org.jmol.adapter.readers.quantum

Class GamessUSReader

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.GamessUSReader

public class GamessUSReader
extends GamessReader

Field Summary

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, 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

Constructor Summary

Constructors

Constructor and Description
GamessUSReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkLine()
protected java.lang.String	fixShellTag(java.lang.String tag)
private void	readAtomsInAngstromCoordinates()
protected void	readAtomsInBohrCoordinates()
(package private) void	readDipoleMoment()
protected void	readEFPInBohrCoordinates()
protected void	readMolecularOrbitals(int headerType)
(package private) void	readPartialCharges()

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, setMOData, setMOType

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDFMap, isQuantumBasisSupported, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, 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

Constructor Detail

GamessUSReader

public GamessUSReader()

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

readMolecularOrbitals

protected void readMolecularOrbitals(int headerType)
                              throws java.lang.Exception

Overrides:

readMolecularOrbitals in class MOReader

Throws:

java.lang.Exception

readEFPInBohrCoordinates

protected void readEFPInBohrCoordinates()
                                 throws java.lang.Exception

Throws:

java.lang.Exception

readAtomsInBohrCoordinates

protected void readAtomsInBohrCoordinates()
                                   throws java.lang.Exception

Specified by:

readAtomsInBohrCoordinates in class GamessReader

Throws:

java.lang.Exception

readAtomsInAngstromCoordinates

private void readAtomsInAngstromCoordinates()
                                     throws java.lang.Exception

Throws:

java.lang.Exception

fixShellTag

protected java.lang.String fixShellTag(java.lang.String tag)

Specified by:

fixShellTag in class GamessReader

readPartialCharges

void readPartialCharges()
                  throws java.lang.Exception

Throws:

java.lang.Exception

readDipoleMoment

void readDipoleMoment()
                throws java.lang.Exception

Throws:

java.lang.Exception