public 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 String |
alphaBeta |
protected int[][] |
dfCoefMaps |
private boolean |
filterIsNot |
private String[] |
filterTokens |
protected boolean |
ignoreMOs |
Map<String,Object> |
moData |
protected int |
nCoef |
protected int |
nOrbitals |
javajs.util.Lst<Map<String,Object>> |
orbitals |
javajs.util.Lst<int[]> |
shells |
private String |
spin |
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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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BasisFunctionReader() |
Modifier and Type | Method and Description |
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protected static String |
canonicalizeQuantumSubshellTag(String tag) |
protected void |
discardPreviousAtoms() |
protected boolean |
filterMO()
check line for filter options
|
protected int |
fixSlaterTypes(int typeOld,
int typeNew) |
int[][] |
getDfCoefMaps() |
protected boolean |
getDFMap(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) |
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, 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
public javajs.util.Lst<int[]> shells
protected int nOrbitals
protected boolean ignoreMOs
protected String alphaBeta
protected int[][] dfCoefMaps
private String[] filterTokens
private boolean filterIsNot
private String spin
protected int nCoef
protected boolean filterMO()
protected boolean getDFMap(String fileList, int shellType, String jmolList, int minLength)
fileList
- shellType
- jmolList
- minLength
- public int[][] getDfCoefMaps()
protected static final String canonicalizeQuantumSubshellTag(String tag)
protected int fixSlaterTypes(int typeOld, int typeNew)
public static int getQuantumShellTagIDSpherical(String tag)
public static int getQuantumShellTagID(String tag)
public static String getQuantumShellTag(int id)
protected void discardPreviousAtoms()
discardPreviousAtoms
in class AtomSetCollectionReader