org.jmol.adapter.readers.quantum
Class GamessUKReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.BasisFunctionReader
          extended by org.jmol.adapter.readers.quantum.MOReader
              extended by org.jmol.adapter.readers.quantum.GamessReader
                  extended by org.jmol.adapter.readers.quantum.GamessUKReader

public class GamessUKReader
extends GamessReader


Field Summary
private  java.util.List<java.lang.Float> occupancies
           
private  java.util.List<java.lang.String> symmetries
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.GamessReader
atomNames
 
Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
 
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
 
Constructor Summary
GamessUKReader()
           
 
Method Summary
protected  boolean checkLine()
           
protected  java.lang.String fixShellTag(java.lang.String tag)
           
protected  void readAtomsInBohrCoordinates()
           
private  void readOrbitalSymmetryAndOccupancy()
           
private  void setOrbitalSymmetryAndOccupancy()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.GamessReader
fixBasisLine, readBasisInfo, readControlInfo, readFrequencies, readGaussianBasis, setCalculationType
 
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addMOData, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals, setMOData, setMOType
 
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, 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.List<java.lang.String> symmetries

occupancies

private java.util.List<java.lang.Float> occupancies
Constructor Detail

GamessUKReader

public GamessUKReader()
Method Detail

checkLine

protected boolean checkLine()
                     throws java.lang.Exception
Overrides:
checkLine in class AtomSetCollectionReader
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()