Package org.jmol.adapter.readers.quantum
Class MopacGraphfReader
- 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.SlaterReader
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- org.jmol.adapter.readers.quantum.MopacSlaterReader
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- org.jmol.adapter.readers.quantum.MopacGraphfReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class MopacGraphfReader extends MopacSlaterReader
Reads Mopac 2007 GRAPHF output files- Author:
- Bob Hanson <hansonr@stolaf.edu>
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Nested Class Summary
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
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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 private int
ac
private float[][]
invMatrix
private boolean
isNewFormat
private int
nCoefficients
private javajs.util.Lst<float[]>
orbitalData
private javajs.util.Lst<String>
orbitalInfo
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Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
atomicNumbers, MIN_COEF
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Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
slaterArray, slaters
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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 MopacGraphfReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
checkLine()
protected void
initializeReader()
private void
readAtoms()
private boolean
readKeywords()
private void
readMolecularOrbitals(boolean isBeta)
private void
readSlaterBasis()
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Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
createSphericalSlaterByType, scaleSlater
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Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
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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, 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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Field Detail
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ac
private int ac
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nCoefficients
private int nCoefficients
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invMatrix
private float[][] invMatrix
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isNewFormat
private boolean isNewFormat
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orbitalData
private javajs.util.Lst<float[]> orbitalData
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orbitalInfo
private javajs.util.Lst<String> orbitalInfo
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Method Detail
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initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in classAtomSetCollectionReader
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checkLine
protected boolean checkLine() throws Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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readMolecularOrbitals
private void readMolecularOrbitals(boolean isBeta) throws Exception
- Throws:
Exception
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