org.jmol.adapter.readers.xml

Class XmlXsdReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xml.XmlReader

org.jmol.adapter.readers.xml.XmlXsdReader

public class XmlXsdReader
extends XmlReader

An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09

Field Summary

Fields

Modifier and Type	Field and Description
private BS	bsBackbone
private int	iAtom
private int	iChain
private int	iGroup

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

atom, atts, chars, domAttributes, 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, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterAtomTypeStr, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, mustFinalizeModelSet, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
XmlXsdReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String[]	getDOMAttributes()
(package private) void	processEndElement(java.lang.String localName)
void	processStartElement(java.lang.String localName)
protected void	processXml(XmlReader parent, java.lang.Object saxReader)

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

applySymmetryAndSetTrajectory, initializeReader, processDOM, PX, setKeepChars

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, read3Vectors, readDataObject, readLine, readLines, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setLoadNote, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

bsBackbone

private BS bsBackbone

iChain

private int iChain

iGroup

private int iGroup

iAtom

private int iAtom

Constructor Detail

XmlXsdReader

public XmlXsdReader()

Method Detail

getDOMAttributes

protected java.lang.String[] getDOMAttributes()

Overrides:

getDOMAttributes in class XmlReader

processXml

protected void processXml(XmlReader parent,
              java.lang.Object saxReader)
                   throws java.lang.Exception

Overrides:

processXml in class XmlReader

Throws:

java.lang.Exception

processStartElement

public void processStartElement(java.lang.String localName)

Overrides:

processStartElement in class XmlReader

processEndElement

void processEndElement(java.lang.String localName)

Overrides:

processEndElement in class XmlReader