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
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"
-
-
Field Summary
Fields Modifier and Type Field Description private javajs.util.BS
bsFree
private int
crystGroup
private int
nAtoms
private int
nFree
private int
nModels
private float[]
xAll
private float[]
yAll
private float[]
zAll
-
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, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, 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, modDim, modelNumber, ms, mustFinalizeModelSet, next, 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
-
-
Constructor Summary
Constructors Constructor Description BinaryDcdReader()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private float[]
calcUnitCell(double[] abc)
private boolean
getTrajectoryStep(javajs.util.P3[] trajectoryStep)
protected void
initializeReader()
protected void
processBinaryDocument()
private void
readCoordinates()
private double[]
readDoubleArray()
private float[]
readFloatArray()
protected void
setup(java.lang.String fullPath, java.util.Map<java.lang.String,java.lang.Object> htParams, java.lang.Object reader)
private java.lang.String
trimString(java.lang.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
-
-
-
-
Method Detail
-
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
-
initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in classAtomSetCollectionReader
-
processBinaryDocument
protected void processBinaryDocument() throws java.lang.Exception
- Overrides:
processBinaryDocument
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
-
trimString
private java.lang.String trimString(java.lang.String s)
-
readFloatArray
private float[] readFloatArray() throws java.lang.Exception
- Throws:
java.lang.Exception
-
readDoubleArray
private double[] readDoubleArray() throws java.lang.Exception
- Throws:
java.lang.Exception
-
readCoordinates
private void readCoordinates() throws java.lang.Exception
- Throws:
java.lang.Exception
-
getTrajectoryStep
private boolean getTrajectoryStep(javajs.util.P3[] trajectoryStep) throws java.lang.Exception
- Throws:
java.lang.Exception
-
calcUnitCell
private float[] calcUnitCell(double[] abc)
-
-