Package org.openscience.cdk.libio.cml
Class Convertor
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- org.openscience.cdk.libio.cml.Convertor
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description org.xmlcml.cml.element.CMLMoleculeList
cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet)
org.xmlcml.cml.element.CMLMolecule
cdkAtomContainerToCMLMolecule(IAtomContainer structure)
org.xmlcml.cml.element.CMLAtom
cdkAtomToCMLAtom(IAtom cdkAtom)
org.xmlcml.cml.element.CMLAtom
cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)
org.xmlcml.cml.element.CMLBond
cdkBondToCMLBond(IBond cdkBond)
org.xmlcml.cml.element.CMLCml
cdkChemFileToCMLList(IChemFile file)
org.xmlcml.cml.element.CMLList
cdkChemModelToCMLList(IChemModel model)
org.xmlcml.cml.element.CMLList
cdkChemSequenceToCMLList(IChemSequence sequence)
org.xmlcml.cml.element.CMLMolecule
cdkCrystalToCMLMolecule(ICrystal crystal)
org.xmlcml.cml.element.CMLMolecule
cdkMonomerToCMLMolecule(IMonomer monomer)
org.xmlcml.cml.element.CMLMolecule
cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer)
org.xmlcml.cml.element.CMLReactionScheme
cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme)
org.xmlcml.cml.element.CMLCml
cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme cdkScheme)
org.xmlcml.cml.element.CMLReactionList
cdkReactionSetToCMLReactionList(IReactionSet reactionSet)
org.xmlcml.cml.element.CMLReaction
cdkReactionToCMLReaction(IReaction reaction)
org.xmlcml.cml.element.CMLReactionStep
cdkReactionToCMLReactionStep(IReaction reaction)
void
registerCustomizer(ICMLCustomizer customizer)
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Field Detail
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NS_CML
public static final String NS_CML
- See Also:
- Constant Field Values
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Constructor Detail
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Convertor
public Convertor(boolean useCMLIDs, String prefix)
Constructs a CML convertor.- Parameters:
useCMLIDs
- Uses object IDs like 'a1' instead of 'a<hash>'.prefix
- Namespace prefix to use. If null, then no prefix is used;
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Method Detail
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registerCustomizer
public void registerCustomizer(ICMLCustomizer customizer)
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cdkChemFileToCMLList
public org.xmlcml.cml.element.CMLCml cdkChemFileToCMLList(IChemFile file)
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cdkChemSequenceToCMLList
public org.xmlcml.cml.element.CMLList cdkChemSequenceToCMLList(IChemSequence sequence)
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cdkChemModelToCMLList
public org.xmlcml.cml.element.CMLList cdkChemModelToCMLList(IChemModel model)
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cdkReactionSchemeToCMLReactionSchemeAndMoleculeList
public org.xmlcml.cml.element.CMLCml cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme cdkScheme)
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cdkReactionSchemeToCMLReactionScheme
public org.xmlcml.cml.element.CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme)
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cdkReactionToCMLReactionStep
public org.xmlcml.cml.element.CMLReactionStep cdkReactionToCMLReactionStep(IReaction reaction)
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cdkReactionSetToCMLReactionList
public org.xmlcml.cml.element.CMLReactionList cdkReactionSetToCMLReactionList(IReactionSet reactionSet)
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cdkAtomContainerSetToCMLList
public org.xmlcml.cml.element.CMLMoleculeList cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet)
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cdkReactionToCMLReaction
public org.xmlcml.cml.element.CMLReaction cdkReactionToCMLReaction(IReaction reaction)
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cdkCrystalToCMLMolecule
public org.xmlcml.cml.element.CMLMolecule cdkCrystalToCMLMolecule(ICrystal crystal)
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cdkPDBPolymerToCMLMolecule
public org.xmlcml.cml.element.CMLMolecule cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer)
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cdkMonomerToCMLMolecule
public org.xmlcml.cml.element.CMLMolecule cdkMonomerToCMLMolecule(IMonomer monomer)
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cdkAtomContainerToCMLMolecule
public org.xmlcml.cml.element.CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure)
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cdkAtomToCMLAtom
public org.xmlcml.cml.element.CMLAtom cdkAtomToCMLAtom(IAtom cdkAtom)
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cdkAtomToCMLAtom
public org.xmlcml.cml.element.CMLAtom cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)
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cdkBondToCMLBond
public org.xmlcml.cml.element.CMLBond cdkBondToCMLBond(IBond cdkBond)
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