WebMOReader

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.WebMOReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class WebMOReader
extends MopacSlaterReader
```
A molecular orbital reader for WebMO files.
http://www.webmo.net/demo/ right now WebMO files don't allow for multiple MOS, but we will assume here that that may change.

Nested Class Summary
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
  BasisFunctionReader.MOEnergySorter
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
  SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter

Field Summary

Fields
Modifier and Type	Field	Description
`private static java.lang.String`	`DC_LIST`
`private static java.lang.String`	`DS_LIST`
`private static java.lang.String`	`FC_LIST`
`private static java.lang.String`	`FS_LIST`

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

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.readers.quantum.MopacSlaterReader
atomicNumbers, MIN_COEF

Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
slaterArray, slaters

Constructor Summary

Constructors
Constructor Description

WebMOReader()

Constructors
Constructor	Description
`WebMOReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private boolean`	`getLine()`
`(package private) void`	`readAtomicOrbitalOrder()`
`(package private) void`	`readAtoms()`
`(package private) void`	`readBonds()`
`(package private) void`	`readGaussianBasis()`
`(package private) void`	`readHeader()`
`(package private) void`	`readMolecularOrbital()`
`(package private) void`	`readSlaterBasis()`

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, initializeReader, 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 org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
createSphericalSlaterByType, scaleSlater

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

Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals

Field Detail

DS_LIST

private static java.lang.String DS_LIST

DC_LIST

private static java.lang.String DC_LIST

FS_LIST

private static java.lang.String FS_LIST

FC_LIST

private static java.lang.String FC_LIST

Constructor Detail
- WebMOReader
```
public WebMOReader()
```

Method Detail

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

finalizeSubclassReader
```
protected 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

readHeader

void readHeader()
         throws java.lang.Exception

Throws:: java.lang.Exception

readAtoms

void readAtoms()
        throws java.lang.Exception

Throws:: java.lang.Exception

readBonds

void readBonds()
        throws java.lang.Exception

Throws:: java.lang.Exception

readAtomicOrbitalOrder

void readAtomicOrbitalOrder()
                     throws java.lang.Exception

Throws:: java.lang.Exception

getLine

private boolean getLine()
                 throws java.lang.Exception

Throws:: java.lang.Exception

readGaussianBasis

void readGaussianBasis()
                throws java.lang.Exception

Throws:: java.lang.Exception

readSlaterBasis

void readSlaterBasis()
              throws java.lang.Exception

Throws:: java.lang.Exception

readMolecularOrbital

void readMolecularOrbital()
                   throws java.lang.Exception

Throws:: java.lang.Exception

Class WebMOReader

Nested Class Summary

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

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

Field Summary

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

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

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

Field Detail

DS_LIST

DC_LIST

FS_LIST

FC_LIST

Constructor Detail

WebMOReader

Method Detail

checkLine

finalizeSubclassReader

readHeader

readAtoms

readBonds

readAtomicOrbitalOrder

getLine

readGaussianBasis

readSlaterBasis

readMolecularOrbital