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