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

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

XmlReader.DummyResolver, XmlReader.JmolXmlHandler

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.Map<java.lang.String,java.lang.Object>	moData
private java.util.List<java.util.Map<java.lang.String,java.lang.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, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
XmlChem3dReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String[]	getImplementedAttributes()
void	processEndElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
void	processStartElement(java.lang.String namespaceURI, java.lang.String localName, java.lang.String qName, java.util.Map<java.lang.String,java.lang.String> atts)
protected void	processXml(XmlReader parent, AtomSetCollection atomSetCollection, java.io.BufferedReader reader, java.lang.Object xmlReader, XmlReader.JmolXmlHandler handler)

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

applySymmetryAndSetTrajectory, getHandler, initializeReader, parseReaderXML, processXml, setKeepChars

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, 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, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setElementAndIsotope, 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

orbitals

private java.util.List<java.util.Map<java.lang.String,java.lang.Object>> orbitals

moData

private java.util.Map<java.lang.String,java.lang.Object> moData

Constructor Detail

XmlChem3dReader

XmlChem3dReader()

Method Detail

getImplementedAttributes

protected java.lang.String[] getImplementedAttributes()

Overrides:

getImplementedAttributes in class XmlReader

processXml

protected void processXml(XmlReader parent,
              AtomSetCollection atomSetCollection,
              java.io.BufferedReader reader,
              java.lang.Object xmlReader,
              XmlReader.JmolXmlHandler handler)

Overrides:

processXml in class XmlReader

processStartElement

public void processStartElement(java.lang.String namespaceURI,
                       java.lang.String localName,
                       java.lang.String qName,
                       java.util.Map<java.lang.String,java.lang.String> atts)

Overrides:

processStartElement in class XmlReader

processEndElement

public void processEndElement(java.lang.String uri,
                     java.lang.String localName,
                     java.lang.String qName)

Overrides:

processEndElement in class XmlReader