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, 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, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, 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

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(String fullPath, Map<String,Object> htParams, Object reader)

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- 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
Constructor Details
- BinaryDcdReader
  
  public BinaryDcdReader()
Method Details
- setup
  
  protected void setup(String fullPath, Map<String,Object> htParams, Object reader)
  
  Overrides:
  
  setup in class AtomSetCollectionReader
- initializeReader
  
  protected void initializeReader()
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
- processBinaryDocument
  
  protected void processBinaryDocument() throws Exception
  
  Overrides:
  
  processBinaryDocument in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- trimString
  
  private String trimString(String s)
- readFloatArray
  
  private float[] readFloatArray() throws Exception
  
  Throws:
  
  Exception
- readDoubleArray
  
  private double[] readDoubleArray() throws Exception
  
  Throws:
  
  Exception
- readCoordinates
  
  private void readCoordinates() throws Exception
  
  Throws:
  
  Exception
- getTrajectoryStep
  
  private boolean getTrajectoryStep(javajs.util.P3[] trajectoryStep) throws Exception
  
  Throws:
  
  Exception
- calcUnitCell
  
  private float[] calcUnitCell(double[] abc)

Class BinaryDcdReader

Field Summary

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Details

nModels

nAtoms

nFree

bsFree

xAll

yAll

zAll

crystGroup

Constructor Details

BinaryDcdReader

Method Details

setup

initializeReader

processBinaryDocument

trimString

readFloatArray

readDoubleArray

readCoordinates

getTrajectoryStep

calcUnitCell