org.jmol.adapter.readers.xml
Class XmlArgusReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xml.XmlReader
org.jmol.adapter.readers.xml.XmlArgusReader
public class XmlArgusReader
- extends XmlReader
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/
Use this reader as a template for adding new XML readers.
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 |
(package private) int |
parseBondToken(java.lang.String str)
|
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 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, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, 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 |
argusImplementedAttributes
private java.lang.String[] argusImplementedAttributes
keepCharsList
private java.lang.String[] keepCharsList
atomName1
private java.lang.String atomName1
atomName2
private java.lang.String atomName2
bondOrder
private int bondOrder
elementContext
private int elementContext
UNSET
private static final int UNSET
- See Also:
- Constant Field Values
MOLECULE
private static final int MOLECULE
- See Also:
- Constant Field Values
ATOM
private static final int ATOM
- See Also:
- Constant Field Values
BOND
private static final int BOND
- See Also:
- Constant Field Values
TRANSFORMMAT
private static final int TRANSFORMMAT
- See Also:
- Constant Field Values
trans
private float[] trans
ptTrans
private int ptTrans
XmlArgusReader
XmlArgusReader()
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
public void processStartElement(java.lang.String namespaceURI,
java.lang.String localName,
java.lang.String qName,
java.util.Map atts)
parseBondToken
int parseBondToken(java.lang.String str)
processEndElement
public void processEndElement(java.lang.String uri,
java.lang.String localName,
java.lang.String qName)
- Overrides:
processEndElement
in class XmlReader