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.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
orbitals |
protected javajs.util.Lst<int[]> |
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 |
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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.
|
static int[][] |
getNewDfCoefMap() |
static java.lang.String |
getQuantumShellTag(int id) |
static int |
getQuantumShellTagID(java.lang.String tag) |
static int |
getQuantumShellTagIDSpherical(java.lang.String tag) |
protected void |
setMO(java.util.Map<java.lang.String,java.lang.Object> mo) |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, 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, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, 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
protected javajs.util.Lst<int[]> shells
protected java.util.Map<java.lang.String,java.lang.Object> moData
protected javajs.util.Lst<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 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)
public static int getQuantumShellTagIDSpherical(java.lang.String tag)
public static int getQuantumShellTagID(java.lang.String tag)
public static java.lang.String getQuantumShellTag(int id)
public static final int[][] getNewDfCoefMap()