffsetPercent(char XorY)

isNavigating

public boolean isNavigating()

isInPosition

public boolean isInPosition(Vector3f axis,
                            float degrees)

move

public void move(Vector3f dRot,
                 float dZoom,
                 Vector3f dTrans,
                 float dSlab,
                 float floatSecondsTotal,
                 int fps)

waitForMoveTo

public boolean waitForMoveTo()

stopMotion

public void stopMotion()

setRotationMatrix

void setRotationMatrix(Matrix3f rotationMatrix)

moveTo

public void moveTo(float floatSecondsTotal,
                   Point3f center,
                   Vector3f rotAxis,
                   float degrees,
                   Matrix3f rotationMatrix,
                   float zoom,
                   float xTrans,
                   float yTrans,
                   float rotationRadius,
                   Point3f navCenter,
                   float xNav,
                   float yNav,
                   float navDepth)

moveUpdate

private void moveUpdate(float floatSecondsTotal)

getMoveToText

String getMoveToText(float timespan)

navigate

public void navigate(float timeSeconds,
                     Point3f[] path,
                     float[] theta,
                     int indexStart,
                     int indexEnd)

navigate

public void navigate(float timeSeconds,
                     Point3f center)

navigate

public void navigate(float timeSeconds,
                     Point3f[][] pathGuide)

navigateSurface

public void navigateSurface(float timeSeconds,
                            String name)

navigate

public void navigate(float timeSeconds,
                     Vector3f rotAxis,
                     float degrees)

navTranslate

public void navTranslate(float timeSeconds,
                         Point3f center)

navTranslatePercent

public void navTranslatePercent(float timeSeconds,
                                float x,
                                float y)

setMouseEnabled

public void setMouseEnabled(boolean TF)

processEvent

public void processEvent(int groupID,
                         int eventType,
                         int touchID,
                         int iData,
                         Point3f pt,
                         long time)
Specified by:
processEvent in class JmolViewer

zoomBy

void zoomBy(int pixels)

zoomByFactor

void zoomByFactor(float factor,
                  int x,
                  int y)

rotateXYBy

void rotateXYBy(float xDelta,
                float yDelta)

spinXYBy

public void spinXYBy(int xDelta,
                     int yDelta,
                     float speed)

rotateZBy

public void rotateZBy(int zDelta,
                      int x,
                      int y)

rotateSelected

void rotateSelected(float deltaX,
                    float deltaY,
                    BitSet bsSelected)

setMovableBitSet

private BitSet setMovableBitSet(BitSet bsSelected,
                                boolean checkMolecule)

translateXYBy

public void translateXYBy(int xDelta,
                          int yDelta)

centerAt

void centerAt(int x,
              int y,
              Point3f pt)

rotateFront

public void rotateFront()
Specified by:
rotateFront in class JmolViewer

rotateX

public void rotateX(float angleRadians)
Specified by:
rotateX in class JmolViewer

rotateY

public void rotateY(float angleRadians)
Specified by:
rotateY in class JmolViewer

rotateZ

public void rotateZ(float angleRadians)
Specified by:
rotateZ in class JmolViewer

rotateX

public void rotateX(int angleDegrees)
Specified by:
rotateX in class JmolViewer

rotateY

public void rotateY(int angleDegrees)
Specified by:
rotateY in class JmolViewer

translate

public void translate(char xyz,
                      float x,
                      char type,
                      BitSet bsAtoms)

getTranslationXPercent

public float getTranslationXPercent()

getTranslationYPercent

public float getTranslationYPercent()

getTranslationZPercent

float getTranslationZPercent()

getTranslationScript

public String getTranslationScript()

getZoomPercent

public int getZoomPercent()
Specified by:
getZoomPercent in class JmolViewer

getZoomSetting

public float getZoomSetting()

getZoomPercentFloat

public float getZoomPercentFloat()
Specified by:
getZoomPercentFloat in class JmolViewer

getMaxZoomPercent

public float getMaxZoomPercent()

slabReset

public void slabReset()

getZoomEnabled

public boolean getZoomEnabled()

getSlabEnabled

public boolean getSlabEnabled()

getSlabByMolecule

public boolean getSlabByMolecule()

getSlabByAtom

public boolean getSlabByAtom()

slabByPixels

void slabByPixels(int pixels)

depthByPixels

void depthByPixels(int pixels)

slabDepthByPixels

void slabDepthByPixels(int pixels)

slabInternal

public void slabInternal(Point4f plane,
                         boolean isDepth)

slabToPercent

public void slabToPercent(int percentSlab)

depthToPercent

public void depthToPercent(int percentDepth)

setSlabDepthInternal

public void setSlabDepthInternal(boolean isDepth)

zValueFromPercent

public int zValueFromPercent(int zPercent)

getUnscaledTransformMatrix

public Matrix4f getUnscaledTransformMatrix()
Specified by:
getUnscaledTransformMatrix in class JmolViewer

finalizeTransformParameters

void finalizeTransformParameters()

rotatePoint

public void rotatePoint(Point3f pt,
                        Point3f ptRot)

transformPoint

public Point3i transformPoint(Point3f pointAngstroms)

transformPoint

public Point3i transformPoint(Point3f pointAngstroms,
                              Vector3f vibrationVector)

transformPoint

public void transformPoint(Point3f pointAngstroms,
                           Point3i pointScreen)

transformPointNoClip

public void transformPointNoClip(Point3f pointAngstroms,
                                 Point3f pt)

transformPoint

public void transformPoint(Point3f pointAngstroms,
                           Point3f pointScreen)

transformPoints

public void transformPoints(Point3f[] pointsAngstroms,
                            Point3i[] pointsScreens)

transformVector

public void transformVector(Vector3f vectorAngstroms,
                            Vector3f vectorTransformed)

unTransformPoint

public void unTransformPoint(Point3f pointScreen,
                             Point3f pointAngstroms)

getScalePixelsPerAngstrom

public float getScalePixelsPerAngstrom(boolean asAntialiased)

scaleToScreen

public short scaleToScreen(int z,
                           int milliAngstroms)

unscaleToScreen

public float unscaleToScreen(float z,
                             float screenDistance)

scaleToPerspective

public float scaleToPerspective(int z,
                                float sizeAngstroms)

setSpin

public void setSpin(String key,
                    int value)

getSpinState

public String getSpinState()

setSpinOn

public void setSpinOn(boolean spinOn)

getSpinOn

boolean getSpinOn()

setNavOn

public void setNavOn(boolean navOn)

getNavOn

boolean getNavOn()

setNavXYZ

public void setNavXYZ(float x,
                      float y,
                      float z)

getOrientationText

public String getOrientationText(int type,
                                 String name)

getOrientationInfo

Map<String,Object> getOrientationInfo()

getMatrixRotate

Matrix3f getMatrixRotate()

getAxisAngle

public void getAxisAngle(AxisAngle4f axisAngle)

getTransformText

public String getTransformText()

getRotation

void getRotation(Matrix3f matrixRotation)

getCurrentColorRange

public float[] getCurrentColorRange()

setDefaultColors

private void setDefaultColors(boolean isRasmol)

getDefaultTranslucent

public float getDefaultTranslucent()

getColorArgbOrGray

public int getColorArgbOrGray(short colix)

setRubberbandArgb

public void setRubberbandArgb(int argb)

getColixRubberband

public short getColixRubberband()

setElementArgb

public void setElementArgb(int elementNumber,
                           int argb)

getVectorScale

public float getVectorScale()

setVectorScale

public void setVectorScale(float scale)
Specified by:
setVectorScale in class JmolViewer

getDefaultDrawArrowScale

public float getDefaultDrawArrowScale()

getVibrationScale

float getVibrationScale()

getVibrationPeriod

public float getVibrationPeriod()

isVibrationOn

public boolean isVibrationOn()

setVibrationScale

public void setVibrationScale(float scale)
Specified by:
setVibrationScale in class JmolViewer

setVibrationOff

public void setVibrationOff()

setVibrationPeriod

public void setVibrationPeriod(float period)
Specified by:
setVibrationPeriod in class JmolViewer

setObjectColor

void setObjectColor(String name,
                    String colorName)

setObjectArgb

public void setObjectArgb(String name,
                          int argb)

setBackgroundImage

public void setBackgroundImage(String fileName,
                               Object image)

getObjectArgb

int getObjectArgb(int objId)

getObjectColix

public short getObjectColix(int objId)

getObjectState

public String getObjectState(String name)

setColorBackground

public void setColorBackground(String colorName)
Specified by:
setColorBackground in class JmolViewer

getBackgroundArgb

public int getBackgroundArgb()
Specified by:
getBackgroundArgb in class JmolViewer

setObjectMad

public void setObjectMad(int iShape,
                         String name,
                         int mad)

getObjectMad

public int getObjectMad(int objId)

setPropertyColorScheme

public void setPropertyColorScheme(String scheme,
                                   boolean isTranslucent,
                                   boolean isOverloaded)

getPropertyColorScheme

public String getPropertyColorScheme()

getColixBackgroundContrast

public short getColixBackgroundContrast()

getSpecularState

public String getSpecularState()

getColixAtomPalette

public short getColixAtomPalette(Atom atom,
                                 byte pid)

getColixBondPalette

public short getColixBondPalette(Bond bond,
                                 int pid)

getColorSchemeList

public String getColorSchemeList(String colorScheme)

setUserScale

public void setUserScale(int[] scale)

getColixForPropertyValue

public short getColixForPropertyValue(float val)

getColorPointForPropertyValue

public Point3f getColorPointForPropertyValue(float val)

select

public void select(BitSet bs,
                   boolean isGroup,
                   Boolean addRemove,
                   boolean isQuiet)

setSelectionSet

public void setSelectionSet(BitSet set)
Specified by:
setSelectionSet in class JmolViewer

selectBonds

public void selectBonds(BitSet bs)

display

public void display(BitSet bs,
                    boolean isDisplay,
                    boolean isGroup,
                    Boolean addRemove,
                    boolean isQuiet)

getUndeletedGroupAtomBits

private BitSet getUndeletedGroupAtomBits(BitSet bs)

getHiddenSet

public BitSet getHiddenSet()

isSelected

public boolean isSelected(int atomIndex)

isInSelectionSubset

boolean isInSelectionSubset(int atomIndex)

reportSelection

void reportSelection(String msg)

getAtomSetCenter

public Point3f getAtomSetCenter(BitSet bs)

clearAtomSets

private void clearAtomSets()

selectAll

public void selectAll()
Specified by:
selectAll in class JmolViewer

setNoneSelected

public void setNoneSelected(boolean noneSelected)

