public class XmlOdysseyReader extends XmlReader
Modifier and Type | Class and Description |
---|---|
(package private) class |
XmlOdysseyReader.OdysseyHandler |
XmlReader.DummyResolver, XmlReader.JmolXmlHandler
Modifier and Type | Field and Description |
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(package private) java.lang.String |
formula |
(package private) java.lang.String |
modelName |
(package private) java.lang.String[] |
odysseyImplementedAttributes |
(package private) java.lang.String |
phase |
atom, chars, implementedAttributes, keepChars, parent
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 and Description |
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XmlOdysseyReader() |
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) |
initializeReader, parseReaderXML, processXml, setKeepChars
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
java.lang.String[] odysseyImplementedAttributes
java.lang.String modelName
java.lang.String formula
java.lang.String phase
protected void processXml(XmlReader parent, AtomSetCollection atomSetCollection, java.io.BufferedReader reader, org.xml.sax.XMLReader xmlReader)
processXml
in class XmlReader
protected void processXml(XmlReader parent, AtomSetCollection atomSetCollection, java.io.BufferedReader reader, netscape.javascript.JSObject DOMNode)
processXml
in class XmlReader
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)
processStartElement
in class XmlReader
public void applySymmetryAndSetTrajectory()
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
int parseBondToken(java.lang.String str)
protected void processEndElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
processEndElement
in class XmlReader