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

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	formula
private java.lang.String	modelName
private java.lang.String[]	myAttributes
private java.lang.String	phase

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
XmlOdysseyReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String[]	getDOMAttributes()
private int	parseBondToken(java.lang.String str)
(package private) void	processEndElement(java.lang.String localName)
protected void	processStartElement(java.lang.String localName)

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

applySymmetryAndSetTrajectory, initializeReader, processDOM, processXml, 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

modelName

private java.lang.String modelName

formula

private java.lang.String formula

phase

private java.lang.String phase

myAttributes

private java.lang.String[] myAttributes

Constructor Detail

XmlOdysseyReader

XmlOdysseyReader()

Method Detail

getDOMAttributes

protected java.lang.String[] getDOMAttributes()

Overrides:

getDOMAttributes in class XmlReader

processStartElement

protected void processStartElement(java.lang.String localName)

Overrides:

processStartElement in class XmlReader

parseBondToken

private int parseBondToken(java.lang.String str)

processEndElement

void processEndElement(java.lang.String localName)

Overrides:

processEndElement in class XmlReader