getNoneSelected

public Boolean getNoneSelected()

clearSelection

public void clearSelection()
Specified by:
clearSelection in class JmolViewer

setSelectionSubset

public void setSelectionSubset(BitSet subset)

getSelectionSubset

public BitSet getSelectionSubset()

invertSelection

public void invertSelection()

getSelectionSet

public BitSet getSelectionSet(boolean includeDeleted)

setSelectedAtom

public void setSelectedAtom(int atomIndex,
                            boolean TF)

isAtomSelected

public boolean isAtomSelected(int atomIndex)

getSelectionCount

public int getSelectionCount()
Specified by:
getSelectionCount in class JmolViewer

setFormalCharges

public void setFormalCharges(int formalCharge)

addSelectionListener

public void addSelectionListener(JmolSelectionListener listener)
Specified by:
addSelectionListener in class JmolViewer

removeSelectionListener

public void removeSelectionListener(JmolSelectionListener listener)
Specified by:
removeSelectionListener in class JmolViewer

getAtomBitSet

BitSet getAtomBitSet(ScriptEvaluator eval,
                     Object atomExpression)

getAtomBitSet

public BitSet getAtomBitSet(Object atomExpression)

getAtomBitSetVector

List<Integer> getAtomBitSetVector(Object atomExpression)

setModeMouse

public void setModeMouse(int modeMouse)
Specified by:
setModeMouse in class JmolViewer

getRubberBandSelection

Rectangle getRubberBandSelection()

isBound

public boolean isBound(int action,
                       int gesture)

getCursorX

public int getCursorX()

getCursorY

public int getCursorY()

getDefaultDirectory

String getDefaultDirectory()

getBufferedInputStream

public BufferedInputStream getBufferedInputStream(String fullPathName)
Specified by:
getBufferedInputStream in interface AtomDataServer

getBufferedReaderOrErrorMessageFromName

public Object getBufferedReaderOrErrorMessageFromName(String name,
                                                      String[] fullPathNameReturn,
                                                      boolean isBinary)

setLoadParameters

private Map<String,Object> setLoadParameters(Map<String,Object> htParams,
                                             boolean isAppend)

openFileAsynchronously

public void openFileAsynchronously(String fileName)
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

Specified by:
openFileAsynchronously in class JmolViewer
Parameters:
fileName -

openFile

public String openFile(String fileName)
for JmolSimpleViewer -- external applications only

Specified by:
openFile in class JmolSimpleViewer
Parameters:
fileName -
Returns:
null or error

openFiles

public String openFiles(String[] fileNames)
for JmolSimpleViewer -- external applications only

Specified by:
openFiles in class JmolSimpleViewer
Parameters:
fileNames -
Returns:
null or error

openReader

public String openReader(String fullPathName,
                         String fileName,
                         Reader reader)
Opens the file, given an already-created reader.

Specified by:
openReader in class JmolViewer
Parameters:
fullPathName -
fileName -
reader -
Returns:
null or error message

openDOM

public String openDOM(Object DOMNode)
applet DOM method -- does not preserve state

Specified by:
openDOM in class JmolSimpleViewer
Parameters:
DOMNode -
Returns:
null or error

loadModelFromFile

public String loadModelFromFile(String fullPathName,
                                String fileName,
                                String[] fileNames,
                                Object reader,
                                boolean isAppend,
                                Map<String,Object> htParams,
                                StringBuffer loadScript,
                                int tokType)
Used by the ScriptEvaluator LOAD command to open one or more files. Now necessary for EVERY load of a file, as loadScript must be passed to the ModelLoader.

Parameters:
fullPathName - TODO
fileName -
fileNames -
reader - TODO
isAppend -
htParams -
loadScript -
tokType -
Returns:
null or error

setLigandModel

public void setLigandModel(String id,
                           String data)

getLigandModel

public Object getLigandModel(String id)
obtain CIF data for a ligand for purposes of adding hydrogens

Parameters:
id - if null, clear "bad" entries from the set.
Returns:
a ligand model or null

getAtomSetCollection

private Object getAtomSetCollection(String fileName,
                                    boolean isAppend,
                                    Map<String,Object> htParams,
                                    StringBuffer loadScript)
Parameters:
fileName -
isAppend -
htParams -
loadScript - only necessary for string reading
Returns:
an AtomSetCollection or a String (error)

openStringInline

public String openStringInline(String strModel)
Specified by:
openStringInline in class JmolSimpleViewer

loadInline

public String loadInline(String strModel)
Specified by:
loadInline in class JmolViewer

loadInline

public String loadInline(String strModel,
                         char newLine)
Specified by:
loadInline in class JmolViewer

loadInline

public String loadInline(String strModel,
                         boolean isAppend)
Specified by:
loadInline in class JmolViewer

loadInline

public String loadInline(String[] arrayModels)
Specified by:
loadInline in class JmolViewer

loadInline

public String loadInline(String[] arrayModels,
                         boolean isAppend)
Specified by:
loadInline in class JmolViewer
Parameters:
arrayModels - and array of models, each of which is a String
Returns:
null or error message

loadInline

public String loadInline(List<Object> arrayData,
                         boolean isAppend)
does not preserver state, intentionally!

Specified by:
loadInline in class JmolViewer
Parameters:
arrayData -
isAppend -
Returns:
null or error string

loadInline

public String loadInline(String strModel,
                         char newLine,
                         boolean isAppend,
                         Map<String,Object> htParams)

fixInlineString

public String fixInlineString(String strModel,
                              char newLine)

openStringInline

private String openStringInline(String strModel,
                                Map<String,Object> htParams,
                                boolean isAppend)

openStringsInline

private String openStringsInline(String[] arrayModels,
                                 Map<String,Object> htParams,
                                 boolean isAppend)

getInlineChar

public char getInlineChar()

getDataSeparator

String getDataSeparator()

createModelSetAndReturnError

private String createModelSetAndReturnError(Object atomSetCollection,
                                            boolean isAppend,
                                            StringBuffer loadScript)
finally(!) we are ready to create the "model set" from the "atom set collection"

Parameters:
atomSetCollection -
isAppend -
loadScript - if null, then some special method like DOM; turn of preserveState
Returns:
errMsg

loadAtomDataAndReturnError

private String loadAtomDataAndReturnError(Object atomSetCollection,
                                          int tokType)
or just apply the data to the current model set

Parameters:
atomSetCollection -
tokType -
Returns:
error or null

writeCurrentFile

public String writeCurrentFile(OutputStream os)

getFileAsBytes

public Object getFileAsBytes(String pathName,
                             OutputStream os)
Specified by:
getFileAsBytes in class JmolViewer

getCurrentFileAsString

public String getCurrentFileAsString()

getFullPathName

public String getFullPathName()

getFileName

public String getFileName()

getFullPathNameOrError

public String[] getFullPathNameOrError(String filename)
Parameters:
filename -
Returns:
String[2] where [0] is fullpathname and [1] is error message or null

getFileAsString

public String getFileAsString(String name)
Specified by:
getFileAsString in class JmolViewer

getFileAsString

public String getFileAsString(String name,
                              int nBytesMax,
                              boolean doSpecialLoad)

getFilePath

public String getFilePath(String name,
                          boolean asShortName)

getFileAsString

public boolean getFileAsString(String[] data,
                               int nBytesMax,
                               boolean doSpecialLoad)
Specified by:
getFileAsString in class JmolViewer

getFileInfo

public String[] getFileInfo()

setFileInfo

public void setFileInfo(String[] fileInfo)

autoCalculate

public void autoCalculate(int tokProperty)

getVolume

public float getVolume(BitSet bs,
                       String type)

getSurfaceDistanceMax

int getSurfaceDistanceMax()

calculateStraightness

public void calculateStraightness()

calculateSurface

public Point3f[] calculateSurface(BitSet bsSelected,
                                  float envelopeRadius)

getStructureList

public Map<EnumStructure,float[]> getStructureList()

setStructureList

public void setStructureList(float[] list,
                             EnumStructure type)

getDefaultStructureDSSP

public boolean getDefaultStructureDSSP()

getDefaultStructure

public String getDefaultStructure(BitSet bsAtoms,
                                  BitSet bsAllAtoms)

calculateStructures

public String calculateStructures(BitSet bsAtoms,
                                  boolean asDSSP,
                                  boolean setStructure)

getSelectedAtomIterator

public AtomIndexIterator getSelectedAtomIterator(BitSet bsSelected,
                                                 boolean isGreaterOnly,
                                                 boolean modelZeroBased,
                                                 boolean isMultiModel)
Specified by:
getSelectedAtomIterator in interface AtomDataServer

setIteratorForAtom

public void setIteratorForAtom(AtomIndexIterator iterator,
                               int atomIndex,
                               float distance)
Specified by:
setIteratorForAtom in interface AtomDataServer

setIteratorForPoint

public void setIteratorForPoint(AtomIndexIterator iterator,
                                int modelIndex,
                                Point3f pt,
                                float distance)
Specified by:
setIteratorForPoint in interface AtomDataServer

fillAtomData

public void fillAtomData(AtomData atomData,
                         int mode)
Specified by:
fillAtomData in interface AtomDataServer

addStateScript

public ModelCollection.StateScript addStateScript(String script,
                                                  boolean addFrameNumber,
                                                  boolean postDefinitions)

addStateScript

public ModelCollection.StateScript addStateScript(String script1,
                                                  BitSet bsBonds,
                                                  BitSet bsAtoms1,
                                                  BitSet bsAtoms2,
                                                  String script2,
                                                  boolean addFrameNumber,
                                                  boolean postDefinitions)

getEchoStateActive

public boolean getEchoStateActive()

setEchoStateActive

public void setEchoStateActive(boolean TF)

zap

public void zap(boolean notify,
                boolean resetUndo,
                boolean zapModelKit)

zap

private void zap(String msg)

echoMessage

void echoMessage(String msg)

initializeModel

private void initializeModel(boolean isAppend)

getModelSetName

public String getModelSetName()
Specified by:
getModelSetName in class JmolViewer

getModelSetFileName

public String getModelSetFileName()
Specified by:
getModelSetFileName in class JmolViewer

getUnitCellInfoText

public String getUnitCellInfoText()

getUnitCellInfo

public float getUnitCellInfo(int infoType)

getSpaceGroupInfo

public Map<String,Object> getSpaceGroupInfo(String spaceGroup)

getPolymerPointsAndVectors

public void getPolymerPointsAndVectors(BitSet bs,
                                       List<Point3f[]> vList)

getModelSetProperty

public String getModelSetProperty(String strProp)

getModelSetAuxiliaryInfo

public Object getModelSetAuxiliaryInfo(String strKey)

