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 |
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, 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, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, 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, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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, processBinaryDocument, 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, setup, setupASCRprivate boolean isSlab
private boolean isPolymer
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 AtomSetCollectionReaderjava.lang.Exceptionprotected void finalizeSubclassReader()
AtomSetCollectionReaderfinalizeSubclassReader in class AtomSetCollectionReaderprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate boolean readDimensionality()
throws java.lang.Exception
java.lang.Exceptionprivate void readSpaceGroup()
throws java.lang.Exception
java.lang.Exceptionprivate 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.Exceptionprivate void readFinalCell()
throws java.lang.Exception
java.lang.Exceptionprivate void scalePrimitiveData(int i,
float value)
public void applySymmetryAndSetTrajectory()
throws java.lang.Exception
applySymmetryAndSetTrajectory in class AtomSetCollectionReaderjava.lang.Exceptionprivate void readAtomicPos(boolean finalizeSymmetry)
throws java.lang.Exception
java.lang.Exceptionprivate void readPartialCharges()
throws java.lang.Exception
java.lang.Exceptionprivate void readEnergy()
throws java.lang.Exception
java.lang.Exceptionprivate void setEnergy()