public IReaction LabelReaction(IReaction reaction, ICanonicalMoleculeLabeller labeller)
{
Console.Out.WriteLine("labelling");
var canonReaction = new Reaction();
var permutationMap = new Dictionary <IAtomContainer, int[]>();
var canonicalProducts = ChemObjectBuilder.Instance.NewChemObjectSet <IAtomContainer>();
foreach (var product in reaction.Products)
{
var canonicalForm = labeller.GetCanonicalMolecule(product);
if (fixAtomMappingCastType)
{
FixAtomMapping(canonicalForm);
}
var canonicalMolecule = canonicalForm.Builder.NewAtomContainer(canonicalForm);
permutationMap[canonicalMolecule] = labeller.GetCanonicalPermutation(product);
canonicalProducts.Add(canonicalMolecule);
}
var canonicalReactants = ChemObjectBuilder.Instance.NewChemObjectSet <IAtomContainer>();
foreach (var reactant in reaction.Reactants)
{
var canonicalForm = labeller.GetCanonicalMolecule(reactant);
if (fixAtomMappingCastType)
{
FixAtomMapping(canonicalForm);
}
var canonicalMolecule = canonicalForm.Builder.NewAtomContainer(canonicalForm);
permutationMap[canonicalMolecule] = labeller.GetCanonicalPermutation(reactant);
canonicalReactants.Add(canonicalMolecule);
}
canonReaction.Products.AddRange(canonicalProducts);
canonReaction.Reactants.AddRange(canonicalReactants);
CloneAndSortMappings(reaction, canonReaction, permutationMap);
return(canonReaction);
}
