public class BinaryDcdReader extends BinaryReader
Modifier and Type | Field and Description |
---|---|
private java.util.BitSet |
bsFree |
private int |
nAtoms |
private int |
nFree |
private int |
nModels |
private float[] |
xAll |
private float[] |
yAll |
private float[] |
zAll |
doc
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
BinaryDcdReader() |
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() |
processBinaryDocument
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, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private int nModels
private int nAtoms
private int nFree
private java.util.BitSet bsFree
private float[] xAll
private float[] yAll
private float[] zAll
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected void readDocument() throws java.lang.Exception
readDocument
in class BinaryReader
java.lang.Exception
private float[] readFloatArray() throws java.lang.Exception
java.lang.Exception
private void readCoordinates() throws java.lang.Exception
java.lang.Exception
private boolean getTrajectoryStep(javax.vecmath.Point3f[] trajectoryStep) throws java.lang.Exception
java.lang.Exception