public class MopacGraphfReader extends MopacSlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorterBasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
private int |
atomCount |
private float[][] |
invMatrix |
private boolean |
isNewFormat |
private int |
nCoefficients |
private javajs.util.List<float[]> |
orbitalData |
private javajs.util.List<String> |
orbitalInfo |
atomicNumbers, MIN_COEFslaterArray, slatersalphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shellsaddVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer| Constructor and Description |
|---|
MopacGraphfReader() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
checkLine() |
protected void |
initializeReader() |
private void |
readAtoms() |
private boolean |
readKeywords() |
private void |
readMolecularOrbitals(boolean isBeta) |
private void |
readSlaterBasis() |
createSphericalSlaterByType, scaleSlateraddSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitalscanonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMOaddJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCRprivate int atomCount
private int nCoefficients
private float[][] invMatrix
private boolean isNewFormat
private javajs.util.List<float[]> orbitalData
private javajs.util.List<String> orbitalInfo
protected void initializeReader()
initializeReader in class AtomSetCollectionReaderprotected boolean checkLine()
throws Exception
checkLine in class AtomSetCollectionReaderExceptionprivate void readMolecularOrbitals(boolean isBeta)
throws Exception
Exception