org.jmol.adapter.readers.quantum.MoldenReader

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 Hanson <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 <mczwier@gmail.com>

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
Field Summary

Fields

Modifier and Type

Field

Description

private javajs.util.BS

bsAtomOK

private javajs.util.BS

bsBadIndex

private int

bufLen

protected boolean

doSort

protected boolean

haveEnergy

private javajs.util.Lst<String>

lineBuffer

protected boolean

loadGeometries

protected boolean

loadVibrations

protected int

modelAtomCount

private int[]

nSPDF

protected boolean

optOnly

protected String

orbitalType

private int

ptLineBuf

protected boolean

vibOnly

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
Constructor Summary

Constructors

Constructor

Description

MoldenReader()
Method Summary

Modifier and Type

Method

Description

protected boolean

checkLine()

private boolean

checkOrbitalType(String line)

private boolean

checkSymmetry()

private void

createLineBuffer()

void

finalizeSubclassReader()

optional reader-specific method run first.

private void

fixOrbitalType()

private String[]

getMoTokens(String line)

protected void

initializeReader()

String

rd()

private void

readAtoms()

private void

readAtomSet(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(String key)

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- loadGeometries
  
  protected boolean loadGeometries
- loadVibrations
  
  protected boolean loadVibrations
- vibOnly
  
  protected boolean vibOnly
- optOnly
  
  protected boolean optOnly
- doSort
  
  protected boolean doSort
- orbitalType
  
  protected String orbitalType
- modelAtomCount
  
  protected int modelAtomCount
- lineBuffer
  
  private javajs.util.Lst<String> lineBuffer
- 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
Constructor Details
- MoldenReader
  
  public MoldenReader()
Method Details
- initializeReader
  
  protected void initializeReader()
  
  Overrides:
  
  initializeReader in class MOReader
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- checkSymmetry
  
  private boolean checkSymmetry() throws Exception
  
  Throws:
  
  Exception
- finalizeSubclassReader
  
  public void finalizeSubclassReader() throws Exception
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- readAtoms
  
  private void readAtoms() throws Exception
  
  Throws:
  
  Exception
- readSlaterBasis
  
  boolean readSlaterBasis() throws Exception
  
  Throws:
  
  Exception
- readGaussianBasis
  
  private boolean readGaussianBasis() throws Exception
  
  Throws:
  
  Exception
- readMolecularOrbitals
  
  private boolean readMolecularOrbitals() throws Exception
  
  Throws:
  
  Exception
- rd
  
  public String rd() throws Exception
  
  Overrides:
  
  rd in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- createLineBuffer
  
  private void createLineBuffer() throws Exception
  
  Throws:
  
  Exception
- sortMOs
  
  protected void sortMOs()
- getMoTokens
  
  private String[] getMoTokens(String line) throws Exception
  
  Throws:
  
  Exception
- checkOrbitalType
  
  private boolean checkOrbitalType(String line)
- fixOrbitalType
  
  private void fixOrbitalType()
- readFreqsAndModes
  
  private boolean readFreqsAndModes() throws Exception
  
  Throws:
  
  Exception
- readGeometryOptimization
  
  private boolean readGeometryOptimization() throws Exception
  
  Throws:
  
  Exception
- skipTo
  
  private void skipTo(String key) throws Exception
  
  Throws:
  
  Exception
- readAtomSet
  
  private void readAtomSet(String atomSetName, boolean isBohr, boolean asClone) throws Exception
  
  Throws:
  
  Exception

Class MoldenReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader

Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader

Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Details

loadGeometries

loadVibrations

vibOnly

optOnly

doSort

orbitalType

modelAtomCount

lineBuffer

bsAtomOK

bsBadIndex

nSPDF

haveEnergy

ptLineBuf

bufLen

Constructor Details

MoldenReader

Method Details

initializeReader

checkLine

checkSymmetry

finalizeSubclassReader

readAtoms

readSlaterBasis

readGaussianBasis

readMolecularOrbitals

rd

createLineBuffer

sortMOs

getMoTokens

checkOrbitalType

fixOrbitalType

readFreqsAndModes

readGeometryOptimization

skipTo

readAtomSet