public class GulpReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private float |
a |
private float |
alpha |
private java.util.Map<java.lang.String,java.lang.Float> |
atomCharges |
private float |
b |
private float |
beta |
private boolean |
bTest |
private float |
c |
private boolean |
coordinatesArePrimitive |
private java.lang.String |
energyUnits |
private float |
gamma |
private boolean |
isMolecular |
private boolean |
isPolymer |
private boolean |
isPrimitive |
private boolean |
isSlab |
private float[] |
primitiveData |
private java.lang.String |
sep |
private static java.lang.String[] |
tags |
private java.lang.Double |
totEnergy |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
GulpReader() |
Modifier and Type | Method and Description |
---|---|
void |
applySymmetryAndSetTrajectory() |
protected boolean |
checkLine() |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
protected void |
initializeReader() |
private void |
newAtomSet(boolean doSetUnitCell) |
private static int |
parameterIndex(java.lang.String key) |
private void |
readAtomicPos(boolean finalizeSymmetry) |
private void |
readCellParameters(boolean isLatticeVectors) |
private boolean |
readDimensionality() |
private void |
readEnergy() |
private void |
readFinalCell() |
private void |
readPartialCharges() |
private void |
readSpaceGroup() |
private void |
scalePrimitiveData(int i,
float value) |
private void |
setEnergy() |
private void |
setModelParameters(boolean isPrimitive) |
private void |
setParameter(java.lang.String key,
float value) |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, 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, processBinaryDocument, processDOM, processDSSR, 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, setup, setupASCR
private boolean isSlab
private boolean isPolymer
private boolean isMolecular
private boolean isPrimitive
private java.lang.String sep
private boolean coordinatesArePrimitive
private java.util.Map<java.lang.String,java.lang.Float> atomCharges
private boolean bTest
private float a
private float b
private float c
private float alpha
private float beta
private float gamma
private float[] primitiveData
private static final java.lang.String[] tags
private java.lang.Double totEnergy
private java.lang.String energyUnits
protected void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeSubclassReader()
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private boolean readDimensionality() throws java.lang.Exception
java.lang.Exception
private void readSpaceGroup() throws java.lang.Exception
java.lang.Exception
private static int parameterIndex(java.lang.String key)
private void setParameter(java.lang.String key, float value)
private void newAtomSet(boolean doSetUnitCell)
private void setModelParameters(boolean isPrimitive)
private void readCellParameters(boolean isLatticeVectors) throws java.lang.Exception
java.lang.Exception
private void readFinalCell() throws java.lang.Exception
java.lang.Exception
private void scalePrimitiveData(int i, float value)
public void applySymmetryAndSetTrajectory() throws java.lang.Exception
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
java.lang.Exception
private void readAtomicPos(boolean finalizeSymmetry) throws java.lang.Exception
java.lang.Exception
private void readPartialCharges() throws java.lang.Exception
java.lang.Exception
private void readEnergy() throws java.lang.Exception
java.lang.Exception
private void setEnergy()