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
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer |
Method Summary |
void |
applySymmetryAndSetTrajectory()
|
(package private) int |
parseBondToken(String str)
|
protected void |
processEndElement(String uri,
String localName,
String qName)
|
protected void |
processStartElement(String namespaceURI,
String localName,
String qName,
HashMap 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.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, 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, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
odysseyImplementedAttributes
String[] odysseyImplementedAttributes
modelName
String modelName
formula
String formula
phase
String phase
XmlOdysseyReader
XmlOdysseyReader()
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
protected void processStartElement(String namespaceURI,
String localName,
String qName,
HashMap atts)
- Overrides:
processStartElement
in class XmlReader
applySymmetryAndSetTrajectory
public void applySymmetryAndSetTrajectory()
- Overrides:
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
parseBondToken
int parseBondToken(String str)
processEndElement
protected void processEndElement(String uri,
String localName,
String qName)
- Overrides:
processEndElement
in class XmlReader