getModelSetPathName

public String getModelSetPathName()
Specified by:
getModelSetPathName in class JmolViewer

getModelSetTypeName

public String getModelSetTypeName()

haveFrame

public boolean haveFrame()
Specified by:
haveFrame in class JmolViewer

haveModelSet

boolean haveModelSet()

clearBfactorRange

public void clearBfactorRange()

getHybridizationAndAxes

public String getHybridizationAndAxes(int atomIndex,
                                      Vector3f z,
                                      Vector3f x,
                                      String lcaoType)

getMoleculeBitSet

public BitSet getMoleculeBitSet(int atomIndex)

getModelUndeletedAtomsBitSet

public BitSet getModelUndeletedAtomsBitSet(int modelIndex)

getModelUndeletedAtomsBitSet

public BitSet getModelUndeletedAtomsBitSet(BitSet bsModels)

excludeAtoms

public void excludeAtoms(BitSet bs,
                         boolean ignoreSubset)

getModelBitSet

public BitSet getModelBitSet(BitSet atomList,
                             boolean allTrajectories)

getModelSet

public ModelSet getModelSet()

getBoundBoxCommand

public String getBoundBoxCommand(boolean withOptions)

setBoundBox

public void setBoundBox(Point3f pt1,
                        Point3f pt2,
                        boolean byCorner,
                        float scale)

getBoundBoxCenter

public Point3f getBoundBoxCenter()
Specified by:
getBoundBoxCenter in class JmolViewer

getAverageAtomPoint

Point3f getAverageAtomPoint()

calcBoundBoxDimensions

public void calcBoundBoxDimensions(BitSet bs,
                                   float scale)

getBoxInfo

public BoxInfo getBoxInfo(BitSet bs,
                          float scale)

calcRotationRadius

float calcRotationRadius(Point3f center)

calcRotationRadius

public float calcRotationRadius(BitSet bs)

getBoundBoxCornerVector

public Vector3f getBoundBoxCornerVector()
Specified by:
getBoundBoxCornerVector in class JmolViewer

getBoundBoxVertices

public Point3f[] getBoundBoxVertices()

getBoundBoxInfo

Map<String,Object> getBoundBoxInfo()

getBoundBoxModels

public BitSet getBoundBoxModels()

getBoundBoxCenterX

public int getBoundBoxCenterX()

getBoundBoxCenterY

public int getBoundBoxCenterY()

getModelCount

public int getModelCount()
Specified by:
getModelCount in class JmolViewer

getModelInfoAsString

public String getModelInfoAsString()

getSymmetryInfoAsString

public String getSymmetryInfoAsString()

getSymmetryOperation

public String getSymmetryOperation(String spaceGroup,
                                   int symop,
                                   Point3f pt1,
                                   Point3f pt2,
                                   boolean labelOnly)

getModelSetProperties

public Properties getModelSetProperties()
Specified by:
getModelSetProperties in class JmolViewer

getModelSetAuxiliaryInfo

public Map<String,Object> getModelSetAuxiliaryInfo()
Specified by:
getModelSetAuxiliaryInfo in class JmolViewer

getModelNumber

public int getModelNumber(int modelIndex)
Specified by:
getModelNumber in class JmolViewer

getModelFileNumber

public int getModelFileNumber(int modelIndex)

getModelNumberDotted

public String getModelNumberDotted(int modelIndex)
Specified by:
getModelNumberDotted in class JmolViewer

getModelName

public String getModelName(int modelIndex)
Specified by:
getModelName in class JmolViewer

getModelProperties

public Properties getModelProperties(int modelIndex)
Specified by:
getModelProperties in class JmolViewer

getModelProperty

public String getModelProperty(int modelIndex,
                               String propertyName)
Specified by:
getModelProperty in class JmolViewer

getModelFileInfo

public String getModelFileInfo()

getModelFileInfoAll

public String getModelFileInfoAll()

getModelAuxiliaryInfo

public Map<String,Object> getModelAuxiliaryInfo(int modelIndex)
Specified by:
getModelAuxiliaryInfo in class JmolViewer

getModelAuxiliaryInfo

public Object getModelAuxiliaryInfo(int modelIndex,
                                    String keyName)
Specified by:
getModelAuxiliaryInfo in class JmolViewer

getModelNumberIndex

public int getModelNumberIndex(int modelNumber,
                               boolean useModelNumber,
                               boolean doSetTrajectory)

modelSetHasVibrationVectors

boolean modelSetHasVibrationVectors()

modelHasVibrationVectors

public boolean modelHasVibrationVectors(int modelIndex)
Specified by:
modelHasVibrationVectors in class JmolViewer

getChainCount

public int getChainCount()
Specified by:
getChainCount in class JmolViewer

getChainCountInModel

public int getChainCountInModel(int modelIndex)
Specified by:
getChainCountInModel in class JmolViewer

getChainCountInModel

public int getChainCountInModel(int modelIndex,
                                boolean countWater)

getGroupCount

public int getGroupCount()
Specified by:
getGroupCount in class JmolViewer

getGroupCountInModel

public int getGroupCountInModel(int modelIndex)
Specified by:
getGroupCountInModel in class JmolViewer

getPolymerCount

public int getPolymerCount()
Specified by:
getPolymerCount in class JmolViewer

getPolymerCountInModel

public int getPolymerCountInModel(int modelIndex)
Specified by:
getPolymerCountInModel in class JmolViewer

getAtomCount

public int getAtomCount()
Specified by:
getAtomCount in class JmolViewer

getAtomCountInModel

public int getAtomCountInModel(int modelIndex)
Specified by:
getAtomCountInModel in class JmolViewer

getBondCount

public int getBondCount()
For use in setting a for() construct max value

Specified by:
getBondCount in class JmolViewer
Returns:
used size of the bonds array;

getBondCountInModel

public int getBondCountInModel(int modelIndex)
from JmolPopup.udateModelSetComputedMenu

Specified by:
getBondCountInModel in class JmolViewer
Parameters:
modelIndex - the model of interest or -1 for all
Returns:
the actual number of connections

getBondsForSelectedAtoms

public BitSet getBondsForSelectedAtoms(BitSet bsAtoms)

frankClicked

public boolean frankClicked(int x,
                            int y)

frankClickedModelKit

public boolean frankClickedModelKit(int x,
                                    int y)

findNearestAtomIndex

public int findNearestAtomIndex(int x,
                                int y)
Specified by:
findNearestAtomIndex in class JmolViewer

findNearestAtomIndex

public int findNearestAtomIndex(int x,
                                int y,
                                boolean mustBeMovable)

findAtomsInRectangle

BitSet findAtomsInRectangle(Rectangle rect)

toCartesian

public void toCartesian(Point3f pt,
                        boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z}

Parameters:
pt -
asAbsolute - TODO

toFractional

public void toFractional(Point3f pt,
                         boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z}

Parameters:
pt -
asAbsolute - TODO

toUnitCell

public void toUnitCell(Point3f pt,
                       Point3f offset)
relative to origin without regard to UNITCELL {x y z}

Parameters:
pt -
offset -

setCurrentUnitCellOffset

public void setCurrentUnitCellOffset(int ijk)

setCurrentUnitCellOffset

public void setCurrentUnitCellOffset(Point3f pt)

getFractionalRelative

public boolean getFractionalRelative()

addUnitCellOffset

public void addUnitCellOffset(Point3f pt)

setAtomData

public void setAtomData(int type,
                        String name,
                        String coordinateData,
                        boolean isDefault)

setCenterSelected

public void setCenterSelected()
Specified by:
setCenterSelected in class JmolViewer

getApplySymmetryToBonds

public boolean getApplySymmetryToBonds()

setApplySymmetryToBonds

void setApplySymmetryToBonds(boolean TF)

setBondTolerance

public void setBondTolerance(float bondTolerance)
Specified by:
setBondTolerance in class JmolViewer

getBondTolerance

public float getBondTolerance()
Specified by:
getBondTolerance in class JmolViewer

setMinBondDistance

public void setMinBondDistance(float minBondDistance)
Specified by:
setMinBondDistance in class JmolViewer

getMinBondDistance

public float getMinBondDistance()
Specified by:
getMinBondDistance in class JmolViewer

getAtomIndices

public int[] getAtomIndices(BitSet bs)

getAtomBits

public BitSet getAtomBits(int tokType,
                          Object specInfo)

getSequenceBits

public BitSet getSequenceBits(String specInfo,
                              BitSet bs)

getAtomsWithin

public BitSet getAtomsWithin(float distance,
                             Point3f coord)

getAtomsWithin

public BitSet getAtomsWithin(float distance,
                             Point3f[] points,
                             BitSet bsInclude)

getAtomsWithin

public BitSet getAtomsWithin(float distance,
                             Point4f plane)

getAtomsWithin

public BitSet getAtomsWithin(float distance,
                             BitSet bs,
                             boolean withinAllModels,
                             RadiusData rd)

getAtomsConnected

public BitSet getAtomsConnected(float min,
                                float max,
                                int intType,
                                BitSet bs)

getBranchBitSet

public BitSet getBranchBitSet(int atomIndex,
                              int atomIndexNot)

getAtomIndexFromAtomNumber

public int getAtomIndexFromAtomNumber(int atomNumber)

getElementsPresentBitSet

public BitSet getElementsPresentBitSet(int modelIndex)
Specified by:
getElementsPresentBitSet in class JmolViewer

getHeteroList

public Map<String,String> getHeteroList(int modelIndex)
Specified by:
getHeteroList in class JmolViewer

getVisibleSet

public BitSet getVisibleSet()

getClickableSet

public BitSet getClickableSet()

calcSelectedGroupsCount

public void calcSelectedGroupsCount()

calcSelectedMonomersCount

public void calcSelectedMonomersCount()

calcSelectedMoleculesCount

public void calcSelectedMoleculesCount()

getFileHeader

String getFileHeader()

getFileData

Object getFileData()

getCifData

public Map<String,Object> getCifData(int modelIndex)

getPDBHeader

public String getPDBHeader()

getModelInfo

public Map<String,Object> getModelInfo(Object atomExpression)

getLigandInfo

public Map<String,Object> getLigandInfo(Object atomExpression)

getAuxiliaryInfo

public Map<String,Object> getAuxiliaryInfo(Object atomExpression)

getAllAtomInfo

List<Map<String,Object>> getAllAtomInfo(Object atomExpression)

getAllBondInfo

List<Map<String,Object>> getAllBondInfo(Object atomExpression)

getMoleculeInfo

List<Map<String,Object>> getMoleculeInfo(Object atomExpression)

