Package 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

All Implemented Interfaces:

javajs.api.GenericLineReader

public class GamessUSReader
extends GamessReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

BasisFunctionReader.MOEnergySorter

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	lowdenCharges

Fields inherited from class org.jmol.adapter.readers.quantum.GamessReader

atomNames

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader

allowNoOrbitals, 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, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells

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

addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor	Description
GamessUSReader()

Method Summary

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

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

fixBasisLine, readBasisInfo, readControlInfo, readEnergy, readFrequencies, readGaussianBasis, setCalculationType

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

addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, setMOData

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

canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

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

addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

lowdenCharges

private boolean lowdenCharges

Constructor Detail

GamessUSReader

public GamessUSReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws Exception

Overrides:

initializeReader in class MOReader

Throws:

Exception

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

readInputDeck

private boolean readInputDeck()
                       throws Exception

Throws:

Exception

readMolecularOrbitals

protected void readMolecularOrbitals(int headerType)
                              throws Exception

Overrides:

readMolecularOrbitals in class MOReader

Throws:

Exception

readEFPInBohrCoordinates

protected void readEFPInBohrCoordinates()
                                 throws Exception

Throws:

Exception

readAtomsInBohrCoordinates

protected void readAtomsInBohrCoordinates()
                                   throws Exception

Specified by:

readAtomsInBohrCoordinates in class GamessReader

Throws:

Exception

readAtomsInAngstromCoordinates

private void readAtomsInAngstromCoordinates()
                                     throws Exception

Throws:

Exception

fixShellTag

protected String fixShellTag(String tag)

Specified by:

fixShellTag in class GamessReader

readPartialCharges

void readPartialCharges()
                 throws Exception

Throws:

Exception

readDipoleMoment

void readDipoleMoment()
               throws Exception

Throws:

Exception