org.jmol.adapter.readers.more
Class MopacGraphfReader

java.lang.Object
  org.jmol.adapter.smarter.AtomSetCollectionReader
      org.jmol.adapter.readers.more.MopacDataReader
          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, 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

MopacGraphfReader()

Method Summary

(package private) void	readAtoms()
void	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, 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

atomicNumbers

int[] atomicNumbers

atomCount

int atomCount

invMatrix

float[][] invMatrix

Constructor Detail

MopacGraphfReader

public MopacGraphfReader()

Method Detail

readAtomSetCollection

public void 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