getChimeInfo

public String getChimeInfo(int tok)

getAllChainInfo

public Map<String,List<Map<String,Object>>> getAllChainInfo(Object atomExpression)

getAllPolymerInfo

public Map<String,List<Map<String,Object>>> getAllPolymerInfo(Object atomExpression)

getWrappedState

public String getWrappedState(boolean isImage,
                              int width,
                              int height)

getStateInfo

public String getStateInfo()
Specified by:
getStateInfo in class JmolViewer

getStateInfo

public String getStateInfo(String type,
                           int width,
                           int height)

getStructureState

public String getStructureState()

getProteinStructureState

public String getProteinStructureState()

getCoordinateState

public String getCoordinateState(BitSet bsSelected)

setCurrentColorRange

public void setCurrentColorRange(String label)

setCurrentColorRange

public void setCurrentColorRange(float[] data,
                                 BitSet bs)

setCurrentColorRange

public void setCurrentColorRange(float min,
                                 float max)

setData

public void setData(String type,
                    Object[] data,
                    int atomCount,
                    int matchField,
                    int matchFieldColumnCount,
                    int field,
                    int fieldColumnCount)

getData

public Object[] getData(String type)

getDataFloat

public float[] getDataFloat(String label)

getDataFloat2D

public float[][] getDataFloat2D(String label)

getDataFloat3D

public float[][][] getDataFloat3D(String label)

getDataFloat

public float getDataFloat(String label,
                          int atomIndex)

getAltLocListInModel

public String getAltLocListInModel(int modelIndex)
Specified by:
getAltLocListInModel in class JmolViewer

setConformation

public BitSet setConformation()

getConformation

public BitSet getConformation(int iModel,
                              int conformationIndex,
                              boolean doSet)

autoHbond

public int autoHbond(BitSet bsFrom,
                     BitSet bsTo)

getHbondsAngleMin

public float getHbondsAngleMin()

getHbondsDistanceMax

public float getHbondsDistanceMax()

getHbondsRasmol

public boolean getHbondsRasmol()

hasCalculatedHBonds

public boolean hasCalculatedHBonds(BitSet bsAtoms)

havePartialCharges

public boolean havePartialCharges()
Specified by:
havePartialCharges in class JmolViewer

getCurrentUnitCell

public SymmetryInterface getCurrentUnitCell()

getModelUnitCell

public SymmetryInterface getModelUnitCell(int modelIndex)

getDefaultMeasurementLabel

public String getDefaultMeasurementLabel(int nPoints)

getMeasurementCount

public int getMeasurementCount()
Specified by:
getMeasurementCount in class JmolViewer

getMeasurementStringValue

public String getMeasurementStringValue(int i)
Specified by:
getMeasurementStringValue in class JmolViewer

getMeasurementInfo

List<Map<String,Object>> getMeasurementInfo()

getMeasurementInfoAsString

public String getMeasurementInfoAsString()

getMeasurementCountPlusIndices

public int[] getMeasurementCountPlusIndices(int i)
Specified by:
getMeasurementCountPlusIndices in class JmolViewer

setPendingMeasurement

void setPendingMeasurement(MeasurementPending measurementPending)

getPendingMeasurement

MeasurementPending getPendingMeasurement()

clearAllMeasurements

public void clearAllMeasurements()

clearMeasurements

public void clearMeasurements()
Specified by:
clearMeasurements in class JmolViewer

getJustifyMeasurements

public boolean getJustifyMeasurements()

setAnimation

public void setAnimation(int tok)

setAnimationDirection

public void setAnimationDirection(int direction)

getAnimationDirection

int getAnimationDirection()

getAnimationInfo

Map<String,Object> getAnimationInfo()

setAnimationFps

public void setAnimationFps(int fps)
Specified by:
setAnimationFps in class JmolViewer

getAnimationFps

public int getAnimationFps()
Specified by:
getAnimationFps in class JmolViewer

setAnimationReplayMode

public void setAnimationReplayMode(EnumAnimationMode replayMode,
                                   float firstFrameDelay,
                                   float lastFrameDelay)

getAnimationReplayMode

EnumAnimationMode getAnimationReplayMode()

setAnimationOn

public void setAnimationOn(boolean animationOn)

setAnimationRange

public void setAnimationRange(int modelIndex1,
                              int modelIndex2)

getVisibleFramesBitSet

public BitSet getVisibleFramesBitSet()
Specified by:
getVisibleFramesBitSet in class JmolViewer

isAnimationOn

boolean isAnimationOn()

setCurrentModelIndex

public void setCurrentModelIndex(int modelIndex)

setTrajectory

void setTrajectory(int modelIndex)

setTrajectory

public void setTrajectory(BitSet bsModels)

isTrajectory

public boolean isTrajectory(int modelIndex)

getBitSetTrajectories

public BitSet getBitSetTrajectories()

getTrajectoryInfo

public String getTrajectoryInfo()

setFrameOffset

void setFrameOffset(int modelIndex)

setFrameOffsets

public void setFrameOffsets(BitSet bsAtoms)

getFrameOffsets

public BitSet getFrameOffsets()

setCurrentModelIndex

public void setCurrentModelIndex(int modelIndex,
                                 boolean clearBackground)

getCurrentModelIndex

public int getCurrentModelIndex()

getDisplayModelIndex

public int getDisplayModelIndex()
Specified by:
getDisplayModelIndex in class JmolViewer

haveFileSet

public boolean haveFileSet()

setBackgroundModelIndex

public void setBackgroundModelIndex(int modelIndex)

setFrameVariables

void setFrameVariables(int firstModelIndex,
                       int lastModelIndex)

getMotionEventNumber

public int getMotionEventNumber()
Specified by:
getMotionEventNumber in class JmolViewer

setInMotion

void setInMotion(boolean inMotion)

getInMotion

public boolean getInMotion()

pushHoldRepaint

public void pushHoldRepaint()
Specified by:
pushHoldRepaint in class JmolViewer

pushHoldRepaint

public void pushHoldRepaint(String why)
Parameters:
why -

popHoldRepaint

public void popHoldRepaint()
Specified by:
popHoldRepaint in class JmolViewer

popHoldRepaint

public void popHoldRepaint(String why)

setRefreshing

private void setRefreshing(boolean TF)

getRefreshing

public boolean getRefreshing()

refresh

public void refresh(int mode,
                    String strWhy)
initiate a repaint/update sequence if it has not already been requested. invoked whenever any operation causes changes that require new rendering. The repaint/update sequence will only be invoked if (a) no repaint is already pending and (b) there is no hold flag set in repaintManager. Sequence is as follows: 1) RepaintManager.refresh() checks flags and then calls Viewer.repaint() 2) Viewer.repaint() invokes display.repaint(), provided display is not null (headless) 3) The system responds with an invocation of Jmol.update(Graphics g), which we are routing through Jmol.paint(Graphics g). 4) Jmol.update invokes Viewer.setScreenDimension(size), which makes the necessary changes in parameters for any new window size. 5) Jmol.update invokes Viewer.renderScreenImage(g, size, rectClip) 6) Viewer.renderScreenImage checks object visibility, invokes render1 to do the actual creation of the image pixel map and send it to the screen, and then invokes repaintView() 7) Viewer.repaintView() invokes RepaintManager.repaintDone(), to clear the flags and then use notify() to release any threads holding on wait().

Specified by:
refresh in class JmolViewer
Parameters:
mode -
strWhy -

requestRepaintAndWait

public void requestRepaintAndWait()

setSync

private void setSync()

notifyViewerRepaintDone

public void notifyViewerRepaintDone()
Specified by:
notifyViewerRepaintDone in class JmolViewer

areAxesTainted

public boolean areAxesTainted()

setMaximumSize

private void setMaximumSize(int x)

setScreenDimension

public void setScreenDimension(int width,
                               int height)
Specified by:
setScreenDimension in class JmolViewer

getImageFontScaling

public float getImageFontScaling()

resizeImage

private void resizeImage(int width,
                         int height,
                         boolean isImageWrite,
                         boolean isExport,
                         boolean isReset)

getScreenWidth

public int getScreenWidth()
Specified by:
getScreenWidth in class JmolViewer

getScreenHeight

public int getScreenHeight()
Specified by:
getScreenHeight in class JmolViewer

getScreenDim

public int getScreenDim()

generateOutput

public String generateOutput(String type,
                             String[] fileName,
                             int width,
                             int height)
Specified by:
generateOutput in class JmolViewer

renderScreenImage

public void renderScreenImage(Object gLeft,
                              Object gRight,
                              int width,
                              int height)
Description copied from class: JmolViewer
an added class for rendering stereo in two independent applets

Specified by:
renderScreenImage in class JmolViewer

renderScreenImage

public void renderScreenImage(Object g,
                              int width,
                              int height)
Specified by:
renderScreenImage in class JmolSimpleViewer

getImage

private Object getImage(boolean isDouble)

isAntialiased

boolean isAntialiased()

render

private void render()

getStereoImage

private Object getStereoImage(EnumStereoMode stereoMode)

render1

private void render1(Object g,
                     Object img,
                     int x,
                     int y)

getScreenImage

public Object getScreenImage(Object g)
Specified by:
getScreenImage in class JmolViewer

getImageAs

public Object getImageAs(String type,
                         int quality,
                         int width,
                         int height,
                         String fileName,
                         OutputStream os)
Specified by:
getImageAs in class JmolViewer
Parameters:
type - "PNG", "JPG", "JPEG", "JPG64", "PPM", "GIF"
Returns:
base64-encoded or binary version of the image

getImageAs

Object getImageAs(String type,
                  int quality,
                  int width,
                  int height,
                  String fileName,
                  OutputStream os,
                  String comment)
Parameters:
type - "PNG", "JPG", "JPEG", "JPG64", "PPM", "GIF"
quality -
width -
height -
fileName -
os -
comment -
Returns:
base64-encoded or binary version of the image

releaseScreenImage

public void releaseScreenImage()
Specified by:
releaseScreenImage in class JmolViewer

getAllowEmbeddedScripts

public boolean getAllowEmbeddedScripts()

evalFile

public String evalFile(String strFilename)
Specified by:
evalFile in class JmolSimpleViewer

getInterruptScript

public String getInterruptScript()

script

public String script(String strScript)
Specified by:
script in class JmolViewer

evalString

public String evalString(String strScript)
Specified by:
evalString in class JmolSimpleViewer

evalStringQuiet

public String evalStringQuiet(String strScript)
Specified by:
evalStringQuiet in class JmolViewer

evalStringQuiet

String evalStringQuiet(String strScript,
                       boolean isQuiet,
                       boolean allowSyncScript)

