public class BinaryDcdReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private BS |
bsFree |
private int |
nAtoms |
private int |
nFree |
private int |
nModels |
private float[] |
xAll |
private float[] |
yAll |
private float[] |
zAll |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
BinaryDcdReader() |
Modifier and Type | Method and Description |
---|---|
private boolean |
getTrajectoryStep(javajs.util.P3[] trajectoryStep) |
protected void |
initializeReader() |
protected void |
processBinaryDocument() |
private void |
readCoordinates() |
private float[] |
readFloatArray() |
protected void |
setup(java.lang.String fullPath,
java.util.Map<java.lang.String,java.lang.Object> htParams,
java.lang.Object reader) |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processDOM, processDSSR, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setupASCR
private int nModels
private int nAtoms
private int nFree
private BS bsFree
private float[] xAll
private float[] yAll
private float[] zAll
protected void setup(java.lang.String fullPath, java.util.Map<java.lang.String,java.lang.Object> htParams, java.lang.Object reader)
setup
in class AtomSetCollectionReader
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected void processBinaryDocument() throws java.lang.Exception
processBinaryDocument
in class AtomSetCollectionReader
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(javajs.util.P3[] trajectoryStep) throws java.lang.Exception
java.lang.Exception