java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.quantum.BasisFunctionReader
  - - org.jmol.adapter.readers.quantum.MOReader
    - - 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 for Jmol 12.0/12.1 adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7

Author:

Matthew Zwier

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 java.util.Map<java.lang.String,java.lang.Object>`	`job`
`private int`	`jobCount`
`(package private) java.lang.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
_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, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, paramsCentroid, paramsLattice, 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

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)`

Methods inherited from class org.jmol.adapter.readers.quantum.MoldenReader
checkLine, rd, readSlaterBasis

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, 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 java.util.Map<java.lang.String,java.lang.Object> job

jobCount
```
private int jobCount
```

modelCount
```
private int modelCount
```

haveEnergy
```
private boolean haveEnergy
```

lastBasisID
```
java.lang.String lastBasisID
```

Constructor Detail
- QCJSONReader
```
public QCJSONReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
```
Overrides:

initializeReader in class MoldenReader

processJob

private void processJob(java.util.Map<java.lang.String,java.lang.Object> job)
                 throws java.lang.Exception

Parameters:: job -
Throws:: java.lang.Exception

finalizeSubclassReader
```
public void finalizeSubclassReader()
                            throws java.lang.Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class MoldenReader

Throws:

java.lang.Exception

readSteps

private void readSteps()
                throws java.lang.Exception

Throws:: java.lang.Exception

readFreqsAndModes

private boolean readFreqsAndModes(java.util.ArrayList<java.lang.Object> vibrations)
                           throws java.lang.Exception

Throws:: java.lang.Exception

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

toFloatArray

private float[] toFloatArray(double[] da)

readBasis

private boolean readBasis(java.lang.String moBasisID)
                   throws java.lang.Exception

Throws:: java.lang.Exception

readSlaterBasis

boolean readSlaterBasis(java.util.ArrayList<java.lang.Object> listS)
                 throws java.lang.Exception

Throws:: java.lang.Exception

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

sortMOs
```
private void sortMOs()
```

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

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 Detail

job

jobCount

modelCount

haveEnergy

lastBasisID

Constructor Detail

QCJSONReader

Method Detail

initializeReader

processJob

finalizeSubclassReader

readSteps

readFreqsAndModes

readMolecularOrbitals

toFloatArray

readBasis

readSlaterBasis

readGaussianBasis

sortMOs

getMapSafely