abstract class BasisFunctionReader extends AtomSetCollectionReader
Modifier and Type | Class and Description |
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class |
BasisFunctionReader.MOEnergySorter |
Modifier and Type | Field and Description |
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protected java.lang.String |
alphaBeta |
protected static java.lang.String |
CANONICAL_DC_LIST |
protected static java.lang.String |
CANONICAL_DS_LIST |
protected static java.lang.String |
CANONICAL_FC_LIST |
protected static java.lang.String |
CANONICAL_FS_LIST |
protected int[][] |
dfCoefMaps |
private boolean |
filterIsNot |
private java.lang.String[] |
filterTokens |
protected boolean |
ignoreMOs |
protected java.util.Map<java.lang.String,java.lang.Object> |
moData |
protected int |
nCoef |
protected int |
nOrbitals |
protected javajs.util.List<java.util.Map<java.lang.String,java.lang.Object>> |
orbitals |
protected javajs.util.List<int[]> |
shells |
addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, vwr
Constructor and Description |
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BasisFunctionReader() |
Modifier and Type | Method and Description |
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protected static java.lang.String |
canonicalizeQuantumSubshellTag(java.lang.String tag) |
protected boolean |
filterMO() |
protected int |
fixSlaterTypes(int typeOld,
int typeNew) |
protected int[][] |
getDfCoefMaps() |
protected boolean |
getDFMap(java.lang.String fileList,
int shellType,
java.lang.String jmolList,
int minLength)
finds the position in the Jmol-required list of function types.
|
protected boolean |
isQuantumBasisSupported(char ch) |
protected void |
setMO(java.util.Map<java.lang.String,java.lang.Object> mo) |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR
protected javajs.util.List<int[]> shells
protected java.util.Map<java.lang.String,java.lang.Object> moData
protected javajs.util.List<java.util.Map<java.lang.String,java.lang.Object>> orbitals
protected int nOrbitals
protected boolean ignoreMOs
protected java.lang.String alphaBeta
protected int[][] dfCoefMaps
private java.lang.String[] filterTokens
private boolean filterIsNot
protected static java.lang.String CANONICAL_DC_LIST
protected static java.lang.String CANONICAL_FC_LIST
protected static java.lang.String CANONICAL_DS_LIST
protected static java.lang.String CANONICAL_FS_LIST
protected int nCoef
protected boolean filterMO()
protected void setMO(java.util.Map<java.lang.String,java.lang.Object> mo)
protected boolean isQuantumBasisSupported(char ch)
protected boolean getDFMap(java.lang.String fileList, int shellType, java.lang.String jmolList, int minLength)
fileList
- shellType
- jmolList
- minLength
- protected int[][] getDfCoefMaps()
protected static final java.lang.String canonicalizeQuantumSubshellTag(java.lang.String tag)
protected int fixSlaterTypes(int typeOld, int typeNew)