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

Fields

Modifier and Type	Field and Description
private java.util.BitSet	bsFree
private int	nAtoms
private int	nFree
private int	nModels
private java.util.List<javax.vecmath.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

Constructors

Constructor and Description
BinaryDcdReader()

Method Summary

Methods

Modifier and Type	Method and Description
private boolean	getTrajectoryStep(javax.vecmath.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 java.util.List<javax.vecmath.Point3f[]> trajectorySteps

nModels

private int nModels

nAtoms

private int nAtoms

nFree

private int nFree

bsFree

private java.util.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 java.lang.Exception

Specified by:

readDocument in class BinaryReader

Throws:

java.lang.Exception

readFloatArray

private float[] readFloatArray()
                        throws java.lang.Exception

Throws:

java.lang.Exception

readCoordinates

private void readCoordinates()
                      throws java.lang.Exception

Throws:

java.lang.Exception

getTrajectoryStep

private boolean getTrajectoryStep(javax.vecmath.Point3f[] trajectoryStep)
                           throws java.lang.Exception

Throws:

java.lang.Exception