Package org.jmol.adapter.readers.quantum
Class QCJSONReader
- java.lang.Object
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class QCJSONReader extends MoldenReader
A molecular structure and orbital reader for MolDen files. See http://www.cmbi.ru.nl/molden/molden_format.html updated by Bob Hansonfor Jmol 12.0/12.1 adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7 - Author:
- Matthew Zwier
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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 boolean
haveEnergy
private java.util.Map<java.lang.String,java.lang.Object>
job
private int
jobCount
(package private) java.lang.String
lastBasisID
private int
modelCount
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Fields inherited from class org.jmol.adapter.readers.quantum.MoldenReader
doSort, loadGeometries, loadVibrations, modelAtomCount, optOnly, orbitalType, vibOnly
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Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
_AM1_C, allowMopacDCoef, atomicNumbers, MIN_COEF, MOPAC_TYPES, mopacBasis
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Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
scaleSlaters
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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
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Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters
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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, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterCased, 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, 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 Constructor Description QCJSONReader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
finalizeSubclassReader()
optional reader-specific method run first.private static java.util.Map<java.lang.String,java.lang.Object>
getMapSafely(java.util.Map<java.lang.String,java.lang.Object> map, java.lang.String key)
Safely get a Map from a Map using a key.protected void
initializeReader()
private void
processJob(java.util.Map<java.lang.String,java.lang.Object> job)
private boolean
readBasis(java.lang.String moBasisID)
private boolean
readFreqsAndModes(java.util.ArrayList<java.lang.Object> vibrations)
private boolean
readGaussianBasis(java.util.ArrayList<java.lang.Object> listG, java.util.ArrayList<java.lang.Object> listS)
private boolean
readMolecularOrbitals(java.util.Map<java.lang.String,java.lang.Object> molecular_orbitals)
Read basis and orbital information.(package private) boolean
readSlaterBasis(java.util.ArrayList<java.lang.Object> listS)
private void
readSteps()
private void
sortMOs()
private float[]
toFloatArray(double[] da)
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Methods inherited from class org.jmol.adapter.readers.quantum.MoldenReader
checkLine, rd, readSlaterBasis
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Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
addSlaterBasis, createMopacSlaters, createSphericalSlaterByType, getMopacAtomZetaSPD, scaleSlater, setMOData
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Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, getSlaters, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
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Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals
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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, 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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Method Detail
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initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in classMoldenReader
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processJob
private void processJob(java.util.Map<java.lang.String,java.lang.Object> job) throws java.lang.Exception
- Parameters:
job
-- Throws:
java.lang.Exception
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finalizeSubclassReader
public void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classMoldenReader
- Throws:
java.lang.Exception
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readSteps
private void readSteps() throws java.lang.Exception
- Throws:
java.lang.Exception
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readFreqsAndModes
private boolean readFreqsAndModes(java.util.ArrayList<java.lang.Object> vibrations) throws java.lang.Exception
- Throws:
java.lang.Exception
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readMolecularOrbitals
private boolean readMolecularOrbitals(java.util.Map<java.lang.String,java.lang.Object> molecular_orbitals) throws java.lang.Exception
Read basis and orbital information.- Parameters:
molecular_orbitals
-- Returns:
- true if successful
- Throws:
java.lang.Exception
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toFloatArray
private float[] toFloatArray(double[] da)
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readBasis
private boolean readBasis(java.lang.String moBasisID) throws java.lang.Exception
- Throws:
java.lang.Exception
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readSlaterBasis
boolean readSlaterBasis(java.util.ArrayList<java.lang.Object> listS) throws java.lang.Exception
- Throws:
java.lang.Exception
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readGaussianBasis
private boolean readGaussianBasis(java.util.ArrayList<java.lang.Object> listG, java.util.ArrayList<java.lang.Object> listS) throws java.lang.Exception
- Throws:
java.lang.Exception
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sortMOs
private void sortMOs()
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getMapSafely
private static java.util.Map<java.lang.String,java.lang.Object> getMapSafely(java.util.Map<java.lang.String,java.lang.Object> map, java.lang.String key)
Safely get a Map from a Map using a key.- Parameters:
map
-key
-- Returns:
- the Map or null
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