MOReader
, SlaterReader
, SpartanInputReader
, SpartanReader
public abstract class BasisFunctionReader extends AtomSetCollectionReader
Modifier and Type | Class | Description |
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class |
BasisFunctionReader.MOEnergySorter |
Modifier and Type | Field | Description |
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protected java.lang.String |
alphaBeta |
|
protected int[][] |
dfCoefMaps |
|
private boolean |
filterIsNot |
|
private java.lang.String[] |
filterTokens |
|
protected boolean |
ignoreMOs |
|
java.util.Map<java.lang.String,java.lang.Object> |
moData |
|
protected int |
nCoef |
|
protected int |
nOrbitals |
|
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, 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 | Description |
---|---|
BasisFunctionReader() |
Modifier and Type | Method | Description |
---|---|---|
protected static java.lang.String |
canonicalizeQuantumSubshellTag(java.lang.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(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, 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
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
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 fileList, int shellType, java.lang.String jmolList, int minLength)
fileList
- shellType
- jmolList
- minLength
- 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