Package org.jmol.adapter.readers.quantum
Class MoldenReader
- java.lang.Object
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- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
QCJSONReader
public class MoldenReader extends MopacSlaterReader
A molecular structure and orbital reader for MolDen files. See http://www.cmbi.ru.nl/molden/molden_format.html updated by Bob Hansonfor 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
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Nested Class Summary
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
Fields Modifier and Type Field Description private javajs.util.BS
bsAtomOK
private javajs.util.BS
bsBadIndex
private int
bufLen
protected boolean
doSort
private boolean
haveEnergy
private javajs.util.Lst<java.lang.String>
lineBuffer
protected boolean
loadGeometries
protected boolean
loadVibrations
protected int
modelAtomCount
private int[]
nSPDF
protected boolean
optOnly
protected java.lang.String
orbitalType
private int
ptLineBuf
protected boolean
vibOnly
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Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
_AM1_C, allowMopacDCoef, atomicNumbers, MIN_COEF, MOPAC_TYPES, mopacBasis
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Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
scaleSlaters
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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
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Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters
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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, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description MoldenReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
checkLine()
private boolean
checkOrbitalType(java.lang.String line)
private boolean
checkSymmetry()
private void
createLineBuffer()
void
finalizeSubclassReader()
optional reader-specific method run first.private void
fixOrbitalType()
private java.lang.String[]
getMoTokens(java.lang.String line)
protected void
initializeReader()
java.lang.String
rd()
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()
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Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
addSlaterBasis, createMopacSlaters, createSphericalSlaterByType, getMopacAtomZetaSPD, scaleSlater, setMOData
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Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, getSlaters, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
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Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals
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Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
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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, 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 Detail
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loadGeometries
protected boolean loadGeometries
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loadVibrations
protected boolean loadVibrations
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vibOnly
protected boolean vibOnly
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optOnly
protected boolean optOnly
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doSort
protected boolean doSort
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orbitalType
protected java.lang.String orbitalType
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modelAtomCount
protected int modelAtomCount
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lineBuffer
private javajs.util.Lst<java.lang.String> lineBuffer
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bsAtomOK
private javajs.util.BS bsAtomOK
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bsBadIndex
private javajs.util.BS bsBadIndex
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nSPDF
private int[] nSPDF
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haveEnergy
private boolean haveEnergy
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ptLineBuf
private int ptLineBuf
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bufLen
private int bufLen
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Method Detail
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initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in classMOReader
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checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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checkSymmetry
private boolean checkSymmetry() throws java.lang.Exception
- Throws:
java.lang.Exception
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finalizeSubclassReader
public void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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readAtoms
private void readAtoms() throws java.lang.Exception
- Throws:
java.lang.Exception
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readSlaterBasis
boolean readSlaterBasis() throws java.lang.Exception
- Throws:
java.lang.Exception
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readGaussianBasis
private boolean readGaussianBasis() throws java.lang.Exception
- Throws:
java.lang.Exception
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readMolecularOrbitals
private boolean readMolecularOrbitals() throws java.lang.Exception
- Throws:
java.lang.Exception
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rd
public java.lang.String rd() throws java.lang.Exception
- Overrides:
rd
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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createLineBuffer
private void createLineBuffer() throws java.lang.Exception
- Throws:
java.lang.Exception
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sortMOs
private void sortMOs()
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getMoTokens
private java.lang.String[] getMoTokens(java.lang.String line) throws java.lang.Exception
- Throws:
java.lang.Exception
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checkOrbitalType
private boolean checkOrbitalType(java.lang.String line)
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fixOrbitalType
private void fixOrbitalType()
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readFreqsAndModes
private boolean readFreqsAndModes() throws java.lang.Exception
- Throws:
java.lang.Exception
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readGeometryOptimization
private boolean readGeometryOptimization() throws java.lang.Exception
- Throws:
java.lang.Exception
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skipTo
private void skipTo(java.lang.String key) throws java.lang.Exception
- Throws:
java.lang.Exception
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readAtomSet
private void readAtomSet(java.lang.String atomSetName, boolean isBohr, boolean asClone) throws java.lang.Exception
- Throws:
java.lang.Exception
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