org.jmol.adapter.readers.quantum
Class BasisFunctionReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
- Direct Known Subclasses:
- MOReader, SlaterReader, SpartanInputReader, SpartanReader
abstract class BasisFunctionReader
- extends AtomSetCollectionReader
- Author:
- hansonr
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer |
Method Summary |
protected static java.lang.String |
canonicalizeQuantumSubshellTag(java.lang.String tag)
|
protected boolean |
filterMO()
|
protected void |
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)
|
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
shells
protected java.util.List<int[]> shells
moData
protected java.util.Map<java.lang.String,java.lang.Object> moData
orbitals
protected java.util.List<java.util.Map<java.lang.String,java.lang.Object>> orbitals
nOrbitals
protected int nOrbitals
ignoreMOs
protected boolean ignoreMOs
alphaBeta
protected java.lang.String alphaBeta
dfCoefMaps
protected int[][] dfCoefMaps
filterTokens
private java.lang.String[] filterTokens
filterIsNot
private boolean filterIsNot
CANONICAL_DC_LIST
protected static java.lang.String CANONICAL_DC_LIST
CANONICAL_FC_LIST
protected static java.lang.String CANONICAL_FC_LIST
CANONICAL_DS_LIST
protected static java.lang.String CANONICAL_DS_LIST
CANONICAL_FS_LIST
protected static java.lang.String CANONICAL_FS_LIST
BasisFunctionReader
BasisFunctionReader()
filterMO
protected boolean filterMO()
setMO
protected void setMO(java.util.Map<java.lang.String,java.lang.Object> mo)
isQuantumBasisSupported
protected boolean isQuantumBasisSupported(char ch)
getDFMap
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. This list is
reader-dependent.
- Parameters:
fileList
- shellType
- jmolList
- minLength
-
- Returns:
- true if successful
getDfCoefMaps
protected int[][] getDfCoefMaps()
canonicalizeQuantumSubshellTag
protected static final java.lang.String canonicalizeQuantumSubshellTag(java.lang.String tag)
fixSlaterTypes
protected void fixSlaterTypes(int typeOld,
int typeNew)