org.jmol.adapter.readers.xml

Class XmlCmlReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xml.XmlReader

org.jmol.adapter.readers.xml.XmlCmlReader

Direct Known Subclasses:

XmlMolproReader

public class XmlCmlReader
extends XmlReader

A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection. If passed a JSObject (from LiveConnect) we treat it as a JS DOM tree, and walk the tree, (using the same processing as the SAX parser) to construct the AtomSetCollection. symmetry added by Bob Hanson: setSpaceGroupName() setUnitCellItem() setFractionalCoordinates() setAtomCoord() applySymmetryAndSetTrajectory() "isotope" added 4/6/2009 Bob Hanson

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	XmlCmlReader.CmlHandler

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 Atom[]	atomArray
private int	atomCount
private java.util.Properties	atomIdNames
private Bond[]	bondArray
private int	bondCount
private java.lang.String	cellParameterType
private boolean	checkedSerial
protected int	CML state constants
private java.lang.String[]	cmlImplementedAttributes
protected int	CRYSTAL state constants
protected int	CRYSTAL_SCALAR state constants
protected int	CRYSTAL_SYMMETRY state constants
protected int	CRYSTAL_SYMMETRY_TRANSFORM3 state constants
private boolean	embeddedCrystal
private boolean	haveMolecule
private boolean	isSerial
protected int	LATTICE_VECTOR state constants
private int	latticeVectorPtr
private java.lang.String	localSpaceGroupName
protected int	MODULE state constants
private int	moduleNestingLevel
protected int	MOLECULE state constants
protected int	MOLECULE_ATOM state constants
protected int	MOLECULE_ATOM_ARRAY state constants
protected int	MOLECULE_ATOM_BUILTIN state constants
protected int	MOLECULE_ATOM_SCALAR state constants
protected int	MOLECULE_BOND state constants
protected int	MOLECULE_BOND_ARRAY state constants
protected int	MOLECULE_BOND_BUILTIN state constants
protected int	MOLECULE_FORMULA state constants
private int	moleculeNesting
private int	nModules
private boolean	processing
private java.lang.String	scalarDictRef
private java.lang.String	scalarDictValue
private java.lang.String	scalarTitle
protected int	START state constants
protected int	state the current state
protected int	SYMMETRY state constants
private int	tokenCount
(package private) java.lang.String[]	tokens

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, 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 Summary

Constructors

Constructor and Description
XmlCmlReader()

Method Summary

Methods

Modifier and Type	Method and Description
private void	addAtom(Atom atom)
private void	addNewBond(java.lang.String a1, java.lang.String a2, int order)
void	applySymmetryAndSetTrajectory()
(package private) void	breakOutAtomTokens(java.lang.String str)
(package private) void	breakOutBondTokens(java.lang.String str)
(package private) void	breakOutTokens(java.lang.String str)
(package private) void	checkAtomArrayLength(int newAtomCount)
(package private) void	checkBondArrayLength(int newBondCount)
private void	checkUnitCellItem(java.lang.String[] tags, java.lang.String value)
private void	createNewAtomSet(java.util.Map<java.lang.String,java.lang.String> atts)
private void	getDictRefValue(java.util.Map<java.lang.String,java.lang.String> atts)
(package private) int	parseBondToken(java.lang.String str)
void	processEndElement(java.lang.String uri, java.lang.String name, java.lang.String qName)
void	processStartElement(java.lang.String uri, java.lang.String name, 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)

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

initializeReader, parseReaderXML, 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, 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

Methods inherited from class java.lang.Object

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

Field Detail

cmlImplementedAttributes

private java.lang.String[] cmlImplementedAttributes

atomCount

private int atomCount

atomArray

private Atom[] atomArray

bondCount

private int bondCount

bondArray

private Bond[] bondArray

tokenCount

private int tokenCount

tokens

java.lang.String[] tokens

nModules

private int nModules

moduleNestingLevel

private int moduleNestingLevel

haveMolecule

private boolean haveMolecule

localSpaceGroupName

private java.lang.String localSpaceGroupName

processing

private boolean processing

START

protected final int START

state constants

See Also:

