org.jmol.adapter.readers.quantum
Class MOReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.BasisFunctionReader
          extended by org.jmol.adapter.readers.quantum.MOReader
Direct Known Subclasses:
GamessReader, GaussianReader, GenNBOReader, JaguarReader, PsiReader, QchemReader

public abstract class MOReader
extends BasisFunctionReader

General methods for reading molecular orbital data, including embedded output from the NBO program. In particular, when the AONBO keyword is included. requires the following sort of construct: public AtomSetCollection readAtomSetCollection(BufferedReader reader) { readAtomSetCollection(reader, "some type"); } protected boolean checkLine() { if (line.indexOf(...)) { doThis(); return true/false; } if (line.indexOf(...)) { doThat(); return true/false; } return checkNboLine(); }


Field Summary
private static java.lang.String DC_LIST
           
private static java.lang.String DS_LIST
           
protected  java.lang.String energyUnits
           
private static java.lang.String FC_LIST
           
private static java.lang.String FS_LIST
           
protected  int gaussianCount
           
protected  float[][] gaussians
           
private  boolean getNBOCharges
           
private  boolean getNBOs
           
private  boolean haveCoeffMap
           
protected  boolean haveNboCharges
           
protected  boolean haveNboOrbitals
           
protected  int HEADER_GAMESS_OCCUPANCIES
           
protected  int HEADER_GAMESS_ORIGINAL
           
protected  int HEADER_GAMESS_UK_MO
           
protected  int HEADER_NONE
           
protected  java.util.List moTypes
           
protected  boolean orbitalsRead
           
private static java.lang.String P_LIST
           
protected  int shellCount
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, 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
MOReader()
           
 
Method Summary
protected  void addMOData(int nColumns, java.util.List[] data, java.util.Hashtable[] mos)
           
protected  boolean checkNboLine()
           
protected  void getMOHeader(int headerType, java.lang.String[] tokens, java.util.Hashtable[] mos, int nThisLine)
           
private  void getNboCharges()
           
protected  void getNboTypes()
           
protected  void initializeReader()
           
protected  void readMolecularOrbitals(int headerType)
           
protected  void setMOData(boolean clearOrbitals)
           
protected  int setMOType(java.util.Hashtable mo, int i)
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDFMap, isQuantumBasisSupported, setMO
 
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, 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

shellCount

protected int shellCount

gaussianCount

protected int gaussianCount

gaussians

protected float[][] gaussians

energyUnits

protected java.lang.String energyUnits

moTypes

protected java.util.List moTypes

getNBOs

private boolean getNBOs

getNBOCharges

private boolean getNBOCharges

haveNboCharges

protected boolean haveNboCharges

haveNboOrbitals

protected boolean haveNboOrbitals

orbitalsRead

protected boolean orbitalsRead

HEADER_GAMESS_UK_MO

protected final int HEADER_GAMESS_UK_MO
See Also:
Constant Field Values

HEADER_GAMESS_OCCUPANCIES

protected final int HEADER_GAMESS_OCCUPANCIES
See Also:
Constant Field Values

HEADER_GAMESS_ORIGINAL

protected final int HEADER_GAMESS_ORIGINAL
See Also:
Constant Field Values

HEADER_NONE

protected final int HEADER_NONE
See Also:
Constant Field Values

haveCoeffMap

private boolean haveCoeffMap

P_LIST

private static final java.lang.String P_LIST
See Also:
Constant Field Values

DS_LIST

private static final java.lang.String DS_LIST
See Also:
Constant Field Values

DC_LIST

private static final java.lang.String DC_LIST
See Also:
Constant Field Values

FS_LIST

private static final java.lang.String FS_LIST
See Also:
Constant Field Values

FC_LIST

private static java.lang.String FC_LIST
Constructor Detail

MOReader

public MOReader()
Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception
Overrides:
initializeReader in class AtomSetCollectionReader
Throws:
java.lang.Exception

checkNboLine

protected boolean checkNboLine()
                        throws java.lang.Exception
Returns:
true if need to read line
Throws:
java.lang.Exception

getNboCharges

private void getNboCharges()
                    throws java.lang.Exception
Throws:
java.lang.Exception

getNboTypes

protected void getNboTypes()
                    throws java.lang.Exception
Throws:
java.lang.Exception

readMolecularOrbitals

protected void readMolecularOrbitals(int headerType)
                              throws java.lang.Exception
Throws:
java.lang.Exception

setMOType

protected int setMOType(java.util.Hashtable mo,
                        int i)

getMOHeader

protected void getMOHeader(int headerType,
                           java.lang.String[] tokens,
                           java.util.Hashtable[] mos,
                           int nThisLine)
                    throws java.lang.Exception
Throws:
java.lang.Exception

addMOData

protected void addMOData(int nColumns,
                         java.util.List[] data,
                         java.util.Hashtable[] mos)

setMOData

protected void setMOData(boolean clearOrbitals)