internal IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents, int length, bool checkPrev, AtomCheck atomCheck)
{
CheckInitiateParams(reactants, agents);
IReactionSet setOfReactions = reactants.Builder.NewReactionSet();
IAtomContainer reactant = reactants[0];
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
Aromaticity.CDKLegacy.Apply(reactant);
AllRingsFinder arf = new AllRingsFinder();
IRingSet ringSet = arf.FindAllRings(reactant);
for (int ir = 0; ir < ringSet.Count; ir++)
{
IRing ring = (IRing)ringSet[ir];
for (int jr = 0; jr < ring.Atoms.Count; jr++)
{
IAtom aring = ring.Atoms[jr];
aring.IsInRing = true;
}
}
// 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, length, checkPrev, atomCheck);
}
HOSECodeGenerator hcg = new HOSECodeGenerator();
foreach (var atomi in reactant.Atoms)
{
if (atomi.IsReactiveCenter && reactant.GetConnectedSingleElectrons(atomi).Count() == 1)
{
IEnumerable <IAtom> atom1s = null;
if (checkPrev)
{
hcg.GetSpheres(reactant, atomi, length - 1, true);
atom1s = hcg.GetNodesInSphere(length - 1);
}
hcg.GetSpheres(reactant, atomi, length, true);
foreach (var atoml in hcg.GetNodesInSphere(length))
{
if (atoml != null &&
atoml.IsReactiveCenter &&
!atoml.IsInRing &&
(atoml.FormalCharge ?? 0) == 0 &&
!atoml.AtomicNumber.Equals(AtomicNumbers.H) &&
reactant.GetMaximumBondOrder(atoml) == BondOrder.Single)
{
foreach (var atomR in reactant.GetConnectedAtoms(atoml))
{
if (atom1s != null && atom1s.Contains(atomR))
{
continue;
}
if (reactant.GetBond(atomR, atoml).IsReactiveCenter &&
atomR.IsReactiveCenter &&
atomCheck(atomR))
{
var atomList = new List <IAtom>
{
atomR,
atomi,
atoml
};
var bondList = new List <IBond>
{
reactant.GetBond(atomR, atoml)
};
var moleculeSet = reactant.Builder.NewChemObjectSet <IAtomContainer>();
moleculeSet.Add(reactant);
var reaction = Mechanism.Initiate(moleculeSet, atomList, bondList);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
}
}
}
}
return(setOfReactions);
}
private static void SetActiveCenters(IAtomContainer reactant, int length, bool checkPrev, AtomCheck atomCheck)
{
var hcg = new HOSECodeGenerator();
foreach (var atomi in reactant.Atoms)
{
if (reactant.GetConnectedSingleElectrons(atomi).Count() == 1)
{
IEnumerable <IAtom> atom1s = null;
if (checkPrev)
{
hcg.GetSpheres(reactant, atomi, length - 1, true);
atom1s = hcg.GetNodesInSphere(length - 1);
}
hcg.GetSpheres(reactant, atomi, length, true);
foreach (var atoml in hcg.GetNodesInSphere(length))
{
if (atoml != null &&
!atoml.IsInRing &&
(atoml.FormalCharge ?? 0) == 0 &&
!atoml.AtomicNumber.Equals(AtomicNumbers.H) &&
reactant.GetMaximumBondOrder(atoml) == BondOrder.Single)
{
foreach (var atomR in reactant.GetConnectedAtoms(atoml))
{
if (atom1s != null && atom1s.Contains(atomR))
{
continue;
}
if (atomCheck(atomR))
{
atomi.IsReactiveCenter = true;
atoml.IsReactiveCenter = true;
atomR.IsReactiveCenter = true;
reactant.GetBond(atomR, atoml).IsReactiveCenter = true;;
}
}
}
}
}
}
}
