Package org.jmol.adapter.readers.quantum
Class MoldenReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
QCJSONReader
A molecular structure and orbital reader for MolDen files.
See http://www.cmbi.ru.nl/molden/molden_format.html
updated by Bob Hanson invalid input: '<'hansonr@stolaf.edu> for Jmol 12.0/12.1
adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7
adding [STO] ANGS MOPAC
-- optional zeta in ANGS
-- optional mopac scaling
- Author:
- Matthew Zwier invalid input: '<'mczwier@gmail.com>
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Nested Class Summary
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate javajs.util.BS
private javajs.util.BS
private int
protected boolean
protected boolean
private javajs.util.Lst
<String> protected boolean
protected boolean
protected int
private int[]
protected boolean
protected String
private int
protected boolean
Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
_AM1_C, allowMopacDCoef, atomicNumbers, MIN_COEF, MOPAC_TYPES, mopacBasis
Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
scaleSlaters
Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
allowNoOrbitals, energyUnits, forceMOPAC, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, lastMoData, moTypes, orbitalsRead, shellCount
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
private boolean
checkOrbitalType
(String line) private boolean
private void
void
optional reader-specific method run first.private void
private String[]
getMoTokens
(String line) protected void
rd()
private void
private void
readAtomSet
(String atomSetName, boolean isBohr, boolean asClone) private boolean
private boolean
private boolean
private boolean
(package private) boolean
private void
protected void
sortMOs()
Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
addSlaterBasis, createMopacSlaters, createSphericalSlaterByType, getMopacAtomZetaSPD, scaleSlater, setMOData
Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, getSlaters, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, 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, getFilterWithCase, 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, 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
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Field Details
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loadGeometries
protected boolean loadGeometries -
loadVibrations
protected boolean loadVibrations -
vibOnly
protected boolean vibOnly -
optOnly
protected boolean optOnly -
doSort
protected boolean doSort -
orbitalType
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modelAtomCount
protected int modelAtomCount -
lineBuffer
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bsAtomOK
private javajs.util.BS bsAtomOK -
bsBadIndex
private javajs.util.BS bsBadIndex -
nSPDF
private int[] nSPDF -
haveEnergy
protected boolean haveEnergy -
ptLineBuf
private int ptLineBuf -
bufLen
private int bufLen
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Constructor Details
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MoldenReader
public MoldenReader()
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Method Details
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initializeReader
protected void initializeReader()- Overrides:
initializeReader
in classMOReader
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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checkSymmetry
- Throws:
Exception
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
Exception
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readAtoms
- Throws:
Exception
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readSlaterBasis
- Throws:
Exception
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readGaussianBasis
- Throws:
Exception
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readMolecularOrbitals
- Throws:
Exception
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rd
- Overrides:
rd
in classAtomSetCollectionReader
- Throws:
Exception
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createLineBuffer
- Throws:
Exception
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sortMOs
protected void sortMOs() -
getMoTokens
- Throws:
Exception
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checkOrbitalType
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fixOrbitalType
private void fixOrbitalType() -
readFreqsAndModes
- Throws:
Exception
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readGeometryOptimization
- Throws:
Exception
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skipTo
- Throws:
Exception
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readAtomSet
- Throws:
Exception
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