org.jmol.adapter.readers.more
Class PsiReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.MOReader
          extended by org.jmol.adapter.readers.more.PsiReader

public class PsiReader
extends MOReader

Reader for Psi3 output files. -- http://www.psicode.org/ preliminary version: -- coordinates only -- final geometry only; not reading steps -- no charges -- no frequencies -- no orbitals (Can't handle irreducible representations here.)


Field Summary
(package private)  java.util.Vector atomNames
           
(package private)  java.util.Vector shellsByUniqueAtom
           
(package private)  java.util.Hashtable uniqueAtomMap
           
 
Fields inherited from class org.jmol.adapter.readers.more.MOReader
alphaBeta, continuing, energyUnits, gaussianCount, gaussians, haveNboCharges, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, ignoreMOs, iHaveAtoms, moData, moTypes, orbitals, shellCount, 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
PsiReader()
           
 
Method Summary
protected  boolean checkLine()
           
private  void readAtoms(boolean isInitial)
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readBasis()
           
(package private)  void readPsiMolecularOrbitals()
           
private  void readSCFDone()
          Interprets the SCF Done: section.
private  void readUniqueAtoms()
           
 
Methods inherited from class org.jmol.adapter.readers.more.MOReader
addMOData, checkNboLine, filterMO, finalizeMoReader, getMOHeader, getNboTypes, readAtomSetCollection, readMolecularOrbitals, setMOData
 
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

atomNames

java.util.Vector atomNames

shellsByUniqueAtom

java.util.Vector shellsByUniqueAtom

uniqueAtomMap

java.util.Hashtable uniqueAtomMap
Constructor Detail

PsiReader

public PsiReader()
Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class MOReader
Parameters:
reader - BufferedReader associated with the Gaussian output text.

checkLine

protected boolean checkLine()
                     throws java.lang.Exception
Specified by:
checkLine in class MOReader
Returns:
true if need to read new line
Throws:
java.lang.Exception

readSCFDone

private void readSCFDone()
                  throws java.lang.Exception
Interprets the SCF Done: section.

Throws:
java.lang.Exception - If an error occurs

readAtoms

private void readAtoms(boolean isInitial)
                throws java.lang.Exception
Throws:
java.lang.Exception

readBasis

void readBasis()
         throws java.lang.Exception
Throws:
java.lang.Exception

readUniqueAtoms

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

readPsiMolecularOrbitals

void readPsiMolecularOrbitals()
                        throws java.lang.Exception
Throws:
java.lang.Exception