Class CMLBridge

java.lang.Object

org.episteme.natural.chemistry.loaders.cml.CMLBridge

public class CMLBridge
extends Object

Bridge for converting CML (Chemical Markup Language) DTOs to core Episteme chemistry objects.

CML is the XML standard for representing molecular data in chemistry. This bridge converts parsed CML structures to the core Episteme chemistry domain model.

Architecture

CML XML → CMLReader → CML DTOs → CMLBridge → Core Episteme Objects
                                             ├── Molecule
                                             ├── Atom
                                             ├── Bond
                                             └── Element

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• CMLReader
• Molecule
• Atom

Constructor Summary

Constructors

Constructor	Description
CMLBridge()

Method Summary

Modifier and Type	Method	Description
Atom	convertAtom(CMLAtom cmlAtom)	Converts a CML atom to a Episteme Atom.
Bond	convertBond(CMLBond cmlBond, Map<String,Atom> atomMap)	Converts a CML bond to a Episteme Bond.
Molecule	toMolecule(CMLMolecule cmlMolecule)	Converts a CML molecule representation to a Episteme Molecule.
List<Molecule>	toMolecules(List<CMLMolecule> cmlMolecules)	Converts multiple CML molecules to Episteme Molecules.

Methods inherited from class Object

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

Constructor Details

CMLBridge

public CMLBridge()

Method Details

toMolecule

public Molecule toMolecule(CMLMolecule cmlMolecule)

Converts a CML molecule representation to a Episteme Molecule.

Parameters:

cmlMolecule - the CML molecule DTO

Returns:

a fully populated Molecule object

convertAtom

public Atom convertAtom(CMLAtom cmlAtom)

Converts a CML atom to a Episteme Atom.

convertBond

public Bond convertBond(CMLBond cmlBond,
 Map<String,Atom> atomMap)

Converts a CML bond to a Episteme Bond.

toMolecules

public List<Molecule> toMolecules(List<CMLMolecule> cmlMolecules)

Converts multiple CML molecules to Episteme Molecules.