org.jmol.adapter.readers.more
Class BinaryDcdReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.BinaryReader
          extended by 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  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
BinaryDcdReader()
           
 
Method Summary
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