Package org.jmol.adapter.readers.quantum
Class GamessReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.quantum.BasisFunctionReader
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- org.jmol.adapter.readers.quantum.MOReader
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- org.jmol.adapter.readers.quantum.GamessReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
GamessUKReader
,GamessUSReader
public abstract class GamessReader extends MOReader
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Nested Class Summary
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
Fields Modifier and Type Field Description protected javajs.util.Lst<java.lang.String>
atomNames
private java.util.Map<java.lang.String,java.lang.String>
calcOptions
private boolean
isTypeSet
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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
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Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description GamessReader()
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description protected static java.lang.String
fixBasisLine(java.lang.String line)
protected abstract java.lang.String
fixShellTag(java.lang.String tag)
protected abstract void
readAtomsInBohrCoordinates()
protected void
readBasisInfo()
private void
readCalculationInfo(java.lang.String type)
protected void
readControlInfo()
protected void
readEnergy()
protected void
readFrequencies()
protected void
readGaussianBasis(java.lang.String initiator, java.lang.String terminator)
protected void
setCalculationType()
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Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals, setMOData
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Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, 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
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Method Detail
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readAtomsInBohrCoordinates
protected abstract void readAtomsInBohrCoordinates() throws java.lang.Exception
- Throws:
java.lang.Exception
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readEnergy
protected void readEnergy()
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readGaussianBasis
protected void readGaussianBasis(java.lang.String initiator, java.lang.String terminator) throws java.lang.Exception
- Throws:
java.lang.Exception
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fixShellTag
protected abstract java.lang.String fixShellTag(java.lang.String tag)
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readFrequencies
protected void readFrequencies() throws java.lang.Exception
- Throws:
java.lang.Exception
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fixBasisLine
protected static java.lang.String fixBasisLine(java.lang.String line)
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setCalculationType
protected void setCalculationType()
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readControlInfo
protected void readControlInfo() throws java.lang.Exception
- Throws:
java.lang.Exception
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readBasisInfo
protected void readBasisInfo() throws java.lang.Exception
- Throws:
java.lang.Exception
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readCalculationInfo
private void readCalculationInfo(java.lang.String type) throws java.lang.Exception
- Throws:
java.lang.Exception
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