org.jmol.adapter.readers.quantum
Class GamessUKReader

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

public class GamessUKReader
extends GamessReader

Field Summary

private List<Float>	occupancies
private List<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 String	fixShellTag(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 List<String> symmetries

occupancies

private List<Float> occupancies

Constructor Detail

GamessUKReader

public GamessUKReader()

Method Detail

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

readAtomsInBohrCoordinates

protected void readAtomsInBohrCoordinates()
                                   throws Exception

Specified by:

readAtomsInBohrCoordinates in class GamessReader

Throws:

Exception

fixShellTag

protected String fixShellTag(String tag)

Specified by:

fixShellTag in class GamessReader

readOrbitalSymmetryAndOccupancy

private void readOrbitalSymmetryAndOccupancy()
                                      throws Exception

Throws:

Exception

setOrbitalSymmetryAndOccupancy

private void setOrbitalSymmetryAndOccupancy()