org.jmol.adapter.readers.more
Class JaguarReader

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

public class JaguarReader
extends AtomSetCollectionReader

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)  int atomCount
           
(package private)  int gaussianCount
           
(package private)  float lumoEnergy
           
(package private)  int moCount
           
(package private)  java.util.Hashtable moData
           
(package private)  java.util.Vector orbitals
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup
 
Constructor Summary
JaguarReader()
           
 
Method Summary
private  void readAtoms()
           
 AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readBasis()
           
(package private)  void readBasisNormalized()
           
private  void readCharges()
           
private  void readFrequencies()
           
private  void readMolecularOrbitals()
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetry, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

atomCount

int atomCount

moCount

int moCount

gaussianCount

int gaussianCount

lumoEnergy

float lumoEnergy

moData

java.util.Hashtable moData

orbitals

java.util.Vector orbitals
Constructor Detail

JaguarReader

public JaguarReader()
Method Detail

readAtomSetCollection

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

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

readMolecularOrbitals

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

readFrequencies

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