checkScriptExecution

private String checkScriptExecution(String strScript,
                                    boolean isInterrupt)

usingScriptQueue

public boolean usingScriptQueue()

clearScriptQueue

public void clearScriptQueue()

setScriptQueue

private void setScriptQueue(boolean TF)

checkResume

public boolean checkResume(String str)

checkStepping

public boolean checkStepping(String str)

checkHalt

public boolean checkHalt(String str,
                         boolean isInterrupt)
Specified by:
checkHalt in class JmolViewer

scriptWait

public String scriptWait(String strScript)
Specified by:
scriptWait in class JmolViewer

scriptWaitStatus

public Object scriptWaitStatus(String strScript,
                               String statusList)
Specified by:
scriptWaitStatus in class JmolViewer

evalStringWaitStatus

public Object evalStringWaitStatus(String returnType,
                                   String strScript,
                                   String statusList)

evalStringWaitStatus

Object evalStringWaitStatus(String returnType,
                            String strScript,
                            String statusList,
                            boolean isScriptFile,
                            boolean isQuiet,
                            boolean isQueued)

exitJmol

public void exitJmol()

scriptCheck

private Object scriptCheck(String strScript,
                           boolean returnContext)

scriptCheck

public Object scriptCheck(String strScript)
Specified by:
scriptCheck in class JmolViewer

isScriptExecuting

public boolean isScriptExecuting()
Specified by:
isScriptExecuting in class JmolViewer

haltScriptExecution

public void haltScriptExecution()
Specified by:
haltScriptExecution in class JmolViewer

resumeScriptExecution

public void resumeScriptExecution()

stepScriptExecution

public void stepScriptExecution()

pauseScriptExecution

public void pauseScriptExecution()

getDefaultLoadFilter

public String getDefaultLoadFilter()

getDefaultLoadScript

public String getDefaultLoadScript()

setLoadFormat

public Object setLoadFormat(String name,
                            char type,
                            boolean withPrefix)

getElectronDensityLoadInfo

public String[] getElectronDensityLoadInfo()

getStandardLabelFormat

public String getStandardLabelFormat(int type)

getRibbonAspectRatio

public int getRibbonAspectRatio()

getSheetSmoothing

public float getSheetSmoothing()

getSsbondsBackbone

public boolean getSsbondsBackbone()

getHbondsBackbone

public boolean getHbondsBackbone()

getHbondsSolid

public boolean getHbondsSolid()

getAdditionalHydrogens

public Point3f[] getAdditionalHydrogens(BitSet bsAtoms,
                                        boolean doAll,
                                        boolean justCarbon,
                                        List<Atom> vConnections)

addHydrogens

public BitSet addHydrogens(BitSet bsAtoms,
                           boolean asScript,
                           boolean isSilent)

addHydrogensInline

private BitSet addHydrogensInline(BitSet bsAtoms,
                                  List<Atom> vConnections,
                                  Point3f[] pts)
                           throws Exception
Throws:
Exception

setMarBond

public void setMarBond(short marBond)
Specified by:
setMarBond in class JmolViewer

isHoverEnabled

public boolean isHoverEnabled()

setHoverLabel

public void setHoverLabel(String strLabel)

hoverOn

void hoverOn(int atomIndex,
             int action)

getHoverDelay

int getHoverDelay()

hoverOn

public void hoverOn(int x,
                    int y,
                    String text)

hoverOff

void hoverOff()

clearShapeRenderers

public void clearShapeRenderers()

getBfactor100Hi

public int getBfactor100Hi()

getColix

short getColix(Object object)

getRasmolSetting

public boolean getRasmolSetting(int tok)

getDebugScript

public boolean getDebugScript()

setDebugScript

public void setDebugScript(boolean debugScript)
Specified by:
setDebugScript in class JmolViewer

clearClickCount

void clearClickCount()

getCursor

public int getCursor()

setCursor

public void setCursor(int cursor)

setPickingMode

void setPickingMode(String strMode,
                    int pickingMode)

getPickingMode

public int getPickingMode()

getDrawPicking

public boolean getDrawPicking()

isModelKitMode

public boolean isModelKitMode()

getBondPicking

public boolean getBondPicking()

getAtomPicking

private boolean getAtomPicking()

setPickingStyle

void setPickingStyle(String style,
                     int pickingStyle)

getDrawHover

public boolean getDrawHover()

getAtomInfo

public String getAtomInfo(int atomOrPointIndex)
Specified by:
getAtomInfo in class JmolViewer

getAtomInfoXYZ

public String getAtomInfoXYZ(int atomIndex,
                             boolean useChimeFormat)

setJmolCallbackListener

public void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
Specified by:
setJmolCallbackListener in class JmolViewer

setJmolStatusListener

public void setJmolStatusListener(JmolStatusListener jmolStatusListener)
Specified by:
setJmolStatusListener in class JmolViewer

getMessageQueue

public Map<String,List<List<Object>>> getMessageQueue()

getStatusChanged

List<List<List<Object>>> getStatusChanged(String statusNameList)

menuEnabled

public boolean menuEnabled()

popupMenu

void popupMenu(int x,
               int y,
               char type)

getMenu

public String getMenu(String type)

getPopupMenu

private Object getPopupMenu()

setMenu

public void setMenu(String fileOrText,
                    boolean isFile)

setStatusFrameChanged

void setStatusFrameChanged(int frameNo)

scriptEcho

public void scriptEcho(String strEcho)

notifyError

public void notifyError(String errType,
                        String errMsg,
                        String errMsgUntranslated)

jsEval

public String jsEval(String strEval)

setStatusAtomHovered

public void setStatusAtomHovered(int atomIndex,
                                 String info)

setFileLoadStatus

private void setFileLoadStatus(FileManager.EnumFileStatus ptLoad,
                               String fullPathName,
                               String fileName,
                               String modelName,
                               String strError)

getZapName

public String getZapName()

setStatusMeasuring

public void setStatusMeasuring(String status,
                               int intInfo,
                               String strMeasure,
                               float value)

notifyMinimizationStatus

public void notifyMinimizationStatus()

setStatusAtomPicked

public void setStatusAtomPicked(int atomIndex,
                                String info)

setStatusResized

public void setStatusResized(int width,
                             int height)

scriptStatus

public void scriptStatus(String strStatus)

scriptStatus

public void scriptStatus(String strStatus,
                         String statusMessage)

scriptStatus

public void scriptStatus(String strStatus,
                         String statusMessage,
                         int msWalltime,
                         String strErrorMessageUntranslated)

getModelTitle

private String getModelTitle(int modelIndex)

getModelFileName

public String getModelFileName(int modelIndex)
Specified by:
getModelFileName in class JmolViewer

dialogAsk

public String dialogAsk(String type,
                        String fileName)

getScriptDelay

public int getScriptDelay()

showUrl

public void showUrl(String urlString)
Specified by:
showUrl in class JmolViewer

setMeshCreator

public void setMeshCreator(Object meshCreator)
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.

Parameters:
meshCreator -

showConsole

public void showConsole(boolean showConsole)

clearConsole

public void clearConsole()

getParameterEscaped

public Object getParameterEscaped(String key)

getParameter

public Object getParameter(String key)
Specified by:
getParameter in class JmolViewer

getOrSetNewVariable

public ScriptVariable getOrSetNewVariable(String key,
                                          boolean doSet)

setUserVariable

public ScriptVariable setUserVariable(String name,
                                      ScriptVariable value)

unsetProperty

public void unsetProperty(String name)

getVariableList

public String getVariableList()

getBooleanProperty

public boolean getBooleanProperty(String key)
Specified by:
getBooleanProperty in class JmolViewer

setStringProperty

public void setStringProperty(String key,
                              String value)
Specified by:
setStringProperty in class JmolViewer

setStringProperty

private void setStringProperty(String key,
                               int tok,
                               String value)

setFloatProperty

public void setFloatProperty(String key,
                             float value)
Specified by:
setFloatProperty in class JmolViewer

setFloatProperty

private void setFloatProperty(String key,
                              int tok,
                              float value)

setIntProperty

public void setIntProperty(String key,
                           int value)
Specified by:
setIntProperty in class JmolViewer

setIntProperty

private void setIntProperty(String key,
                            int tok,
                            int value)

checkIntRange

private static int checkIntRange(int value,
                                 int min,
                                 int max)

checkFloatRange

private static float checkFloatRange(float value,
                                     float min,
                                     float max)

setBooleanProperty

public void setBooleanProperty(String key,
                               boolean value)
Specified by:
setBooleanProperty in class JmolViewer

setBooleanProperty

private void setBooleanProperty(String key,
                                int tok,
                                boolean value)

setModelKitMode

private void setModelKitMode(boolean value)

getModelkitMode

public boolean getModelkitMode()

getLanguage

public String getLanguage()

setSmilesString

public void setSmilesString(String s)

removeUserVariable

public void removeUserVariable(String key)

isJmolVariable

public boolean isJmolVariable(String key)

jmolTest

private void jmolTest()

isPdbSequential

public boolean isPdbSequential()

getSelectAllModels

boolean getSelectAllModels()

getMessageStyleChime

public boolean getMessageStyleChime()

getFontCaching

public boolean getFontCaching()

getFontScaling

public boolean getFontScaling()

showParameter

public void showParameter(String key,
                          boolean ifNotSet,
                          int nMax)

showString

public void showString(String str,
                       boolean isPrint)

getAllSettings

public String getAllSettings(String prefix)

getBindingInfo

public String getBindingInfo(String qualifiers)

getDelayMaximum

public int getDelayMaximum()

getDotSurfaceFlag

public boolean getDotSurfaceFlag()

getDotsSelectedOnlyFlag

public boolean getDotsSelectedOnlyFlag()

getDotDensity

public int getDotDensity()

getDotScale

public int getDotScale()

isRangeSelected

public boolean isRangeSelected()

getIsosurfaceKey

public boolean getIsosurfaceKey()

getIsosurfacePropertySmoothing

public int getIsosurfacePropertySmoothing(boolean asPower)

getWireframeRotation

public boolean getWireframeRotation()

isWindowCentered

public boolean isWindowCentered()

setNavigationDepthPercent

public void setNavigationDepthPercent(float timeSec,
                                      float percent)

getNavigationSpeed

float getNavigationSpeed()

getShowNavigationPoint

public boolean getShowNavigationPoint()

getSolventProbeRadius

public float getSolventProbeRadius()

getCurrentSolventProbeRadius

public float getCurrentSolventProbeRadius()

getSolventOn

boolean getSolventOn()

getTestFlag

public boolean getTestFlag(int i)

