private DefaultChemObjectBuilder() {
// self reference required for stereo-elements
final IChemObjectBuilder self = this;
// elements
factory.register(IAtom.class, Atom.class);
factory.register(IPseudoAtom.class, PseudoAtom.class);
factory.register(IElement.class, Element.class);
factory.register(IAtomType.class, AtomType.class);
factory.register(IFragmentAtom.class, FragmentAtom.class);
factory.register(IPDBAtom.class, PDBAtom.class);
factory.register(IIsotope.class, Isotope.class);
// electron containers
factory.register(IBond.class, Bond.class);
factory.register(IElectronContainer.class, ElectronContainer.class);
factory.register(ISingleElectron.class, SingleElectron.class);
factory.register(ILonePair.class, LonePair.class);
// atom containers
factory.register(IAtomContainer.class, AtomContainer.class);
factory.register(IRing.class, Ring.class);
factory.register(ICrystal.class, Crystal.class);
factory.register(IPolymer.class, Polymer.class);
factory.register(IPDBPolymer.class, PDBPolymer.class);
factory.register(IMonomer.class, Monomer.class);
factory.register(IPDBMonomer.class, PDBMonomer.class);
factory.register(IBioPolymer.class, BioPolymer.class);
factory.register(IPDBStructure.class, PDBStructure.class);
factory.register(IAminoAcid.class, AminoAcid.class);
factory.register(IStrand.class, Strand.class);
// reactions
factory.register(IReaction.class, Reaction.class);
factory.register(IReactionScheme.class, ReactionScheme.class);
// formula
factory.register(IMolecularFormula.class, MolecularFormula.class);
factory.register(IAdductFormula.class, AdductFormula.class);
// chem object sets
factory.register(IAtomContainerSet.class, AtomContainerSet.class);
factory.register(IMolecularFormulaSet.class, MolecularFormulaSet.class);
factory.register(IReactionSet.class, ReactionSet.class);
factory.register(IRingSet.class, RingSet.class);
factory.register(IChemModel.class, ChemModel.class);
factory.register(IChemFile.class, ChemFile.class);
factory.register(IChemSequence.class, ChemSequence.class);
// stereo components (requires some modification after instantiation)
factory.register(
ITetrahedralChirality.class,
TetrahedralChirality.class,
new DynamicFactory.CreationModifier<TetrahedralChirality>() {
@Override
public void modify(TetrahedralChirality instance) {
instance.setBuilder(self);
}
});
factory.register(
IDoubleBondStereochemistry.class,
DoubleBondStereochemistry.class,
new DynamicFactory.CreationModifier<DoubleBondStereochemistry>() {
@Override
public void modify(DoubleBondStereochemistry instance) {
instance.setBuilder(self);
}
});
// miscellaneous
factory.register(IMapping.class, Mapping.class);
factory.register(IChemObject.class, ChemObject.class);
}
/** @inheritDoc */
@Override
public <T extends ICDKObject> T newInstance(Class<T> clazz, Object... params) {
return factory.ofClass(clazz, params);
}