org.jmol.adapter.readers.more
Class MopacGraphfReader

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

public class MopacGraphfReader
extends MopacDataReader

Reads Mopac 2007 GRAPHF output files

Author:
Bob Hanson

Field Summary
(package private)  int atomCount
           
(package private)  int[] atomicNumbers
           
(package private)  float[][] invMatrix
           
 
Fields inherited from class org.jmol.adapter.readers.more.MopacDataReader
dValues, floatinfo, intinfo, MIN_COEF, moData, nOrbitals, 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
MopacGraphfReader()
           
 
Method Summary
(package private)  void readAtoms()
           
 AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
private  boolean readKeywords()
           
(package private)  void readMOs(boolean isBeta)
           
(package private)  void readSlaterBasis()
           
 
Methods inherited from class org.jmol.adapter.readers.more.MopacDataReader
addSlater, setMOs, setSlaters
 
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

atomicNumbers

int[] atomicNumbers

atomCount

int atomCount

invMatrix

float[][] invMatrix
Constructor Detail

MopacGraphfReader

public MopacGraphfReader()
Method Detail

readAtomSetCollection

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

readAtoms

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

readSlaterBasis

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

readMOs

void readMOs(boolean isBeta)
       throws java.lang.Exception
Throws:
java.lang.Exception

readKeywords

private boolean readKeywords()
                      throws java.lang.Exception
Throws:
java.lang.Exception