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 |
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount |
Method Summary |
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.HashMap 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.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, 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
java.lang.String[] odysseyImplementedAttributes
modelName
java.lang.String modelName
formula
java.lang.String formula
phase
java.lang.String phase
XmlOdysseyReader
XmlOdysseyReader()
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.HashMap 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