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"
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 |
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 |
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
BinaryDcdReader
public BinaryDcdReader()
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