public class MoldenReader extends MopacSlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field and Description |
---|---|
private BS |
bsAtomOK |
private BS |
bsBadIndex |
private boolean |
doSort |
private boolean |
haveEnergy |
private boolean |
loadGeometries |
private boolean |
loadVibrations |
private int |
modelAtomCount |
private int[] |
nSPDF |
private boolean |
optOnly |
private java.lang.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, nCoef, nOrbitals, orbitals, shells
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
MoldenReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
private boolean |
checkOrbitalType(java.lang.String line) |
private boolean |
checkSymmetry() |
void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private void |
fixOrbitalType() |
private java.lang.String[] |
getMoTokens(java.lang.String line) |
protected void |
initializeReader() |
private void |
readAtoms() |
private void |
readAtomSet(java.lang.String atomSetName,
boolean isBohr,
boolean asClone) |
private boolean |
readFreqsAndModes() |
private boolean |
readGaussianBasis() |
private boolean |
readGeometryOptimization() |
private boolean |
readMolecularOrbitals() |
(package private) boolean |
readSlaterBasis() |
private void |
skipTo(java.lang.String key) |
private void |
sortMOs() |
createSphericalSlaterByType, scaleSlater
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getNewDfCoefMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, 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, processDSSR, 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 boolean loadGeometries
private boolean loadVibrations
private boolean vibOnly
private boolean optOnly
private boolean doSort
private java.lang.String orbitalType
private int modelAtomCount
private BS bsAtomOK
private BS bsBadIndex
private int[] nSPDF
private boolean haveEnergy
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private boolean checkSymmetry() throws java.lang.Exception
java.lang.Exception
public void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
private void readAtoms() throws java.lang.Exception
java.lang.Exception
boolean readSlaterBasis() throws java.lang.Exception
java.lang.Exception
private boolean readGaussianBasis() throws java.lang.Exception
java.lang.Exception
private boolean readMolecularOrbitals() throws java.lang.Exception
java.lang.Exception
private void sortMOs()
private java.lang.String[] getMoTokens(java.lang.String line) throws java.lang.Exception
java.lang.Exception
private boolean checkOrbitalType(java.lang.String line)
private void fixOrbitalType()
private boolean readFreqsAndModes() throws java.lang.Exception
java.lang.Exception
private boolean readGeometryOptimization() throws java.lang.Exception
java.lang.Exception
private void skipTo(java.lang.String key) throws java.lang.Exception
java.lang.Exception
private void readAtomSet(java.lang.String atomSetName, boolean isBohr, boolean asClone) throws java.lang.Exception
java.lang.Exception