public class GaussianFchkReader extends GaussianReader
BasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
private static String[] |
AO_TYPES |
private int |
atomCount |
private Map<String,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, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, 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, readFrequencies, readMolecularOrbitalsaddCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMODatacanonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMOaddAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, 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, 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 int atomCount
private static String[] AO_TYPES
protected void initializeReader()
throws Exception
initializeReader in class GaussianReaderExceptionprivate float[] fillFloat(float[] f0,
int i,
int n)
protected void readAtoms()
throws Exception
readAtoms in class GaussianReaderExceptionprotected void readBonds()
protected void readDipoleMoment()
throws Exception
readDipoleMoment in class GaussianReaderExceptionprotected void readPartialCharges()
throws Exception
GaussianReaderreadPartialCharges in class GaussianReaderException - When an I/O error or discardlines error occursprotected void readBasis()
throws Exception
readBasis in class GaussianReaderExceptionprivate void getOrbitals(float[] e,
float[] c,
int occ,
int nElec)