public class QCJSONReader extends MoldenReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorterBasisFunctionReader.MOEnergySorter| Modifier and Type | Field and 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 |
doSort, loadGeometries, loadVibrations, modelAtomCount, optOnly, orbitalType, vibOnlyatomicNumbers, MIN_COEFslaterArray, slatersalphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shellsaddedData, addedDataKey, addVibrations, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr| Constructor and Description |
|---|
QCJSONReader() |
| Modifier and Type | Method and 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) |
checkLine, readSlaterBasiscreateSphericalSlaterByType, scaleSlateraddSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitalscanonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMOaddAtomXYZSymName, 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, rd, 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, setupASCRprivate java.util.Map<java.lang.String,java.lang.Object> job
private int jobCount
private int modelCount
private boolean haveEnergy
java.lang.String lastBasisID
protected void initializeReader()
initializeReader in class MoldenReaderprivate void processJob(java.util.Map<java.lang.String,java.lang.Object> job)
throws java.lang.Exception
job - java.lang.Exceptionpublic void finalizeSubclassReader()
throws java.lang.Exception
AtomSetCollectionReaderfinalizeSubclassReader in class MoldenReaderjava.lang.Exceptionprivate void readSteps()
throws java.lang.Exception
java.lang.Exceptionprivate boolean readFreqsAndModes(java.util.ArrayList<java.lang.Object> vibrations)
throws java.lang.Exception
java.lang.Exceptionprivate boolean readMolecularOrbitals(java.util.Map<java.lang.String,java.lang.Object> molecular_orbitals)
throws java.lang.Exception
molecular_orbitals - java.lang.Exceptionprivate float[] toFloatArray(double[] da)
private boolean readBasis(java.lang.String moBasisID)
throws java.lang.Exception
java.lang.Exceptionboolean readSlaterBasis(java.util.ArrayList<java.lang.Object> listS)
throws java.lang.Exception
java.lang.Exceptionprivate boolean readGaussianBasis(java.util.ArrayList<java.lang.Object> listG,
java.util.ArrayList<java.lang.Object> listS)
throws java.lang.Exception
java.lang.Exceptionprivate void sortMOs()
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)
map - key -