setPerspectiveDepth

public void setPerspectiveDepth(boolean perspectiveDepth)
Specified by:
setPerspectiveDepth in class JmolViewer

setAxesOrientationRasmol

public void setAxesOrientationRasmol(boolean TF)
Specified by:
setAxesOrientationRasmol in class JmolViewer

getAxesOrientationRasmol

public boolean getAxesOrientationRasmol()
Specified by:
getAxesOrientationRasmol in class JmolViewer

setAxesScale

void setAxesScale(float scale)

getAxisPoints

public Point3f[] getAxisPoints()

getAxesScale

public float getAxesScale()

resetError

public void resetError()

setAxesModeMolecular

private void setAxesModeMolecular(boolean TF)

setAxesModeUnitCell

void setAxesModeUnitCell(boolean TF)

getAxesMode

public EnumAxesMode getAxesMode()

getDisplayCellParameters

public boolean getDisplayCellParameters()

getPerspectiveDepth

public boolean getPerspectiveDepth()
Specified by:
getPerspectiveDepth in class JmolViewer

setSelectionHalos

public void setSelectionHalos(boolean TF)
Specified by:
setSelectionHalos in class JmolViewer

getSelectionHaloEnabled

public boolean getSelectionHaloEnabled(boolean isRenderer)

getBondSelectionModeOr

public boolean getBondSelectionModeOr()

getChainCaseSensitive

public boolean getChainCaseSensitive()

getRibbonBorder

public boolean getRibbonBorder()

getCartoonRocketFlag

public boolean getCartoonRocketFlag()

getRocketBarrelFlag

public boolean getRocketBarrelFlag()

getCartoonBaseEdgesFlag

public boolean getCartoonBaseEdgesFlag()

setStrandCount

private void setStrandCount(int type,
                            int value)

getStrandCount

public int getStrandCount(int type)

getHideNameInPopup

boolean getHideNameInPopup()

getNavigationPeriodic

public boolean getNavigationPeriodic()

stopAnimationThreads

private void stopAnimationThreads(String fromWhere)
Parameters:
fromWhere -

setNavigationMode

private void setNavigationMode(boolean TF)

getNavigationMode

public boolean getNavigationMode()

getNavigateSurface

public boolean getNavigateSurface()

setTransformManager

public void setTransformManager(TransformManager transformManager)
for an external application

Parameters:
transformManager -

setPerspectiveModel

private void setPerspectiveModel(int mode)

setTransformManagerDefaults

private void setTransformManagerDefaults()

getCameraFactors

public Point3f[] getCameraFactors()

getZoomLarge

boolean getZoomLarge()

getTraceAlpha

public boolean getTraceAlpha()

getHermiteLevel

public int getHermiteLevel()

getHighResolution

public boolean getHighResolution()

getLoadState

String getLoadState(Map<String,Object> htParams)

setAutoBond

public void setAutoBond(boolean TF)
Specified by:
setAutoBond in class JmolViewer

getAutoBond

public boolean getAutoBond()
Specified by:
getAutoBond in class JmolViewer

makeConnections

public int[] makeConnections(float minDistance,
                             float maxDistance,
                             int order,
                             int connectOperation,
                             BitSet bsA,
                             BitSet bsB,
                             BitSet bsBonds,
                             boolean isBonds,
                             boolean addGroup,
                             float energy)

rebond

public void rebond()
Specified by:
rebond in class JmolViewer

rebond

public void rebond(boolean isStateScript)

setPdbConectBonding

public void setPdbConectBonding(boolean isAuto,
                                boolean isStateScript)

getGreyscaleRendering

boolean getGreyscaleRendering()

getDisablePopupMenu

boolean getDisablePopupMenu()

getForceAutoBond

public boolean getForceAutoBond()

setPercentVdwAtom

public void setPercentVdwAtom(int value)
Specified by:
setPercentVdwAtom in class JmolViewer

getPercentVdwAtom

public int getPercentVdwAtom()
Specified by:
getPercentVdwAtom in class JmolViewer

getDefaultRadiusData

public RadiusData getDefaultRadiusData()

getMadBond

public short getMadBond()
Specified by:
getMadBond in class JmolViewer

getMarBond

public short getMarBond()

getModeMultipleBond

public byte getModeMultipleBond()

getShowMultipleBonds

public boolean getShowMultipleBonds()

getMultipleBondSpacing

public float getMultipleBondSpacing()

getMultipleBondRadiusFactor

public float getMultipleBondRadiusFactor()

setShowHydrogens

public void setShowHydrogens(boolean TF)
Specified by:
setShowHydrogens in class JmolViewer

getShowHydrogens

public boolean getShowHydrogens()
Specified by:
getShowHydrogens in class JmolViewer

getShowHiddenSelectionHalos

public boolean getShowHiddenSelectionHalos()

setShowBbcage

public void setShowBbcage(boolean value)
Specified by:
setShowBbcage in class JmolViewer

getShowBbcage

public boolean getShowBbcage()
Specified by:
getShowBbcage in class JmolViewer

setShowUnitCell

public void setShowUnitCell(boolean value)

getShowUnitCell

public boolean getShowUnitCell()

setShowAxes

public void setShowAxes(boolean value)
Specified by:
setShowAxes in class JmolViewer

getShowAxes

public boolean getShowAxes()
Specified by:
getShowAxes in class JmolViewer

setFrankOn

public void setFrankOn(boolean TF)
Specified by:
setFrankOn in class JmolViewer

getShowFrank

public boolean getShowFrank()

isSignedApplet

public boolean isSignedApplet()

setShowMeasurements

public void setShowMeasurements(boolean TF)
Specified by:
setShowMeasurements in class JmolViewer

getShowMeasurements

public boolean getShowMeasurements()
Specified by:
getShowMeasurements in class JmolViewer

getShowMeasurementLabels

public boolean getShowMeasurementLabels()

getMeasureAllModelsFlag

public boolean getMeasureAllModelsFlag()

setMeasureDistanceUnits

public void setMeasureDistanceUnits(String units)

getMeasureDistanceUnits

public String getMeasureDistanceUnits()

getUseNumberLocalization

public boolean getUseNumberLocalization()

setAppendNew

public void setAppendNew(boolean value)

getAppendNew

public boolean getAppendNew()

getAutoFps

boolean getAutoFps()

setRasmolDefaults

public void setRasmolDefaults()
Specified by:
setRasmolDefaults in class JmolViewer

setJmolDefaults

public void setJmolDefaults()
Specified by:
setJmolDefaults in class JmolViewer

setDefaults

private void setDefaults(String type)

setDefaults

private void setDefaults()

getZeroBasedXyzRasmol

public boolean getZeroBasedXyzRasmol()

setAntialias

private void setAntialias(int mode,
                          boolean TF)

allocTempPoints

public Point3f[] allocTempPoints(int size)

freeTempPoints

public void freeTempPoints(Point3f[] tempPoints)

allocTempScreens

public Point3i[] allocTempScreens(int size)

freeTempScreens

public void freeTempScreens(Point3i[] tempScreens)

allocTempEnum

public EnumStructure[] allocTempEnum(int size)

freeTempEnum

public void freeTempEnum(EnumStructure[] temp)

getFont3D

public Font3D getFont3D(String fontFace,
                        String fontStyle,
                        float fontSize)

formatText

public String formatText(String text0)

getElementSymbol

String getElementSymbol(int i)

getElementNumber

int getElementNumber(int i)

getAtomName

public String getAtomName(int i)
Specified by:
getAtomName in class JmolViewer

getAtomNumber

public int getAtomNumber(int i)
Specified by:
getAtomNumber in class JmolViewer

getAtomGroupQuaternions

public Quaternion[] getAtomGroupQuaternions(BitSet bsAtoms,
                                            int nMax)

getAtomQuaternion

public Quaternion getAtomQuaternion(int i)

getAtomPoint3f

public Point3f getAtomPoint3f(int i)
Specified by:
getAtomPoint3f in class JmolViewer

getAtomPointVector

public List<Point3f> getAtomPointVector(BitSet bs)

getAtomRadius

public float getAtomRadius(int i)
Specified by:
getAtomRadius in class JmolViewer

getAtomArgb

public int getAtomArgb(int i)
Specified by:
getAtomArgb in class JmolViewer

getAtomChain

String getAtomChain(int i)

getAtomModelIndex

public int getAtomModelIndex(int i)
Specified by:
getAtomModelIndex in class JmolViewer

getAtomSequenceCode

String getAtomSequenceCode(int i)

getBondRadius

public float getBondRadius(int i)
Specified by:
getBondRadius in class JmolViewer

getBondOrder

public int getBondOrder(int i)
Specified by:
getBondOrder in class JmolViewer

assignAromaticBonds

public void assignAromaticBonds()

getSmartAromatic

public boolean getSmartAromatic()

resetAromatic

public void resetAromatic()

getBondArgb1

public int getBondArgb1(int i)
Specified by:
getBondArgb1 in class JmolViewer

getBondModelIndex

public int getBondModelIndex(int i)
Specified by:
getBondModelIndex in class JmolViewer

getBondArgb2

public int getBondArgb2(int i)
Specified by:
getBondArgb2 in class JmolViewer

getPolymerLeadMidPoints

public Point3f[] getPolymerLeadMidPoints(int modelIndex,
                                         int polymerIndex)
Specified by:
getPolymerLeadMidPoints in class JmolViewer

setStereoMode

public void setStereoMode(int[] twoColors,
                          EnumStereoMode stereoMode,
                          float degrees)

isStereoDouble

boolean isStereoDouble()

getOperatingSystemName

public String getOperatingSystemName()
Specified by:
getOperatingSystemName in class JmolViewer

getJavaVendor

public String getJavaVendor()
Specified by:
getJavaVendor in class JmolViewer

getJavaVersion

public String getJavaVersion()
Specified by:
getJavaVersion in class JmolViewer

getGraphics3D

public Graphics3D getGraphics3D()

showModelSetDownload

public boolean showModelSetDownload()
Specified by:
showModelSetDownload in class JmolViewer

getProperty

public Object getProperty(String returnType,
                          String infoType,
                          String paramInfo)

isScriptEditorVisible

public boolean isScriptEditorVisible()

getProperty

public Object getProperty(String returnType,
                          String infoType,
                          Object paramInfo)
Specified by:
getProperty in class JmolSimpleViewer
Parameters:
returnType - "JSON", "string", "readable", and anything else returns the Java object.
Returns:
property data -- see org.jmol.viewer.PropertyManager.java

showEditor

void showEditor(String[] file_text)

getModelExtract

public String getModelExtract(Object atomExpression,
                              boolean doTransform,
                              String type)

