Package org.jmol.adapter.readers.quantum

Class BasisFunctionReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

MOReader, SlaterReader, SpartanInputReader, SpartanReader

public abstract class BasisFunctionReader
extends AtomSetCollectionReader

Author:

hansonr <hansonr@stolaf.edu>

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	BasisFunctionReader.MOEnergySorter

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

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addedData, addedDataKey, addVibrations, allow_a_len_1, 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, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor	Description
BasisFunctionReader()

Method Summary

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 options
protected 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)

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

shells

public javajs.util.Lst<int[]> shells

moData

public Map<String,Object> moData

orbitals

public javajs.util.Lst<Map<String,Object>> orbitals

nOrbitals

protected int nOrbitals

ignoreMOs

protected boolean ignoreMOs

alphaBeta

protected String alphaBeta

dfCoefMaps

protected int[][] dfCoefMaps

filterTokens

private String[] filterTokens

filterIsNot

private boolean filterIsNot

spin

private String spin

orbitalMaps

Map<String,String> orbitalMaps

highLEnabled

private int[] highLEnabled

nCoef

protected int nCoef

Constructor Detail

BasisFunctionReader

public BasisFunctionReader()

Method Detail

filterMO

protected boolean filterMO()

check line for filter options

Returns:

true if a match

setMO

public void setMO(Map<String,Object> mo)

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 - TODO

fileList -

shellType -

jmolList -

minLength -

Returns:

true if successful

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 -

getDfCoefMaps

public int[][] getDfCoefMaps()

canonicalizeQuantumSubshellTag

protected static final String canonicalizeQuantumSubshellTag(String tag)

fixSlaterTypes

protected int fixSlaterTypes(int typeOld,
                             int typeNew)

getQuantumShellTagIDSpherical

public static int getQuantumShellTagIDSpherical(String tag)

getQuantumShellTagID

public static int getQuantumShellTagID(String tag)

getQuantumShellTag

public static String getQuantumShellTag(int id)

discardPreviousAtoms

protected void discardPreviousAtoms()

Overrides:

discardPreviousAtoms in class AtomSetCollectionReader

clearOrbitals

protected void clearOrbitals()