Constant Field Values

CML

protected final int CML

state constants

See Also:

Constant Field Values

CRYSTAL

protected final int CRYSTAL

state constants

See Also:

Constant Field Values

CRYSTAL_SCALAR

protected final int CRYSTAL_SCALAR

state constants

See Also:

Constant Field Values

CRYSTAL_SYMMETRY

protected final int CRYSTAL_SYMMETRY

state constants

See Also:

Constant Field Values

CRYSTAL_SYMMETRY_TRANSFORM3

protected final int CRYSTAL_SYMMETRY_TRANSFORM3

state constants

See Also:

Constant Field Values

MOLECULE

protected final int MOLECULE

state constants

See Also:

Constant Field Values

MOLECULE_ATOM_ARRAY

protected final int MOLECULE_ATOM_ARRAY

state constants

See Also:

Constant Field Values

MOLECULE_ATOM

protected final int MOLECULE_ATOM

state constants

See Also:

Constant Field Values

MOLECULE_ATOM_SCALAR

protected final int MOLECULE_ATOM_SCALAR

state constants

See Also:

Constant Field Values

MOLECULE_BOND_ARRAY

protected final int MOLECULE_BOND_ARRAY

state constants

See Also:

Constant Field Values

MOLECULE_BOND

protected final int MOLECULE_BOND

state constants

See Also:

Constant Field Values

MOLECULE_FORMULA

protected final int MOLECULE_FORMULA

state constants

See Also:

Constant Field Values

MOLECULE_ATOM_BUILTIN

protected final int MOLECULE_ATOM_BUILTIN

state constants

See Also:

Constant Field Values

MOLECULE_BOND_BUILTIN

protected final int MOLECULE_BOND_BUILTIN

state constants

See Also:

Constant Field Values

MODULE

protected final int MODULE

state constants

See Also:

Constant Field Values

SYMMETRY

protected final int SYMMETRY

state constants

See Also:

Constant Field Values

LATTICE_VECTOR

protected final int LATTICE_VECTOR

state constants

See Also:

Constant Field Values

state

protected int state

the current state

scalarDictRef

private java.lang.String scalarDictRef

scalarDictValue

private java.lang.String scalarDictValue

scalarTitle

private java.lang.String scalarTitle

cellParameterType

private java.lang.String cellParameterType

checkedSerial

private boolean checkedSerial

isSerial

private boolean isSerial

moleculeNesting

private int moleculeNesting

latticeVectorPtr

private int latticeVectorPtr

embeddedCrystal

private boolean embeddedCrystal

atomIdNames

private java.util.Properties atomIdNames

Constructor Detail

XmlCmlReader

XmlCmlReader()

Method Detail

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 uri,
                       java.lang.String name,
                       java.lang.String qName,
                       java.util.Map<java.lang.String,java.lang.String> atts)

Overrides:

processStartElement in class XmlReader

addNewBond

private void addNewBond(java.lang.String a1,
              java.lang.String a2,
              int order)

getDictRefValue

private void getDictRefValue(java.util.Map<java.lang.String,java.lang.String> atts)

processEndElement

public void processEndElement(java.lang.String uri,
                     java.lang.String name,
                     java.lang.String qName)

Overrides:

processEndElement in class XmlReader

checkUnitCellItem

private void checkUnitCellItem(java.lang.String[] tags,
                     java.lang.String value)

addAtom

private void addAtom(Atom atom)

parseBondToken

int parseBondToken(java.lang.String str)

breakOutTokens

void breakOutTokens(java.lang.String str)

breakOutAtomTokens

void breakOutAtomTokens(java.lang.String str)

checkAtomArrayLength

void checkAtomArrayLength(int newAtomCount)

breakOutBondTokens

void breakOutBondTokens(java.lang.String str)

checkBondArrayLength

void checkBondArrayLength(int newBondCount)

createNewAtomSet

private void createNewAtomSet(java.util.Map<java.lang.String,java.lang.String> atts)

applySymmetryAndSetTrajectory

public void applySymmetryAndSetTrajectory()

Overrides:

applySymmetryAndSetTrajectory in class AtomSetCollectionReader