java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.quantum.BasisFunctionReader
  - - org.jmol.adapter.readers.quantum.MOReader
    - - 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 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

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<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`

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, 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

Constructor Summary

Constructors
Constructor Description

MoldenReader()

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()`

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, 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 java.lang.String orbitalType
```

modelAtomCount
```
protected int modelAtomCount
```

lineBuffer

private javajs.util.Lst<java.lang.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 MOReader

checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

checkSymmetry

private boolean checkSymmetry()
                       throws java.lang.Exception

Throws:: java.lang.Exception

finalizeSubclassReader
```
public void finalizeSubclassReader()
                            throws java.lang.Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

readAtoms

private void readAtoms()
                throws java.lang.Exception

Throws:: java.lang.Exception

readSlaterBasis

boolean readSlaterBasis()
                 throws java.lang.Exception

Throws:: java.lang.Exception

readGaussianBasis

private boolean readGaussianBasis()
                           throws java.lang.Exception

Throws:: java.lang.Exception

readMolecularOrbitals

private boolean readMolecularOrbitals()
                               throws java.lang.Exception

Throws:: java.lang.Exception

rd

public java.lang.String rd()
                    throws java.lang.Exception

Overrides:: rd in class AtomSetCollectionReader
Throws:: java.lang.Exception

createLineBuffer

private void createLineBuffer()
                       throws java.lang.Exception

Throws:: java.lang.Exception

sortMOs
```
private void sortMOs()
```

getMoTokens

private java.lang.String[] getMoTokens(java.lang.String line)
                                throws java.lang.Exception

Throws:: java.lang.Exception

checkOrbitalType

private boolean checkOrbitalType(java.lang.String line)

fixOrbitalType
```
private void fixOrbitalType()
```

readFreqsAndModes

private boolean readFreqsAndModes()
                           throws java.lang.Exception

Throws:: java.lang.Exception

readGeometryOptimization

private boolean readGeometryOptimization()
                                  throws java.lang.Exception

Throws:: java.lang.Exception

readAtomSet

private void readAtomSet(java.lang.String atomSetName,
                         boolean isBohr,
                         boolean asClone)
                  throws java.lang.Exception

Throws:: java.lang.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 Detail

loadGeometries

loadVibrations

vibOnly

optOnly

doSort

orbitalType

modelAtomCount

lineBuffer

bsAtomOK

bsBadIndex

nSPDF

haveEnergy

ptLineBuf

bufLen

Constructor Detail

MoldenReader

Method Detail

initializeReader

checkLine

checkSymmetry

finalizeSubclassReader

readAtoms

readSlaterBasis

readGaussianBasis

readMolecularOrbitals

rd

createLineBuffer

sortMOs

getMoTokens

checkOrbitalType

fixOrbitalType

readFreqsAndModes

readGeometryOptimization

skipTo

readAtomSet