Package org.jmol.adapter.readers.quantum
Class QCJSONReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
A molecular structure and orbital reader for MolDen files.
See http://www.cmbi.ru.nl/molden/molden_format.html
updated by Bob Hanson <hansonr@stolaf.edu> for Jmol 12.0/12.1
adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7
- Author:
- Matthew Zwier <mczwier@gmail.com>
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Nested Class Summary
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
FieldsFields inherited from class org.jmol.adapter.readers.quantum.MoldenReader
doSort, haveEnergy, loadGeometries, loadVibrations, modelAtomCount, optOnly, orbitalType, vibOnly
Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
_AM1_C, allowMopacDCoef, atomicNumbers, MIN_COEF, MOPAC_TYPES, mopacBasis
Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
scaleSlaters
Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
allowNoOrbitals, energyUnits, forceMOPAC, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, lastMoData, moTypes, orbitalsRead, shellCount
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
optional reader-specific method run first.getMapSafely
(Map<String, Object> map, String key) Safely get a Map from a Map using a key.protected void
private void
processJob
(Map<String, Object> job) private boolean
readBasisQC
(String moBasisID) private boolean
readFreqsAndModesQC
(ArrayList<Object> vibrations) private boolean
readGaussianBasisQC
(ArrayList<Object> listG, ArrayList<Object> listS) private boolean
readMolecularOrbitalsQC
(Map<String, Object> molecular_orbitals) Read basis and orbital information.(package private) boolean
readSlaterBasisQC
(ArrayList<Object> listS) private void
private float[]
toFloatArray
(double[] da) Methods inherited from class org.jmol.adapter.readers.quantum.MoldenReader
checkLine, rd, readSlaterBasis, sortMOs
Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
addSlaterBasis, createMopacSlaters, createSphericalSlaterByType, getMopacAtomZetaSPD, scaleSlater, setMOData
Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, getSlaters, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals
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, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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, 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 Details
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job
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jobCount
private int jobCount -
modelCount
private int modelCount -
lastBasisID
String lastBasisID
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Constructor Details
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QCJSONReader
public QCJSONReader()
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Method Details
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initializeReader
protected void initializeReader()- Overrides:
initializeReader
in classMoldenReader
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processJob
- Parameters:
job
-- Throws:
Exception
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classMoldenReader
- Throws:
Exception
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readSteps
- Throws:
Exception
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readFreqsAndModesQC
- Throws:
Exception
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readMolecularOrbitalsQC
Read basis and orbital information.- Parameters:
molecular_orbitals
-- Returns:
- true if successful
- Throws:
Exception
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toFloatArray
private float[] toFloatArray(double[] da) -
readBasisQC
- Throws:
Exception
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readSlaterBasisQC
- Throws:
Exception
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readGaussianBasisQC
private boolean readGaussianBasisQC(ArrayList<Object> listG, ArrayList<Object> listS) throws Exception - Throws:
Exception
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getMapSafely
Safely get a Map from a Map using a key.- Parameters:
map
-key
-- Returns:
- the Map or null
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