org.jmol.adapter.readers.more
public class BinaryDcdReader extends BinaryReader
Modifier and Type | Field and Description |
---|---|
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 |
doc
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 and Description |
---|
BinaryDcdReader() |
Modifier and Type | Method and Description |
---|---|
private boolean |
getTrajectoryStep(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, 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
private int nModels
private int nAtoms
private int nFree
private BitSet bsFree
private float[] xAll
private float[] yAll
private float[] zAll
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected void readDocument() throws Exception
readDocument
in class BinaryReader
Exception