public class GaussianFchkReader extends GaussianReader
BasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
private static java.lang.String[] |
AO_TYPES |
private int |
atomCount |
private java.util.Map<java.lang.String,java.lang.Object> |
fileData |
calculationNumber, namedSetsallowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCountalphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shellsaddedData, 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, isPrimitive, 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 |
|---|
GaussianFchkReader() |
| Modifier and Type | Method and Description |
|---|---|
private void |
checkForFreq() |
private float[] |
fillFloat(float[] f0,
int i,
int n) |
private void |
getOrbitals(float[] e,
float[] c,
int occ,
int nElec) |
protected void |
initializeReader() |
private void |
readAllData() |
protected void |
readAtoms() |
protected void |
readBasis() |
protected void |
readBonds() |
protected void |
readDipoleMoment() |
protected void |
readMolecularObitals() |
protected void |
readPartialCharges()
Reads partial charges and assigns them only to the last atom set.
|
checkLine, finalizeSubclassReader, readFrequencies, readMolecularOrbitalsaddCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMODatacanonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMOaddAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, 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 java.util.Map<java.lang.String,java.lang.Object> fileData
private int atomCount
private static java.lang.String[] AO_TYPES
protected void initializeReader()
throws java.lang.Exception
initializeReader in class GaussianReaderjava.lang.Exceptionprivate void checkForFreq()
throws java.lang.Exception
java.lang.Exceptionprivate float[] fillFloat(float[] f0,
int i,
int n)
private void readAllData()
throws java.lang.Exception
java.lang.Exceptionprotected void readAtoms()
throws java.lang.Exception
readAtoms in class GaussianReaderjava.lang.Exceptionprotected void readBonds()
protected void readDipoleMoment()
throws java.lang.Exception
readDipoleMoment in class GaussianReaderjava.lang.Exceptionprotected void readPartialCharges()
throws java.lang.Exception
GaussianReaderreadPartialCharges in class GaussianReaderjava.lang.Exception - When an I/O error or discardlines error occursprotected void readBasis()
throws java.lang.Exception
readBasis in class GaussianReaderjava.lang.Exceptionprotected void readMolecularObitals()
throws java.lang.Exception
java.lang.Exceptionprivate void getOrbitals(float[] e,
float[] c,
int occ,
int nElec)