Package org.jmol.adapter.readers.more
Class BinaryDcdReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.more.BinaryDcdReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class BinaryDcdReader extends AtomSetCollectionReader
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
Fields Modifier and Type Field Description private BS
bsFree
private int
nAtoms
private int
nFree
private int
nModels
private float[]
xAll
private float[]
yAll
private float[]
zAll
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description BinaryDcdReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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)
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, 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, 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 Detail
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nModels
private int nModels
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nAtoms
private int nAtoms
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nFree
private int nFree
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bsFree
private BS bsFree
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xAll
private float[] xAll
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yAll
private float[] yAll
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zAll
private float[] zAll
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Method Detail
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setup
protected void setup(java.lang.String fullPath, java.util.Map<java.lang.String,java.lang.Object> htParams, java.lang.Object reader)
- Overrides:
setup
in classAtomSetCollectionReader
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initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in classAtomSetCollectionReader
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processBinaryDocument
protected void processBinaryDocument() throws java.lang.Exception
- Overrides:
processBinaryDocument
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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readFloatArray
private float[] readFloatArray() throws java.lang.Exception
- Throws:
java.lang.Exception
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readCoordinates
private void readCoordinates() throws java.lang.Exception
- Throws:
java.lang.Exception
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getTrajectoryStep
private boolean getTrajectoryStep(javajs.util.P3[] trajectoryStep) throws java.lang.Exception
- Throws:
java.lang.Exception
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