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.

Nested Class Summary

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
private static int	ATOM
private java.lang.String	atomName1
private java.lang.String	atomName2
private static int	BOND
private int	bondOrder
private int	elementContext
private static java.lang.String[]	keepCharsList
private static int	MOLECULE
private int	ptTrans
private float[]	trans
private static int	TRANSFORMMAT
private static int	UNSET

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, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
XmlArgusReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String[]	getImplementedAttributes()
(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<java.lang.String,java.lang.String> atts)

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader

applySymmetryAndSetTrajectory, getHandler, initializeReader, parseReaderXML, processXml, 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, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setElementAndIsotope, 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

keepCharsList

private static 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

Constructor Detail

XmlArgusReader

XmlArgusReader()

Method Detail

getImplementedAttributes

protected java.lang.String[] getImplementedAttributes()

Overrides:

getImplementedAttributes in class XmlReader

processStartElement

public 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

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