org.jmol.adapter.readers.more
Class JaguarReader

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.JaguarReader

public class JaguarReader
extends MOReader

Jaguar reader tested for the two samples files in CVS. Both these files were created with Jaguar version 4.0, release 20.


Field Summary
(package private)  float lumoEnergy
           
(package private)  int moCount
           
 
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
JaguarReader()
           
 
Method Summary
protected  boolean checkLine()
           
private  void readAtoms()
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readBasis()
           
(package private)  void readBasisNormalized()
           
private  void readCharges()
           
private  void readFrequencies()
           
private  void readJaguarMolecularOrbitals()
           
 
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

moCount

int moCount

lumoEnergy

float lumoEnergy
Constructor Detail

JaguarReader

public JaguarReader()
Method Detail

readAtomSetCollection

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

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

readAtoms

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

readCharges

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

readBasis

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

readBasisNormalized

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

readJaguarMolecularOrbitals

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

readFrequencies

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