public class GenNBOReader extends MOReader
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field and Description |
---|---|
private static java.lang.String |
DC_LIST |
private static java.lang.String |
DS_LIST |
private static java.lang.String |
FC_LIST |
private static java.lang.String |
FS_LIST |
private boolean |
isArchive |
private boolean |
isOutputFile |
private java.lang.String |
nboType |
private int |
nOrbitals0 |
private static java.lang.String |
P_LIST |
private static java.lang.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, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, 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) |
private void |
getAlphasAndExponents() |
private boolean |
getFile31() |
private void |
getFile46() |
private java.lang.String |
getFileData(java.lang.String ext) |
private int[] |
getIntData() |
protected void |
initializeReader() |
private boolean |
readData31(java.lang.String line1) |
private void |
readData46() |
private void |
readData47() |
private void |
readMOs() |
addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData, setMOType
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getNewDfCoefMap, 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, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, 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, processDSSR, 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 java.lang.String nboType
private int nOrbitals0
private boolean isArchive
private static java.lang.String P_LIST
private static java.lang.String SP_LIST
private static java.lang.String DS_LIST
private static java.lang.String DC_LIST
private static java.lang.String FS_LIST
private static java.lang.String FC_LIST
protected void initializeReader() throws java.lang.Exception
initializeReader
in class MOReader
java.lang.Exception
private void readMOs() throws java.lang.Exception
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private java.lang.String getFileData(java.lang.String ext) throws java.lang.Exception
java.lang.Exception
private boolean getFile31() throws java.lang.Exception
java.lang.Exception
private void getFile46() throws java.lang.Exception
java.lang.Exception
private void readData47() throws java.lang.Exception
java.lang.Exception
private int[] getIntData() throws java.lang.Exception
java.lang.Exception
private boolean fillSlater(int[] slater, int n, int pt, int ng)
private void getAlphasAndExponents() throws java.lang.Exception
java.lang.Exception
private boolean readData31(java.lang.String line1) throws java.lang.Exception
java.lang.Exception
private void readData46() throws java.lang.Exception
java.lang.Exception