Package org.jmol.adapter.readers.quantum
Class BasisFunctionReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.quantum.BasisFunctionReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
MOReader
,SlaterReader
,SpartanInputReader
,SpartanReader
public abstract class BasisFunctionReader extends AtomSetCollectionReader
- Author:
- hansonr <hansonr@stolaf.edu>
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
BasisFunctionReader.MOEnergySorter
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Field Summary
Fields Modifier and Type Field Description protected String
alphaBeta
protected int[][]
dfCoefMaps
private boolean
filterIsNot
private String[]
filterTokens
private int[]
highLEnabled
protected boolean
ignoreMOs
Map<String,Object>
moData
protected int
nCoef
protected int
nOrbitals
(package private) Map<String,String>
orbitalMaps
javajs.util.Lst<Map<String,Object>>
orbitals
javajs.util.Lst<int[]>
shells
private String
spin
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description BasisFunctionReader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected static String
canonicalizeQuantumSubshellTag(String tag)
protected void
clearOrbitals()
protected void
discardPreviousAtoms()
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[][]
getDfCoefMaps()
protected boolean
getDFMap(String shell, String fileList, int shellType, String jmolList, int minLength)
finds the position in the Jmol-required list of function types.static String
getQuantumShellTag(int id)
static int
getQuantumShellTagID(String tag)
static int
getQuantumShellTagIDSpherical(String tag)
void
setMO(Map<String,Object> mo)
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, 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, 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 Detail
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shells
public javajs.util.Lst<int[]> shells
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nOrbitals
protected int nOrbitals
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ignoreMOs
protected boolean ignoreMOs
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alphaBeta
protected String alphaBeta
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dfCoefMaps
protected int[][] dfCoefMaps
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filterTokens
private String[] filterTokens
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filterIsNot
private boolean filterIsNot
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spin
private String spin
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highLEnabled
private int[] highLEnabled
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nCoef
protected int nCoef
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Method Detail
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filterMO
protected boolean filterMO()
check line for filter options- Returns:
- true if a match
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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()
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canonicalizeQuantumSubshellTag
protected static final String canonicalizeQuantumSubshellTag(String tag)
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fixSlaterTypes
protected int fixSlaterTypes(int typeOld, int typeNew)
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getQuantumShellTagIDSpherical
public static int getQuantumShellTagIDSpherical(String tag)
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getQuantumShellTagID
public static int getQuantumShellTagID(String tag)
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getQuantumShellTag
public static String getQuantumShellTag(int id)
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discardPreviousAtoms
protected void discardPreviousAtoms()
- Overrides:
discardPreviousAtoms
in classAtomSetCollectionReader
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clearOrbitals
protected void clearOrbitals()
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