public class GenNBOReader extends MOReader
BasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
private static String |
DC_LIST |
private static String |
DS_LIST |
private static String |
FC_LIST |
private static String |
FS_LIST |
private boolean |
isArchive |
private boolean |
isOutputFile |
private String |
nboType |
private int |
nOrbitals0 |
private static String |
P_LIST |
private static String |
SP_LIST |
allowNoOrbitals, 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 |
|---|
GenNBOReader() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
checkLine() |
private boolean |
fillSlater(int[] slater,
int n,
int pt,
int ng) |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private void |
getAlphasAndExponents() |
private boolean |
getFile31() |
private void |
getFile46() |
private String |
getFileData(String ext) |
private int[] |
getIntData() |
protected void |
initializeReader() |
private boolean |
readData31(String line1) |
private void |
readData46() |
private void |
readData47() |
private void |
readMOs() |
addCoef, 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, 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 isOutputFile
private String nboType
private int nOrbitals0
private boolean isArchive
private static String P_LIST
private static String SP_LIST
private static String DS_LIST
private static String DC_LIST
private static String FS_LIST
private static String FC_LIST
protected void initializeReader()
throws Exception
initializeReader in class MOReaderExceptionprotected void finalizeSubclassReader()
throws Exception
AtomSetCollectionReaderfinalizeSubclassReader in class AtomSetCollectionReaderExceptionprotected boolean checkLine()
throws Exception
checkLine in class AtomSetCollectionReaderExceptionprivate boolean fillSlater(int[] slater,
int n,
int pt,
int ng)