Package org.openscience.cdk.io.cml
Class CMLCoreModule
- java.lang.Object
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- org.openscience.cdk.io.cml.CMLCoreModule
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- All Implemented Interfaces:
ICMLModule
- Direct Known Subclasses:
CDKConvention
,CMLReactionModule
,JMOLANIMATIONConvention
,MDLMolConvention
,MDMoleculeConvention
,PDBConvention
,PMPConvention
,QSARConvention
public class CMLCoreModule extends Object implements ICMLModule
Core CML 1.x and 2.x elements are parsed by this class (see [Willighagen, E.L.. Internet Journal of Chemistry. 2001. 4]).Please file a bug report if this parser fails to parse a certain element or attribute value in a valid CML document.
- Author:
- Egon Willighagen <egonw@sci.kun.nl>
- Source code:
- main
- Belongs to CDK module:
- io
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Field Summary
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Constructor Summary
Constructors Constructor Description CMLCoreModule(IChemFile chemFile)
CMLCoreModule(ICMLModule conv)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
addArrayElementsTo(List<String> toAddto, String array)
void
characterData(org.openscience.cdk.io.cml.CMLStack xpath, char[] ch, int start, int length)
void
endDocument()
void
endElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String name, String raw)
void
inherit(ICMLModule convention)
protected void
newAtomData()
Clean all data about read atoms.protected void
newBondData()
Clean all data about read bonds.protected void
newCrystalData()
Clean all data about read bonds.protected void
newFormulaData()
Clean all data about read formulas.protected void
newMolecule()
Clean all data about parsed data.protected void
newMoleculeData()
Clean all data about the molecule itself.protected void
notify(String message, String systemId, int line, int column)
IChemFile
returnChemFile()
void
startDocument()
void
startElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw, Attributes atts)
protected void
storeAtomData()
protected void
storeBondData()
protected void
storeData()
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Field Detail
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logger
protected ILoggingTool logger
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SYSTEMID
protected final String SYSTEMID
- See Also:
- Constant Field Values
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currentChemFile
protected IChemFile currentChemFile
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currentMolecule
protected IAtomContainer currentMolecule
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currentMoleculeSet
protected IAtomContainerSet currentMoleculeSet
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currentChemModel
protected IChemModel currentChemModel
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currentChemSequence
protected IChemSequence currentChemSequence
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currentReactionSet
protected IReactionSet currentReactionSet
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currentReaction
protected IReaction currentReaction
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currentAtom
protected IAtom currentAtom
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currentBond
protected IBond currentBond
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currentStrand
protected IStrand currentStrand
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currentMonomer
protected IMonomer currentMonomer
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formulaCounter
protected int formulaCounter
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atomCounter
protected int atomCounter
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parityAtomsGiven
protected boolean parityAtomsGiven
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parityGiven
protected boolean parityGiven
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bondCounter
protected int bondCounter
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stereoGiven
protected boolean stereoGiven
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inchi
protected String inchi
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curRef
protected int curRef
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CurrentElement
protected int CurrentElement
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BUILTIN
protected String BUILTIN
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DICTREF
protected String DICTREF
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elementTitle
protected String elementTitle
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currentChars
protected String currentChars
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unitcellparams
protected double[] unitcellparams
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crystalScalar
protected int crystalScalar
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Constructor Detail
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CMLCoreModule
public CMLCoreModule(IChemFile chemFile)
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CMLCoreModule
public CMLCoreModule(ICMLModule conv)
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Method Detail
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inherit
public void inherit(ICMLModule convention)
- Specified by:
inherit
in interfaceICMLModule
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returnChemFile
public IChemFile returnChemFile()
- Specified by:
returnChemFile
in interfaceICMLModule
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newMolecule
protected void newMolecule()
Clean all data about parsed data.
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newMoleculeData
protected void newMoleculeData()
Clean all data about the molecule itself.
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newFormulaData
protected void newFormulaData()
Clean all data about read formulas.
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newAtomData
protected void newAtomData()
Clean all data about read atoms.
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newBondData
protected void newBondData()
Clean all data about read bonds.
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newCrystalData
protected void newCrystalData()
Clean all data about read bonds.
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startDocument
public void startDocument()
- Specified by:
startDocument
in interfaceICMLModule
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endDocument
public void endDocument()
- Specified by:
endDocument
in interfaceICMLModule
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startElement
public void startElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw, Attributes atts)
- Specified by:
startElement
in interfaceICMLModule
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endElement
public void endElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String name, String raw)
- Specified by:
endElement
in interfaceICMLModule
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characterData
public void characterData(org.openscience.cdk.io.cml.CMLStack xpath, char[] ch, int start, int length)
- Specified by:
characterData
in interfaceICMLModule
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storeData
protected void storeData()
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storeAtomData
protected void storeAtomData()
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storeBondData
protected void storeBondData()
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