Package org.jmol.adapter.readers.more
Class BinaryDcdReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.BinaryDcdReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
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"
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate javajs.util.BS
private int
private int
private int
private int
private float[]
private float[]
private float[]
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate float[]
calcUnitCell
(double[] abc) private boolean
getTrajectoryStep
(javajs.util.P3[] trajectoryStep) protected void
protected void
private void
private double[]
private float[]
protected void
private String
trimString
(String s) Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processDOM, 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
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Field Details
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nModels
private int nModels -
nAtoms
private int nAtoms -
nFree
private int nFree -
bsFree
private javajs.util.BS bsFree -
xAll
private float[] xAll -
yAll
private float[] yAll -
zAll
private float[] zAll -
crystGroup
private int crystGroup
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Constructor Details
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BinaryDcdReader
public BinaryDcdReader()
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Method Details
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setup
- Overrides:
setup
in classAtomSetCollectionReader
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initializeReader
protected void initializeReader()- Overrides:
initializeReader
in classAtomSetCollectionReader
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processBinaryDocument
- Overrides:
processBinaryDocument
in classAtomSetCollectionReader
- Throws:
Exception
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trimString
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readFloatArray
- Throws:
Exception
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readDoubleArray
- Throws:
Exception
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readCoordinates
- Throws:
Exception
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getTrajectoryStep
- Throws:
Exception
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calcUnitCell
private float[] calcUnitCell(double[] abc)
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