internal IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents, bool isReverse, CheckReactantAtom checkReactantAtom, CheckAtom checkAtom, CheckBond checkBond) { CheckInitiateParams(reactants, agents); IReactionSet setOfReactions = reactants.Builder.NewReactionSet(); IAtomContainer reactant = reactants[0]; // if the parameter hasActiveCenter is not fixed yet, set the active centers IParameterReaction ipr = base.GetParameterClass(typeof(SetReactionCenter)); if (ipr != null && !ipr.IsSetParameter) { SetActiveCenters(reactant, checkReactantAtom, checkAtom, checkBond); } foreach (var atomi in reactant.Atoms) { if (atomi.IsReactiveCenter && checkReactantAtom(reactant, atomi)) { foreach (var bondi in reactant.GetConnectedBonds(atomi)) { if (bondi.IsReactiveCenter && checkBond(bondi)) { IAtom atomj = bondi.GetOther(atomi); if (atomj.IsReactiveCenter && checkAtom(atomj) && !reactant.GetConnectedSingleElectrons(atomj).Any()) { IAtom[] atomList; if (isReverse) { atomList = new[] { atomj, atomi } } ; else { atomList = new[] { atomi, atomj } }; var bondList = new[] { bondi }; IChemObjectSet <IAtomContainer> moleculeSet = reactant.Builder.NewChemObjectSet <IAtomContainer>(); moleculeSet.Add(reactant); IReaction reaction = Mechanism.Initiate(moleculeSet, atomList, bondList); if (reaction == null) { continue; } else { setOfReactions.Add(reaction); } } } } } } return(setOfReactions); }
private static void SetActiveCenters(IAtomContainer reactant, CheckReactantAtom checkReactantAtom, CheckAtom checkAtom, CheckBond checkBond) { foreach (var atomi in reactant.Atoms) { if (checkReactantAtom(reactant, atomi)) { foreach (var bondi in reactant.GetConnectedBonds(atomi)) { if (checkBond(bondi)) { IAtom atomj = bondi.GetOther(atomi); if (checkAtom(atomj) && !reactant.GetConnectedSingleElectrons(atomj).Any()) { atomi.IsReactiveCenter = true; atomj.IsReactiveCenter = true; bondi.IsReactiveCenter = true; } } } } } }