org.jmol.adapter.readers.xml
Class XmlChem3dReader

java.lang.Object
  org.jmol.adapter.smarter.AtomSetCollectionReader
      org.jmol.adapter.readers.xml.XmlReader
          org.jmol.adapter.readers.xml.XmlChem3dReader

public class XmlChem3dReader
extends XmlReader

An chem3d c3xml reader

Nested Class Summary

(package private) class

XmlChem3dReader.Chem3dHandler

Nested classes/interfaces inherited from class org.jmol.adapter.readers.xml.XmlReader

XmlReader.DummyResolver, XmlReader.JmolXmlHandler

Field Summary

(package private) String[]	chem3dImplementedAttributes
private Map<String,Object>	moData
protected List<Map<String,Object>>	orbitals

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader

atom, chars, implementedAttributes, keepChars, parent

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

XmlChem3dReader()

Method Summary

void	processEndElement(String uri, String localName, String qName)
void	processStartElement(String namespaceURI, String localName, String qName, Map<String,String> atts)
protected void	processXml(XmlReader parent, AtomSetCollection atomSetCollection, BufferedReader reader, netscape.javascript.JSObject DOMNode)
protected void	processXml(XmlReader parent, AtomSetCollection atomSetCollection, BufferedReader reader, XMLReader xmlReader)

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader

initializeReader, parseReaderXML, processXml, setKeepChars

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, 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

chem3dImplementedAttributes

String[] chem3dImplementedAttributes

orbitals

protected List<Map<String,Object>> orbitals

moData

private Map<String,Object> moData

Constructor Detail

XmlChem3dReader

XmlChem3dReader()

Method Detail

processXml

protected void processXml(XmlReader parent,
                          AtomSetCollection atomSetCollection,
                          BufferedReader reader,
                          XMLReader xmlReader)

Overrides:

processXml in class XmlReader

processXml

protected void processXml(XmlReader parent,
                          AtomSetCollection atomSetCollection,
                          BufferedReader reader,
                          netscape.javascript.JSObject DOMNode)

Overrides:

processXml in class XmlReader

processStartElement

public void processStartElement(String namespaceURI,
                                String localName,
                                String qName,
                                Map<String,String> atts)

Overrides:

processStartElement in class XmlReader

processEndElement

public void processEndElement(String uri,
                              String localName,
                              String qName)

Overrides:

processEndElement in class XmlReader