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, shellCount
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
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, 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, setMOData
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
addAtomXYZSymName, 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, setupASCR
private 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 MOReader
Exception
protected void finalizeSubclassReader() throws Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
Exception
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private boolean fillSlater(int[] slater, int n, int pt, int ng)