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 java.lang.String |
alphaBeta |
protected int[][] |
dfCoefMaps |
private boolean |
filterIsNot |
private java.lang.String[] |
filterTokens |
private int[] |
highLEnabled |
protected boolean |
ignoreMOs |
java.util.Map<java.lang.String,java.lang.Object> |
moData |
protected int |
nCoef |
protected int |
nOrbitals |
(package private) java.util.Map<java.lang.String,java.lang.String> |
orbitalMaps |
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
orbitals |
javajs.util.Lst<int[]> |
shells |
private java.lang.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, 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
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 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 options
|
protected int |
fixSlaterTypes(int typeOld,
int typeNew) |
int[][] |
getDfCoefMaps() |
protected boolean |
getDFMap(java.lang.String shell,
java.lang.String fileList,
int shellType,
java.lang.String jmolList,
int minLength)
finds the position in the Jmol-required list of function types.
|
static java.lang.String |
getQuantumShellTag(int id) |
static int |
getQuantumShellTagID(java.lang.String tag) |
static int |
getQuantumShellTagIDSpherical(java.lang.String tag) |
void |
setMO(java.util.Map<java.lang.String,java.lang.Object> mo) |
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
public javajs.util.Lst<int[]> shells
public java.util.Map<java.lang.String,java.lang.Object> moData
public 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
private java.lang.String spin
java.util.Map<java.lang.String,java.lang.String> orbitalMaps
private int[] highLEnabled
protected int nCoef
protected boolean filterMO()
public void setMO(java.util.Map<java.lang.String,java.lang.Object> mo)
protected boolean getDFMap(java.lang.String shell, java.lang.String fileList, int shellType, java.lang.String jmolList, int minLength)
shell
- TODOfileList
- shellType
- jmolList
- minLength
- protected void enableShell(int shellType)
shellType
- public 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)
protected void discardPreviousAtoms()
discardPreviousAtoms
in class AtomSetCollectionReader
protected void clearOrbitals()