org.openscience.cdk.libio.cml

Class Convertor

java.lang.Object

org.openscience.cdk.libio.cml.Convertor

public class Convertor
extends Object

Source code:

master

Belongs to CDK module:

libiocml

Keywords:

CML, class convertor

Requires:

java1.5+

Field Summary

Fields

Modifier and Type	Field and Description
static String	NS_CML

Constructor Summary

Constructors

Constructor and Description
Convertor(boolean useCMLIDs, String prefix) Constructs a CML convertor.

Method Summary

Methods

Modifier and Type	Method and 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)

Methods inherited from class java.lang.Object

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

Field Detail

NS_CML

public static final String NS_CML

See Also:

Constant Field Values

Constructor Detail

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;

Method Detail

registerCustomizer

public void registerCustomizer(ICMLCustomizer customizer)

cdkChemFileToCMLList

public org.xmlcml.cml.element.CMLCml cdkChemFileToCMLList(IChemFile file)

cdkChemSequenceToCMLList

public org.xmlcml.cml.element.CMLList cdkChemSequenceToCMLList(IChemSequence sequence)

cdkChemModelToCMLList

public org.xmlcml.cml.element.CMLList cdkChemModelToCMLList(IChemModel model)

cdkReactionSchemeToCMLReactionSchemeAndMoleculeList

public org.xmlcml.cml.element.CMLCml cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme cdkScheme)

cdkReactionSchemeToCMLReactionScheme

public org.xmlcml.cml.element.CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme)

cdkReactionToCMLReactionStep

public org.xmlcml.cml.element.CMLReactionStep cdkReactionToCMLReactionStep(IReaction reaction)

cdkReactionSetToCMLReactionList

public org.xmlcml.cml.element.CMLReactionList cdkReactionSetToCMLReactionList(IReactionSet reactionSet)

cdkAtomContainerSetToCMLList

public org.xmlcml.cml.element.CMLMoleculeList cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet)

cdkReactionToCMLReaction

public org.xmlcml.cml.element.CMLReaction cdkReactionToCMLReaction(IReaction reaction)

cdkCrystalToCMLMolecule

public org.xmlcml.cml.element.CMLMolecule cdkCrystalToCMLMolecule(ICrystal crystal)

cdkPDBPolymerToCMLMolecule

public org.xmlcml.cml.element.CMLMolecule cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer)

cdkMonomerToCMLMolecule

public org.xmlcml.cml.element.CMLMolecule cdkMonomerToCMLMolecule(IMonomer monomer)

cdkAtomContainerToCMLMolecule

public org.xmlcml.cml.element.CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure)

cdkAtomToCMLAtom

public org.xmlcml.cml.element.CMLAtom cdkAtomToCMLAtom(IAtom cdkAtom)

cdkAtomToCMLAtom

public org.xmlcml.cml.element.CMLAtom cdkAtomToCMLAtom(IAtomContainer container,
                                              IAtom cdkAtom)

cdkBondToCMLBond

public org.xmlcml.cml.element.CMLBond cdkBondToCMLBond(IBond cdkBond)