org.jmol.adapter.readers.quantum
Class BasisFunctionReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.BasisFunctionReader
Direct Known Subclasses:
MOReader, SlaterReader

abstract class BasisFunctionReader
extends AtomSetCollectionReader

Author:
hansonr

Field Summary
protected  java.lang.String alphaBeta
           
protected static java.lang.String CANONICAL_DC_LIST
           
protected static java.lang.String CANONICAL_DS_LIST
           
protected static java.lang.String CANONICAL_FC_LIST
           
protected static java.lang.String CANONICAL_FS_LIST
           
protected  int[][] dfCoefMaps
           
private  boolean filterIsNot
           
private  java.lang.String[] filterTokens
           
protected  boolean ignoreMOs
           
protected  java.util.Hashtable moData
           
protected  int nOrbitals
           
protected  java.util.List orbitals
           
protected  java.util.List shells
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
 
Constructor Summary
BasisFunctionReader()
           
 
Method Summary
protected static java.lang.String canonicalizeQuantumSubshellTag(java.lang.String tag)
           
protected  boolean filterMO()
           
protected  void fixSlaterTypes(int typeOld, int typeNew)
           
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.
protected  boolean isQuantumBasisSupported(char ch)
           
protected  void setMO(java.util.Map mo)
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

shells

protected java.util.List shells

moData

protected java.util.Hashtable moData

orbitals

protected java.util.List orbitals

nOrbitals

protected int nOrbitals

alphaBeta

protected java.lang.String alphaBeta

ignoreMOs

protected boolean ignoreMOs

dfCoefMaps

protected int[][] dfCoefMaps

filterTokens

private java.lang.String[] filterTokens

filterIsNot

private boolean filterIsNot

CANONICAL_DC_LIST

protected static java.lang.String CANONICAL_DC_LIST

CANONICAL_FC_LIST

protected static java.lang.String CANONICAL_FC_LIST

CANONICAL_DS_LIST

protected static java.lang.String CANONICAL_DS_LIST

CANONICAL_FS_LIST

protected static java.lang.String CANONICAL_FS_LIST
Constructor Detail

BasisFunctionReader

BasisFunctionReader()
Method Detail

filterMO

protected boolean filterMO()

setMO

protected void setMO(java.util.Map mo)

isQuantumBasisSupported

protected boolean isQuantumBasisSupported(char ch)

getDFMap

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. This list is reader-dependent.

Parameters:
fileList -
shellType -
jmolList -
minLength -
Returns:
true if successful

canonicalizeQuantumSubshellTag

protected static final java.lang.String canonicalizeQuantumSubshellTag(java.lang.String tag)

fixSlaterTypes

protected void fixSlaterTypes(int typeOld,
                              int typeNew)