org.jmol.adapter.readers.more
Class BinaryDcdReader

java.lang.Object
  org.jmol.adapter.smarter.AtomSetCollectionReader
      org.jmol.adapter.readers.more.BinaryReader
          org.jmol.adapter.readers.more.BinaryDcdReader

public class BinaryDcdReader
extends BinaryReader

DCD binary trajectory file reader. see http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html and http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5651.html Bob Hanson 2/18/2011 requires PDB file load trajectory "c:/temp/t.pdb" coord "c:/temp/t.dcd"

Field Summary

private BitSet	bsFree
private int	nAtoms
private int	nFree
private int	nModels
private List<Point3f[]>	trajectorySteps
private float[]	xAll
private float[]	yAll
private float[]	zAll

Fields inherited from class org.jmol.adapter.readers.more.BinaryReader

doc

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer

Constructor Summary

BinaryDcdReader()

Method Summary

private boolean	getTrajectoryStep(Point3f[] trajectoryStep)
protected void	initializeReader()
private void	readCoordinates()
protected void	readDocument()
private float[]	readFloatArray()

Methods inherited from class org.jmol.adapter.readers.more.BinaryReader

processBinaryDocument

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

trajectorySteps

private List<Point3f[]> trajectorySteps

nModels

private int nModels

nAtoms

private int nAtoms

nFree

private int nFree

bsFree

private BitSet bsFree

xAll

private float[] xAll

yAll

private float[] yAll

zAll

private float[] zAll

Constructor Detail

BinaryDcdReader

public BinaryDcdReader()

Method Detail

initializeReader

protected void initializeReader()

Overrides:

initializeReader in class AtomSetCollectionReader

readDocument

protected void readDocument()
                     throws Exception

Specified by:

readDocument in class BinaryReader

Throws:

Exception

readFloatArray

private float[] readFloatArray()
                        throws Exception

Throws:

Exception

readCoordinates

private void readCoordinates()
                      throws Exception

Throws:

Exception

getTrajectoryStep

private boolean getTrajectoryStep(Point3f[] trajectoryStep)
                           throws Exception

Throws:

Exception