public override ICDKObject Clone(CDKObjectMap map)
{
ChemModel clone = (ChemModel)base.Clone(map);
clone.setOfMolecules = (IChemObjectSet <IAtomContainer>)setOfMolecules?.Clone(map);
clone.setOfReactions = (IReactionSet)setOfReactions?.Clone(map);
clone.ringSet = (IRingSet)ringSet?.Clone(map);
clone.crystal = (ICrystal)crystal?.Clone(map);
return(clone);
}
public virtual void TestChemModel()
{
IChemModel chemModel = new ChemModel();
Assert.IsNotNull(chemModel);
Assert.IsTrue(chemModel.IsEmpty());
IAtom atom = new Atom("N");
IRing mol = new Ring(); // NCDK does not allow to add AtomContainer to RingSet
IChemObjectSet <IAtomContainer> mset = new ChemObjectSet <IAtomContainer>();
mol.Atoms.Add(atom);
mset.Add(mol);
chemModel.MoleculeSet = mset;
Assert.IsFalse(chemModel.IsEmpty());
mol.Atoms.Remove(atom);
Assert.IsFalse(chemModel.IsEmpty());
chemModel.MoleculeSet = null;
Assert.IsTrue(chemModel.IsEmpty());
IChemModel model1 = new ChemModel();
mol.Atoms.Add(atom);
IReaction react = new Reaction();
react.Reactants.Add(mol);
IReactionSet rset = new ReactionSet {
react
};
model1.ReactionSet = rset;
Assert.IsFalse(model1.IsEmpty());
mol.Atoms.Remove(atom);
Assert.IsFalse(model1.IsEmpty());
model1.ReactionSet = null;
Assert.IsTrue(model1.IsEmpty());
IChemModel model2 = new ChemModel();
mol.Atoms.Add(atom);
IRingSet ringset = new RingSet();
ringset.AddRange(mset.Cast <IRing>()); // NCDK does not allow to add AtomContainer to RingSet directly
model2.RingSet = ringset;
Assert.IsFalse(model2.IsEmpty());
mol.Atoms.Remove(atom);
Assert.IsFalse(model2.IsEmpty());
model2.RingSet = null;
Assert.IsTrue(model2.IsEmpty());
IChemModel model3 = new ChemModel();
mol.Atoms.Add(atom);
ICrystal cry = new Crystal(mol);
model3.Crystal = cry;
Assert.IsFalse(model3.IsEmpty());
mol.Atoms.Remove(atom);
Assert.IsFalse(model3.IsEmpty());
model3.Crystal = null;
Assert.IsTrue(model3.IsEmpty());
}