public class QCJSONReader extends MoldenReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
BasisFunctionReader.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, vibOnly
atomicNumbers, MIN_COEF
slaterArray, slaters
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells
addedData, 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, readSlaterBasis
createSphericalSlaterByType, scaleSlater
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
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, 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, setupASCR
private 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 MoldenReader
private void processJob(java.util.Map<java.lang.String,java.lang.Object> job) throws java.lang.Exception
job
- java.lang.Exception
public void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class MoldenReader
java.lang.Exception
private void readSteps() throws java.lang.Exception
java.lang.Exception
private boolean readFreqsAndModes(java.util.ArrayList<java.lang.Object> vibrations) throws java.lang.Exception
java.lang.Exception
private boolean readMolecularOrbitals(java.util.Map<java.lang.String,java.lang.Object> molecular_orbitals) throws java.lang.Exception
molecular_orbitals
- java.lang.Exception
private float[] toFloatArray(double[] da)
private boolean readBasis(java.lang.String moBasisID) throws java.lang.Exception
java.lang.Exception
boolean readSlaterBasis(java.util.ArrayList<java.lang.Object> listS) throws java.lang.Exception
java.lang.Exception
private boolean readGaussianBasis(java.util.ArrayList<java.lang.Object> listG, java.util.ArrayList<java.lang.Object> listS) throws java.lang.Exception
java.lang.Exception
private 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
-