org.jmol.adapter.readers.more
Class MOReader

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

abstract class MOReader
extends AtomSetCollectionReader

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
protected  java.lang.String alphaBeta
           
protected  boolean continuing
           
protected  java.lang.String energyUnits
           
private  boolean filterIsNot
           
private  java.lang.String[] filterTokens
           
protected  int gaussianCount
           
protected  float[][] gaussians
           
private  boolean getNBOCharges
           
private  boolean getNBOs
           
protected  boolean haveNboCharges
           
protected  int HEADER_GAMESS_OCCUPANCIES
           
protected  int HEADER_GAMESS_ORIGINAL
           
protected  int HEADER_GAMESS_UK_MO
           
protected  int HEADER_NONE
           
protected  boolean ignoreMOs
           
protected  boolean iHaveAtoms
           
protected  java.util.Hashtable moData
           
protected  java.util.Vector moTypes
           
protected  java.util.Vector orbitals
           
protected  int shellCount
           
protected  java.util.Vector shells
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount
 
Constructor Summary
MOReader()
           
 
Method Summary
protected  void addMOData(int nColumns, java.util.Vector[] data, java.util.Hashtable[] mos)
           
protected abstract  boolean checkLine()
           
protected  boolean checkNboLine()
           
protected  boolean filterMO()
           
protected  void finalizeMoReader()
           
protected  void getMOHeader(int headerType, java.lang.String[] tokens, java.util.Hashtable[] mos, int nThisLine)
           
private  void getNboCharges()
           
protected  void getNboTypes()
           
private  void initializeMoReader(java.io.BufferedReader reader, java.lang.String type)
           
abstract  void readAtomSetCollection(java.io.BufferedReader reader)
           
 void readAtomSetCollection(java.io.BufferedReader reader, java.lang.String type)
           
protected  void readMolecularOrbitals(int headerType)
           
protected  void setMOData(boolean clearOrbitals)
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, 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

moData

protected java.util.Hashtable moData

shells

protected java.util.Vector shells

gaussians

protected float[][] gaussians

orbitals

protected java.util.Vector orbitals

energyUnits

protected java.lang.String energyUnits

moTypes

protected java.util.Vector moTypes

getNBOs

private boolean getNBOs

getNBOCharges

private boolean getNBOCharges

haveNboCharges

protected boolean haveNboCharges

filterTokens

private java.lang.String[] filterTokens

filterIsNot

private boolean filterIsNot

iHaveAtoms

protected boolean iHaveAtoms

continuing

protected boolean continuing

ignoreMOs

protected boolean ignoreMOs

alphaBeta

protected java.lang.String alphaBeta

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
Constructor Detail

MOReader

MOReader()
Method Detail

readAtomSetCollection

public abstract void readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class AtomSetCollectionReader

checkLine

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

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader,
                                  java.lang.String type)

finalizeMoReader

protected void finalizeMoReader()

initializeMoReader

private void initializeMoReader(java.io.BufferedReader reader,
                                java.lang.String type)

filterMO

protected boolean filterMO()

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

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.Vector[] data,
                         java.util.Hashtable[] mos)

setMOData

protected void setMOData(boolean clearOrbitals)