setTainted

public void setTainted(boolean TF)

notifyMouseClicked

public int notifyMouseClicked(int x,
                              int y,
                              int action,
                              int mode)

checkObjectClicked

Map<String,Object> checkObjectClicked(int x,
                                      int y,
                                      int modifiers)

checkObjectHovered

boolean checkObjectHovered(int x,
                           int y)

checkObjectDragged

void checkObjectDragged(int prevX,
                        int prevY,
                        int x,
                        int y,
                        int action)

rotateAxisAngleAtCenter

public void rotateAxisAngleAtCenter(Point3f rotCenter,
                                    Vector3f rotAxis,
                                    float degreesPerSecond,
                                    float endDegrees,
                                    boolean isSpin,
                                    BitSet bsSelected)

rotateAboutPointsInternal

public void rotateAboutPointsInternal(Point3f point1,
                                      Point3f point2,
                                      float degreesPerSecond,
                                      float endDegrees,
                                      boolean isSpin,
                                      BitSet bsSelected,
                                      Vector3f translation,
                                      List<Point3f> finalPoints)

getPickingSpinRate

int getPickingSpinRate()

startSpinningAxis

public void startSpinningAxis(Point3f pt1,
                              Point3f pt2,
                              boolean isClockwise)

getModelDipole

public Vector3f getModelDipole()

calculateMolecularDipole

public Vector3f calculateMolecularDipole()

getDipoleScale

public float getDipoleScale()

getAtomIdentityInfo

public void getAtomIdentityInfo(int atomIndex,
                                Map<String,Object> info)

setDefaultLattice

public void setDefaultLattice(Point3f ptLattice)

getDefaultLattice

public Point3f getDefaultLattice()

getTaintedAtoms

public BitSet getTaintedAtoms(byte type)

setTaintedAtoms

public void setTaintedAtoms(BitSet bs,
                            byte type)

getData

public String getData(String atomExpression,
                      String type)
Specified by:
getData in class JmolViewer

getModelCml

public String getModelCml(BitSet bs,
                          int nAtomsMax,
                          boolean addBonds)

evaluateExpression

public Object evaluateExpression(Object stringOrTokens)

getHelixData

public Object getHelixData(BitSet bs,
                           int tokType)

getPdbData

public String getPdbData(BitSet bs,
                         OutputStringBuffer sb)

isJmolDataFrame

public boolean isJmolDataFrame(int modelIndex)

isJmolDataFrame

public boolean isJmolDataFrame()

getJmolDataFrameIndex

public int getJmolDataFrameIndex(int modelIndex,
                                 String type)

setJmolDataFrame

public void setJmolDataFrame(String type,
                             int modelIndex,
                             int dataIndex)

setFrameTitle

public void setFrameTitle(int modelIndex,
                          String title)

setFrameTitle

public void setFrameTitle(Object title)

getFrameTitle

public String getFrameTitle()

getJmolFrameType

String getJmolFrameType(int modelIndex)

getJmolDataSourceFrame

public int getJmolDataSourceFrame(int modelIndex)

setAtomProperty

public void setAtomProperty(BitSet bs,
                            int tok,
                            int iValue,
                            float fValue,
                            String sValue,
                            float[] values,
                            String[] list)

checkCoordinatesChanged

public void checkCoordinatesChanged()

setAtomCoord

public void setAtomCoord(int atomIndex,
                         float x,
                         float y,
                         float z)

setAtomCoordRelative

public void setAtomCoordRelative(int atomIndex,
                                 float x,
                                 float y,
                                 float z)

setAtomCoord

public void setAtomCoord(BitSet bs,
                         int tokType,
                         Object xyzValues)

setAtomCoordRelative

public void setAtomCoordRelative(Tuple3f offset,
                                 BitSet bs)

allowRotateSelected

boolean allowRotateSelected()

invertAtomCoord

public void invertAtomCoord(Point3f pt,
                            BitSet bs)

invertAtomCoord

public void invertAtomCoord(Point4f plane,
                            BitSet bs)

invertSelected

public void invertSelected(Point3f pt,
                           Point4f plane,
                           int iAtom,
                           BitSet invAtoms)

moveAtoms

void moveAtoms(Matrix3f mNew,
               Matrix3f matrixRotate,
               Vector3f translation,
               Point3f center,
               boolean isInternal,
               BitSet bsAtoms)

moveSelected

public void moveSelected(int deltaX,
                         int deltaY,
                         int deltaZ,
                         int x,
                         int y,
                         BitSet bsSelected,
                         boolean isTranslation,
                         boolean asAtoms)

highlightBond

public void highlightBond(int index,
                          boolean isHover)

highlight

public void highlight(BitSet bs)

setRotateBondIndex

void setRotateBondIndex(int index)

getRotateBondIndex

int getRotateBondIndex()

actionRotateBond

void actionRotateBond(int deltaX,
                      int deltaY,
                      int x,
                      int y)

refreshMeasures

public void refreshMeasures(boolean andStopMinimization)

setDynamicMeasurements

void setDynamicMeasurements(boolean TF)

getDynamicMeasurements

public boolean getDynamicMeasurements()

functionXY

public float[][] functionXY(String functionName,
                            int nX,
                            int nY)
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. Otherwise it reads the values using individual function calls, which each return Double. If the functionName begins with "file:" then data are read from a file specified after the colon. The sign of nX is not relevant in that case. The file may contain mixed numeric and non-numeric values; the non-numeric values will be skipped by Parser.parseFloatArray

Parameters:
functionName -
nX -
nY -
Returns:
nX by nY array of floating values

functionXYZ

public float[][][] functionXYZ(String functionName,
                               int nX,
                               int nY,
                               int nZ)

getHelp

public void getHelp(String what)

show2D

public void show2D(String smiles)

getChemicalInfo

public String getChemicalInfo(String smiles,
                              char type)

addCommand

public void addCommand(String command)
Adds one or more commands to the command history

Parameters:
command - the command to add

removeCommand

public String removeCommand()
Removes one command from the command history

Returns:
command removed

getSetHistory

public String getSetHistory(int howFarBack)
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;

Specified by:
getSetHistory in class JmolViewer
Parameters:
howFarBack - number of lines (-1 for next line)
Returns:
one or more lines of command history

writeTextFile

public void writeTextFile(String fileName,
                          String data)
Specified by:
writeTextFile in class JmolViewer

clipImage

public String clipImage(String text)
Specified by:
clipImage in class JmolViewer
Parameters:
text - null here clips image; String clips text
Returns:
"OK" for image or "OK [number of bytes]"

createImage

public String createImage(String fileName,
                          String type,
                          Object text_or_bytes,
                          int quality,
                          int width,
                          int height,
                          BitSet bsFrames,
                          String[] fullPath)
from eval write command only includes option to write set of files

Parameters:
fileName -
type -
text_or_bytes -
quality -
width -
height -
bsFrames -
fullPath -
Returns:
message starting with "OK" or an error message

getCreatingImage

public boolean getCreatingImage()

createImage

public Object createImage(String fileName,
                          String type,
                          Object text_or_bytes,
                          int quality,
                          int width,
                          int height)
Specified by:
createImage in class JmolViewer
Returns:
null (canceled) or a message starting with OK or an error message

createImage

public Object createImage(String fileName,
                          String type,
                          Object text_or_bytes,
                          int quality,
                          int width,
                          int height,
                          String[] fullPath)
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

Parameters:
fileName - starts with ? --> use file dialog; null --> to clipboard
type - PNG, JPG, etc.
text_or_bytes - String or byte[] or null if an image
quality - Integer.MIN_VALUE --> not an image
width - image width
height - image height
fullPath -
Returns:
null (canceled) or a message starting with OK or an error message

createImage

private Object createImage(String fileName,
                           String type,
                           Object text_or_bytes,
                           int quality,
                           int width,
                           int height,
                           String[] fullPath,
                           boolean doCheck)

getFileNameFromDialog

private String getFileNameFromDialog(String fileName,
                                     int quality)

setSyncTarget

private void setSyncTarget(int mode,
                           boolean TF)

syncScript

public void syncScript(String script,
                       String applet,
                       int port)
Specified by:
syncScript in class JmolViewer

setSyncDriver

void setSyncDriver(int mode)

getPartialCharges

public float[] getPartialCharges()

getAtomicPotentials

public float[] getAtomicPotentials(boolean isMep,
                                   BitSet bsSelected,
                                   BitSet bsIgnore,
                                   String fileName)
Parameters:
isMep -
bsSelected -
bsIgnore -
fileName -
Returns:
calculated atom potentials

setProteinType

public void setProteinType(EnumStructure type,
                           BitSet bs)

getBondPoint3f1

public Point3f getBondPoint3f1(int i)
Specified by:
getBondPoint3f1 in class JmolViewer

getBondPoint3f2

public Point3f getBondPoint3f2(int i)
Specified by:
getBondPoint3f2 in class JmolViewer

getVibrationVector

public Vector3f getVibrationVector(int atomIndex)

getVanderwaalsMar

public int getVanderwaalsMar(int i)

getVanderwaalsMar

public int getVanderwaalsMar(int i,
                             EnumVdw type)

setDefaultVdw

void setDefaultVdw(String type)

getDefaultVdwTypeNameOrData

public String getDefaultVdwTypeNameOrData(int iMode,
                                          EnumVdw vType)

deleteAtoms

public int deleteAtoms(BitSet bs,
                       boolean fullModels)

deleteBonds

public void deleteBonds(BitSet bsDeleted)

deleteModelAtoms

public void deleteModelAtoms(int firstAtomIndex,
                             int nAtoms,
                             BitSet bsDeleted)

getDeletedAtoms

public BitSet getDeletedAtoms()

getQuaternionFrame

public char getQuaternionFrame()

getHelixStep

public int getHelixStep()

calculatePointGroup

public String calculatePointGroup()

getPointGroupInfo

public Map<String,Object> getPointGroupInfo(Object atomExpression)

getPointGroupAsString

public String getPointGroupAsString(boolean asDraw,
                                    String type,
                                    int index,
                                    float scale)

getPointGroupTolerance

public float getPointGroupTolerance(int type)

getFileAsImage

public Object getFileAsImage(String pathName,
                             String[] retFileNameOrError)

cd

public String cd(String dir)

setErrorMessage

private String setErrorMessage(String errMsg)

setErrorMessage

private String setErrorMessage(String errMsg,
                               String errMsgUntranslated)

getErrorMessage

public String getErrorMessage()
Specified by:
getErrorMessage in class JmolViewer

getErrorMessageUntranslated

public String getErrorMessageUntranslated()
Specified by:
getErrorMessageUntranslated in class JmolViewer

setShapeErrorState

public void setShapeErrorState(int shapeID,
                               String state)

getShapeErrorState

public String getShapeErrorState()

handleError

public void handleError(Error er,
                        boolean doClear)

getAtomicCharges

public float[] getAtomicCharges()

getFunction

public ScriptFunction getFunction(String name)

addFunction

public void addFunction(ScriptFunction f)

clearFunctions

public void clearFunctions()

isFunction

public boolean isFunction(String name)

getFunctionCalls

public String getFunctionCalls(String selectedFunction)

showMessage

public void showMessage(String s)

getMoInfo

public String getMoInfo(int modelIndex)

isRepaintPending

boolean isRepaintPending()

getContextVariables

public Map<String,ScriptVariable> getContextVariables()

checkPrivateKey

public boolean checkPrivateKey(double privateKey)
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. When the image creator is used it requires both a viewer object and that viewer's private key. But the private key is private, so it is not possible to create a useable image creator without working through a viewer's own methods. Bob Hanson, 9/20/2009

