public class MoldenReader extends MopacSlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorterBasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
private javajs.util.BS |
bsAtomOK |
private javajs.util.BS |
bsBadIndex |
protected boolean |
doSort |
private boolean |
haveEnergy |
protected boolean |
loadGeometries |
protected boolean |
loadVibrations |
protected int |
modelAtomCount |
private int[] |
nSPDF |
protected boolean |
optOnly |
protected java.lang.String |
orbitalType |
protected boolean |
vibOnly |
atomicNumbers, 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 |
|---|
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, 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, setupASCRprotected boolean loadGeometries
protected boolean loadVibrations
protected boolean vibOnly
protected boolean optOnly
protected boolean doSort
protected java.lang.String orbitalType
protected int modelAtomCount
private javajs.util.BS bsAtomOK
private javajs.util.BS bsBadIndex
private int[] nSPDF
private boolean haveEnergy
protected void initializeReader()
initializeReader in class AtomSetCollectionReaderprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate boolean checkSymmetry()
throws java.lang.Exception
java.lang.Exceptionpublic void finalizeSubclassReader()
throws java.lang.Exception
AtomSetCollectionReaderfinalizeSubclassReader in class AtomSetCollectionReaderjava.lang.Exceptionprivate void readAtoms()
throws java.lang.Exception
java.lang.Exceptionboolean readSlaterBasis()
throws java.lang.Exception
java.lang.Exceptionprivate boolean readGaussianBasis()
throws java.lang.Exception
java.lang.Exceptionprivate boolean readMolecularOrbitals()
throws java.lang.Exception
java.lang.Exceptionprivate void sortMOs()
private java.lang.String[] getMoTokens(java.lang.String line)
throws java.lang.Exception
java.lang.Exceptionprivate boolean checkOrbitalType(java.lang.String line)
private void fixOrbitalType()
private boolean readFreqsAndModes()
throws java.lang.Exception
java.lang.Exceptionprivate boolean readGeometryOptimization()
throws java.lang.Exception
java.lang.Exceptionprivate void skipTo(java.lang.String key)
throws java.lang.Exception
java.lang.Exceptionprivate void readAtomSet(java.lang.String atomSetName,
boolean isBohr,
boolean asClone)
throws java.lang.Exception
java.lang.Exception