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, 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, 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, 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 Detail

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 Detail
- BinaryDcdReader
```
public BinaryDcdReader()
```

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 class AtomSetCollectionReader

initializeReader
```
protected void initializeReader()
```
Overrides:

initializeReader in class AtomSetCollectionReader

processBinaryDocument
```
protected void processBinaryDocument()
                              throws java.lang.Exception
```
Overrides:

processBinaryDocument in class AtomSetCollectionReader

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)

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 Detail

nModels

nAtoms

nFree

bsFree

xAll

yAll

zAll

crystGroup

Constructor Detail

BinaryDcdReader

Method Detail

setup

initializeReader

processBinaryDocument

trimString

readFloatArray

readDoubleArray

readCoordinates

getTrajectoryStep

calcUnitCell