Specified by:
checkPrivateKey in class JmolViewer
Parameters:
privateKey -
Returns:
true if privateKey matches

bindAction

public void bindAction(String desc,
                       String name,
                       Point3f range1,
                       Point3f range2)

unBindAction

public void unBindAction(String desc,
                         String name)

getMouseInfo

public Object getMouseInfo()

clearTimeout

public void clearTimeout(String name)

setTimeout

public void setTimeout(String name,
                       int mSec,
                       String script)

triggerTimeout

public void triggerTimeout(String name)

showTimeout

public String showTimeout(String name)

getFrontPlane

public int getFrontPlane()

getPlaneIntersection

public List<Object> getPlaneIntersection(int type,
                                         Point4f plane,
                                         float scale,
                                         int flags)

repaint

void repaint()

getOutputStream

public OutputStream getOutputStream(String localName,
                                    String[] fullPath)

calculateStruts

public int calculateStruts(BitSet bs1,
                           BitSet bs2)

getStrutsMultiple

public boolean getStrutsMultiple()

getStrutSpacingMinimum

public int getStrutSpacingMinimum()

getStrutLengthMaximum

public float getStrutLengthMaximum()

getStrutDefaultRadius

public float getStrutDefaultRadius()

getPreserveState

public boolean getPreserveState()
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.

Returns:
TRUE or FALSE

getDragSelected

public boolean getDragSelected()

getLoadAtomDataTolerance

public float getLoadAtomDataTolerance()

getAllowGestures

public boolean getAllowGestures()

getLogGestures

public boolean getLogGestures()

allowMultiTouch

public boolean allowMultiTouch()

logCommands

public boolean logCommands()

getLogFile

public String getLogFile()

setLogFile

private String setLogFile(String value)

log

public void log(String data)
Specified by:
log in interface AtomDataServer

isKiosk

boolean isKiosk()

hasFocus

public boolean hasFocus()

setFocus

public void setFocus()

getMinimizer

public MinimizerInterface getMinimizer(boolean createNew)

stopMinimization

void stopMinimization()

clearMinimization

void clearMinimization()

getMinimizationInfo

public String getMinimizationInfo()

useMinimizationThread

public boolean useMinimizationThread()

checkMinimization

private void checkMinimization()

minimize

public void minimize(int steps,
                     float crit,
                     BitSet bsSelected,
                     BitSet bsFixed,
                     float rangeFixed,
                     boolean addHydrogen,
                     boolean isSilent,
                     boolean asScript)
Parameters:
steps - Integer.MAX_VALUE --> use defaults
crit - -1 --> use defaults
bsSelected -
bsFixed - TODO
rangeFixed -
addHydrogen -
isSilent -
asScript -

setMotionFixedAtoms

public void setMotionFixedAtoms(BitSet bs)

getMotionFixedAtoms

public BitSet getMotionFixedAtoms()

useArcBall

boolean useArcBall()

rotateArcBall

void rotateArcBall(int x,
                   int y,
                   float factor)

getAtomicPropertyState

void getAtomicPropertyState(StringBuffer commands,
                            byte type,
                            BitSet bs,
                            String name,
                            float[] data)

getCenterAndPoints

public Point3f[][] getCenterAndPoints(List<BitSet[]> atomSets,
                                      boolean addCenter)

getSmallMoleculeMaxAtoms

public int getSmallMoleculeMaxAtoms()

streamFileData

public String streamFileData(String fileName,
                             String type,
                             String type2,
                             int modelIndex,
                             Object[] parameters)

getPdbData

public String getPdbData(int modelIndex,
                         String type,
                         Object[] parameters)

getRepaintWait

public int getRepaintWait()

getGroupsWithin

public BitSet getGroupsWithin(int nResidues,
                              BitSet bs)

getExecutor

public Object getExecutor()

eval

public boolean eval(ScriptContext context,
                    ShapeManager shapeManager)

getShapeInfo

public Map<String,Object> getShapeInfo()

togglePickingLabel

public void togglePickingLabel(BitSet bs)

loadShape

public void loadShape(int shapeID)

setShapeSize

public void setShapeSize(int shapeID,
                         int mad,
                         BitSet bsSelected)

setShapeSize

public void setShapeSize(int shapeID,
                         RadiusData rd,
                         BitSet bsAtoms)

setShapeProperty

public void setShapeProperty(int shapeID,
                             String propertyName,
                             Object value)

getShapeProperty

public Object getShapeProperty(int shapeType,
                               String propertyName)

getShapeProperty

public boolean getShapeProperty(int shapeType,
                                String propertyName,
                                Object[] data)

getShapeProperty

public Object getShapeProperty(int shapeType,
                               String propertyName,
                               int index)

getShapePropertyAsInt

private int getShapePropertyAsInt(int shapeID,
                                  String propertyName)

setModelVisibility

public void setModelVisibility()

resetShapes

public void resetShapes()

setAtomLabel

public void setAtomLabel(String value,
                         int i)

deleteShapeAtoms

public void deleteShapeAtoms(Object[] value,
                             BitSet bs)

getShapeState

public void getShapeState(StringBuffer commands,
                          boolean isAll)

resetBioshapes

public void resetBioshapes(BitSet bsAllAtoms)

getAtomShapeValue

public float getAtomShapeValue(int tok,
                               Group group,
                               int atomIndex)

mergeShapes

public void mergeShapes(Shape[] newShapes)

getShapeManager

public ShapeManager getShapeManager()

setParallel

public boolean setParallel(boolean TF)

isParallel

public boolean isParallel()

getRenderableBitSet

public BitSet getRenderableBitSet()

setAtomPickingOption

private void setAtomPickingOption(String option)

setBondPickingOption

private void setBondPickingOption(String option)

undoClear

void undoClear()

undoMoveAction

public void undoMoveAction(int action,
                           int n)
Parameters:
action - Token.undo or Token.redo
n - number of steps to go back/forward; 0 for all; -1 for clear; -2 for clear BOTH

undoMoveAction

void undoMoveAction(int taintedAtom,
                    int type,
                    boolean clearRedo)

assignBond

public void assignBond(int bondIndex,
                       char type)

assignAtom

public void assignAtom(int atomIndex,
                       Point3f pt,
                       String type)

assignConnect

public void assignConnect(int index,
                          int index2)

moveAtomWithHydrogens

protected void moveAtomWithHydrogens(int atomIndex,
                                     int deltaX,
                                     int deltaY,
                                     int deltaZ,
                                     BitSet bsAtoms)

appendLoadStates

void appendLoadStates(StringBuffer commands)

getInlineData

public static void getInlineData(StringBuffer loadScript,
                                 String strModel,
                                 boolean isAppend)

isAtomPDB

public boolean isAtomPDB(int i)

isModelPDB

public boolean isModelPDB(int i)

isAtomAssignable

boolean isAtomAssignable(int i)

deleteMeasurement

public void deleteMeasurement(int i)
Specified by:
deleteMeasurement in class JmolViewer

haveModelKit

boolean haveModelKit()

getModelKitStateBitSet

BitSet getModelKitStateBitSet(BitSet bs,
                              BitSet bsDeleted)

getSmiles

public String getSmiles(int index1,
                        int index2,
                        BitSet bsSelected,
                        boolean isBioSmiles,
                        boolean allowUnmatchedRings,
                        boolean addCrossLinks,
                        boolean addComment)
returns the SMILES string for a sequence or atom set does not include attached protons on groups

Parameters:
index1 -
index2 -
bsSelected -
isBioSmiles -
allowUnmatchedRings - TODO
addCrossLinks - TODO
addComment -
Returns:
SMILES string

connect

public void connect(float[][] connections)

prompt

public String prompt(String label,
                     String data,
                     String[] list,
                     boolean asButtons)

getMenuName

String getMenuName(int i)

getColorEncoder

public ColorEncoder getColorEncoder(String colorScheme)

displayBonds

public void displayBonds(Bond.BondSet bs,
                         boolean isDisplay)

getModelAtomProperty

public String getModelAtomProperty(Atom atom,
                                   String text)

setStateScriptVersion

public void setStateScriptVersion(String version)

checkAutoBondLegacy

public boolean checkAutoBondLegacy()

initializeExporter

boolean initializeExporter(JmolRendererInterface g3dExport,
                           String type,
                           Object output)

setPrivateKeyForShape

public void setPrivateKeyForShape(int iShape)

getMouseEnabled

public boolean getMouseEnabled()

getPartialDots

public boolean getPartialDots()

setZslabPoint

public void setZslabPoint(Point3f pt)

calcAtomsMinMax

public void calcAtomsMinMax(BitSet bs,
                            BoxInfo boxInfo)
Specified by:
calcAtomsMinMax in class JmolViewer

getCrossHairMinMax

public int[] getCrossHairMinMax()

evalFunctionFloat

public float evalFunctionFloat(Object func,
                               Object params,
                               float[] values)
Specified by:
evalFunctionFloat in interface AtomDataServer

getObjectMap

public void getObjectMap(Map<String,Token> map,
                         boolean withDollar)
Description copied from class: JmolViewer
retrieves list of draw/isosurface objects

Specified by:
getObjectMap in class JmolViewer

getPdbBondInfo

public String[][] getPdbBondInfo(String group3)

setPicked

public void setPicked(int iAtom)

runScriptImmediately

public boolean runScriptImmediately(String script)

allowSpecAtom

public boolean allowSpecAtom()

getMinPixelSelRadius

public int getMinPixelSelRadius()

evaluateExpressionAsVariable

public ScriptVariable evaluateExpressionAsVariable(Object stringOrTokens)
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