org.jmol.adapter.readers.quantum
Class GamessReader
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
- Direct Known Subclasses:
- GamessUKReader, GamessUSReader
public abstract class GamessReader
- extends MOReader
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, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, 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, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, 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 |
atomNames
protected java.util.List atomNames
calcOptions
private java.util.Hashtable calcOptions
isTypeSet
private boolean isTypeSet
GamessReader
public GamessReader()
readAtomsInBohrCoordinates
protected abstract void readAtomsInBohrCoordinates()
throws java.lang.Exception
- Throws:
java.lang.Exception
readGaussianBasis
protected void readGaussianBasis(java.lang.String initiator,
java.lang.String terminator)
throws java.lang.Exception
- Throws:
java.lang.Exception
fixShellTag
protected abstract java.lang.String fixShellTag(java.lang.String tag)
readFrequencies
protected void readFrequencies()
throws java.lang.Exception
- Throws:
java.lang.Exception
fixBasisLine
protected static java.lang.String fixBasisLine(java.lang.String line)
setCalculationType
protected void setCalculationType()
readControlInfo
protected void readControlInfo()
throws java.lang.Exception
- Throws:
java.lang.Exception
readBasisInfo
protected void readBasisInfo()
throws java.lang.Exception
- Throws:
java.lang.Exception
readCalculationInfo
private void readCalculationInfo(java.lang.String type)
throws java.lang.Exception
- Throws:
java.lang.Exception