Package org.jmol.adapter.readers.quantum

Class MoldenReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

org.jmol.adapter.readers.quantum.SlaterReader

org.jmol.adapter.readers.quantum.MopacSlaterReader

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

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
private 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

atomicNumbers, MIN_COEF

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

slaterArray, slaters

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

alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells

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

addedData, addedDataKey, addVibrations, allow_a_len_1, 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, 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)
private void	sortMOs()

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

createSphericalSlaterByType, scaleSlater

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

addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals

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, 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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

private boolean haveEnergy

ptLineBuf

private int ptLineBuf

bufLen

private int bufLen

Constructor Detail

MoldenReader

public MoldenReader()

Method Detail

initializeReader

protected void initializeReader()

Overrides:

initializeReader in class AtomSetCollectionReader

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

private 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