Package org.jmol.adapter.readers.quantum

Class QCJSONReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

org.jmol.adapter.readers.quantum.SlaterReader

org.jmol.adapter.readers.quantum.MopacSlaterReader

org.jmol.adapter.readers.quantum.MoldenReader

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 boolean	haveEnergy
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, loadGeometries, loadVibrations, modelAtomCount, optOnly, orbitalType, vibOnly

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

atomicNumbers, MIN_COEF

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

slaterArray, slaters

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

alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells

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

addedData, addedDataKey, addVibrations, allow_a_len_1, 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, 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	readBasis(String moBasisID)
private boolean	readFreqsAndModes(ArrayList<Object> vibrations)
private boolean	readGaussianBasis(ArrayList<Object> listG, ArrayList<Object> listS)
private boolean	readMolecularOrbitals(Map<String,Object> molecular_orbitals)	Read basis and orbital information.
(package private) boolean	readSlaterBasis(ArrayList<Object> listS)
private void	readSteps()
private void	sortMOs()
private float[]	toFloatArray(double[] da)

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

checkLine, rd, readSlaterBasis

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

createSphericalSlaterByType, scaleSlater

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

addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals

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, 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, 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 Detail

job

private Map<String,Object> job

jobCount

private int jobCount

modelCount

private int modelCount

haveEnergy

private boolean haveEnergy

lastBasisID

String lastBasisID

Constructor Detail

QCJSONReader

public QCJSONReader()

Method Detail

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

readFreqsAndModes

private boolean readFreqsAndModes(ArrayList<Object> vibrations)
                           throws Exception

Throws:

Exception

readMolecularOrbitals

private boolean readMolecularOrbitals(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)

readBasis

private boolean readBasis(String moBasisID)
                   throws Exception

Throws:

Exception

readSlaterBasis

boolean readSlaterBasis(ArrayList<Object> listS)
                 throws Exception

Throws:

Exception

readGaussianBasis

private boolean readGaussianBasis(ArrayList<Object> listG,
                                  ArrayList<Object> listS)
                           throws Exception

Throws:

Exception

sortMOs

private void sortMOs()

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