org.jmol.adapter.readers.quantum
public class MoldenReader extends MopacSlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
Modifier and Type | Field and Description |
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private BitSet |
bsAtomOK |
private BitSet |
bsBadIndex |
private boolean |
loadGeometries |
private boolean |
loadVibrations |
private int |
modelAtomCount |
private boolean |
optOnly |
private String |
orbitalType |
private boolean |
vibOnly |
atomicNumbers, MIN_COEF
slaterArray, slaters
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
Constructor and Description |
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MoldenReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
private boolean |
checkOrbitalType(String line) |
void |
finalizeReader() |
private void |
fixOrbitalType() |
private String[] |
getMoTokens(String line) |
protected void |
initializeReader() |
private void |
readAtoms() |
private void |
readAtomSet(String atomSetName,
boolean isBohr,
boolean asClone) |
private boolean |
readFreqsAndModes() |
private boolean |
readGaussianBasis() |
private boolean |
readGeometryOptimization() |
private boolean |
readMolecularOrbitals() |
private void |
skipTo(String key) |
createSphericalSlaterByType, scaleSlater
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private boolean loadGeometries
private boolean loadVibrations
private boolean vibOnly
private boolean optOnly
private String orbitalType
private int modelAtomCount
private BitSet bsAtomOK
private BitSet bsBadIndex
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
public void finalizeReader()
finalizeReader
in class AtomSetCollectionReader
private boolean checkOrbitalType(String line)
private void fixOrbitalType()
private boolean readGeometryOptimization() throws Exception
Exception