org.jmol.adapter.readers.more
Class GamessUKReader

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.GamessReader
              extended by org.jmol.adapter.readers.more.GamessUKReader

public class GamessUKReader
extends GamessReader


Field Summary
private  java.util.Vector occupancies
           
private  java.util.Vector symmetries
           
 
Fields inherited from class org.jmol.adapter.readers.more.GamessReader
atomNames
 
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
GamessUKReader()
           
 
Method Summary
protected  boolean checkLine()
           
protected  java.lang.String fixShellTag(java.lang.String tag)
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
protected  void readAtomsInBohrCoordinates()
           
private  void readOrbitalSymmetryAndOccupancy()
           
private  void setOrbitalSymmetryAndOccupancy()
           
 
Methods inherited from class org.jmol.adapter.readers.more.GamessReader
fixBasisLine, readBasisInfo, readControlInfo, readFrequencies, readGaussianBasis, setCalculationType
 
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

symmetries

private java.util.Vector symmetries

occupancies

private java.util.Vector occupancies
Constructor Detail

GamessUKReader

public GamessUKReader()
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

readAtomsInBohrCoordinates

protected void readAtomsInBohrCoordinates()
                                   throws java.lang.Exception
Specified by:
readAtomsInBohrCoordinates in class GamessReader
Throws:
java.lang.Exception

fixShellTag

protected java.lang.String fixShellTag(java.lang.String tag)
Specified by:
fixShellTag in class GamessReader

readOrbitalSymmetryAndOccupancy

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

setOrbitalSymmetryAndOccupancy

private void setOrbitalSymmetryAndOccupancy()