org.jmol.adapter.readers.quantum
Class WebMOReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.BasisFunctionReader
          extended by org.jmol.adapter.readers.quantum.SlaterReader
              extended by org.jmol.adapter.readers.quantum.MopacSlaterReader
                  extended by org.jmol.adapter.readers.quantum.WebMOReader

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.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
 
Field Summary
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.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, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
 
Constructor Summary
WebMOReader()
           
 
Method Summary
protected  boolean checkLine()
           
protected  void finalizeReader()
           
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.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, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

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

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception
Overrides:
finalizeReader 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