org.jmol.adapter.readers.xml

Class XmlOdysseyReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xml.XmlReader

org.jmol.adapter.readers.xml.XmlOdysseyReader

public class XmlOdysseyReader
extends XmlReader

An Odyssey xodydata reader

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	XmlOdysseyReader.OdysseyHandler

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
(package private) java.lang.String	formula
(package private) java.lang.String	modelName
(package private) java.lang.String[]	odysseyImplementedAttributes
(package private) java.lang.String	phase

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

Constructors

Constructor and Description
XmlOdysseyReader()

Method Summary

Methods

Modifier and Type	Method and Description
void	applySymmetryAndSetTrajectory()
(package private) int	parseBondToken(java.lang.String str)
protected void	processEndElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
protected 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, netscape.javascript.JSObject DOMNode)
protected void	processXml(XmlReader parent, AtomSetCollection atomSetCollection, java.io.BufferedReader reader, org.xml.sax.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, 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

odysseyImplementedAttributes

java.lang.String[] odysseyImplementedAttributes

modelName

java.lang.String modelName

formula

java.lang.String formula

phase

java.lang.String phase

Constructor Detail

XmlOdysseyReader

XmlOdysseyReader()

Method Detail

processXml

protected void processXml(XmlReader parent,
              AtomSetCollection atomSetCollection,
              java.io.BufferedReader reader,
              org.xml.sax.XMLReader xmlReader)

Overrides:

processXml in class XmlReader

processXml

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

Overrides:

processXml in class XmlReader

processStartElement

protected 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

applySymmetryAndSetTrajectory

public void applySymmetryAndSetTrajectory()

Overrides:

applySymmetryAndSetTrajectory in class AtomSetCollectionReader

parseBondToken

int parseBondToken(java.lang.String str)

processEndElement

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

Overrides:

processEndElement in class XmlReader