org.jmol.adapter.readers.quantum.QCJSONReader

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 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>

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
Field Summary

Fields

Modifier and Type

Field

Description

private Map<String,Object>

job

private int

jobCount

(package private) String

lastBasisID

private int

modelCount

Fields 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
Constructor Summary

Constructors

Constructor

Description

QCJSONReader()
Method Summary

Modifier and Type

Method

Description

void

finalizeSubclassReader()

optional reader-specific method run first.

private static Map<String,Object>

getMapSafely(Map<String,Object> map, String key)

Safely get a Map from a Map using a key.

protected void

initializeReader()

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

readSteps()

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- job
  
  private Map<String,Object> job
- jobCount
  
  private int jobCount
- modelCount
  
  private int modelCount
- lastBasisID
  
  String lastBasisID
Constructor Details
- QCJSONReader
  
  public QCJSONReader()
Method Details
- initializeReader
  
  protected void initializeReader()
  
  Overrides:
  
  initializeReader in class MoldenReader
- processJob
  
  private void processJob(Map<String,Object> job) throws Exception
  
  Parameters:
  
  job -
  
  Throws:
  
  Exception
- finalizeSubclassReader
  
  public void finalizeSubclassReader() throws Exception
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class MoldenReader
  
  Throws:
  
  Exception
- readSteps
  
  private void readSteps() throws Exception
  
  Throws:
  
  Exception
- readFreqsAndModesQC
  
  private boolean readFreqsAndModesQC(ArrayList<Object> vibrations) throws Exception
  
  Throws:
  
  Exception
- readMolecularOrbitalsQC
  
  private boolean readMolecularOrbitalsQC(Map<String,Object> molecular_orbitals) throws Exception
  
  Read basis and orbital information.
  
  Parameters:
  
  molecular_orbitals -
  
  Returns:
  
  true if successful
  
  Throws:
  
  Exception
- toFloatArray
  
  private float[] toFloatArray(double[] da)
- readBasisQC
  
  private boolean readBasisQC(String moBasisID) throws Exception
  
  Throws:
  
  Exception
- readSlaterBasisQC
  
  boolean readSlaterBasisQC(ArrayList<Object> listS) throws Exception
  
  Throws:
  
  Exception
- readGaussianBasisQC
  
  private boolean readGaussianBasisQC(ArrayList<Object> listG, ArrayList<Object> listS) throws Exception
  
  Throws:
  
  Exception
- getMapSafely
  
  private static Map<String,Object> getMapSafely(Map<String,Object> map, String key)
  
  Safely get a Map from a Map using a key.
  
  Parameters:
  
  map -
  
  key -
  
  Returns:
  
  the Map or null

Class QCJSONReader

Nested Class Summary

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

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

Field Summary

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

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

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

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

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

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

Constructor Summary

Method Summary

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

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

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

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

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

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

Methods inherited from class java.lang.Object

Field Details

job

jobCount

modelCount

lastBasisID

Constructor Details

QCJSONReader

Method Details

initializeReader

processJob

finalizeSubclassReader

readSteps

readFreqsAndModesQC

readMolecularOrbitalsQC

toFloatArray

readBasisQC

readSlaterBasisQC

readGaussianBasisQC

getMapSafely