Package org.jmol.adapter.readers.quantum
Class BasisFunctionReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
MOReader
,SpartanInputReader
,SpartanReader
- Author:
- hansonr invalid input: '<'hansonr@stolaf.edu>
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Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionprotected String
protected int[][]
private boolean
private String[]
private int[]
protected boolean
protected int
protected int
javajs.util.Lst
<int[]> protected SlaterData[]
protected javajs.util.Lst
<SlaterData> private String
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected static final String
protected void
protected void
protected void
enableShell
(int shellType) This flag must be explicitly set when a reader has been verified to properly sort G, H, I,...protected boolean
filterMO()
check line for filter optionsprotected int
fixSlaterTypes
(int typeOld, int typeNew) int[][]
protected boolean
finds the position in the Jmol-required list of function types.static String
getQuantumShellTag
(int id) static int
static int
void
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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, 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
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Field Details
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shells
public javajs.util.Lst<int[]> shells -
slaters
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slaterArray
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moData
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orbitals
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nOrbitals
protected int nOrbitals -
ignoreMOs
protected boolean ignoreMOs -
alphaBeta
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dfCoefMaps
protected int[][] dfCoefMaps -
filterTokens
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filterIsNot
private boolean filterIsNot -
spin
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orbitalMaps
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highLEnabled
private int[] highLEnabled -
nCoef
protected int nCoef
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Constructor Details
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BasisFunctionReader
public BasisFunctionReader()
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Method Details
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filterMO
protected boolean filterMO()check line for filter options- Returns:
- true if a match
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setMO
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getDFMap
protected boolean getDFMap(String shell, String fileList, int shellType, String jmolList, int minLength) finds the position in the Jmol-required list of function types. This list is reader-dependent.- Parameters:
shell
- TODOfileList
-shellType
-jmolList
-minLength
-- Returns:
- true if successful
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enableShell
protected void enableShell(int shellType) This flag must be explicitly set when a reader has been verified to properly sort G, H, I,... orbitals.- Parameters:
shellType
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getDfCoefMaps
public int[][] getDfCoefMaps() -
canonicalizeQuantumSubshellTag
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fixSlaterTypes
protected int fixSlaterTypes(int typeOld, int typeNew) -
getQuantumShellTagIDSpherical
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getQuantumShellTagID
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getQuantumShellTag
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discardPreviousAtoms
protected void discardPreviousAtoms()- Overrides:
discardPreviousAtoms
in classAtomSetCollectionReader
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clearOrbitals
protected void clearOrbitals()
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