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
```
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

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 and Description
`private BS`	`bsAtomOK`
`private BS`	`bsBadIndex`
`private boolean`	`doSort`
`private boolean`	`haveEnergy`
`private boolean`	`loadGeometries`
`private boolean`	`loadVibrations`
`private int`	`modelAtomCount`
`private int[]`	`nSPDF`
`private boolean`	`optOnly`
`private String`	`orbitalType`
`private 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, orbitals, shells

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor and Description

MoldenReader()

Constructors
Constructor and Description
`MoldenReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected boolean`	`checkLine()`
`private boolean`	`checkOrbitalType(String line)`
`private boolean`	`checkSymmetry()`
`void`	`finalizeSubclassReader()` optional reader-specific method run first.
`private void`	`fixOrbitalType()`
`private String[]`	`getMoTokens(String line)`
`protected void`	`initializeReader()`
`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, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, 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, rd, 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
```
private boolean loadGeometries
```

loadVibrations
```
private boolean loadVibrations
```

vibOnly
```
private boolean vibOnly
```

optOnly
```
private boolean optOnly
```

doSort
```
private boolean doSort
```

orbitalType
```
private String orbitalType
```

modelAtomCount
```
private int modelAtomCount
```

bsAtomOK
```
private BS bsAtomOK
```

bsBadIndex
```
private BS bsBadIndex
```

nSPDF
```
private int[] nSPDF
```

haveEnergy
```
private boolean haveEnergy
```

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

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

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.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.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

bsAtomOK

bsBadIndex

nSPDF

haveEnergy

Constructor Detail

MoldenReader

Method Detail

initializeReader

checkLine

checkSymmetry

finalizeSubclassReader

readAtoms

readSlaterBasis

readGaussianBasis

readMolecularOrbitals

sortMOs

getMoTokens

checkOrbitalType

fixOrbitalType

readFreqsAndModes

readGeometryOptimization

skipTo

readAtomSet