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;
}
}
}
}
}
}
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);
}
internal IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents, CheckReactant checkReactant, CheckReactantAtom checkReatantAtom, CheckAtom checkAtom)
{
CheckInitiateParams(reactants, agents);
IReactionSet setOfReactions = reactants.Builder.NewReactionSet();
IAtomContainer reactant = reactants[0];
// if the parameter hasActiveCenter is not fixed yet, set the active centers
var ipr = base.GetParameterClass(typeof(SetReactionCenter));
if (ipr != null && !ipr.IsSetParameter)
{
SetActiveCenters(reactant, checkReactant, checkReatantAtom, checkAtom);
}
foreach (var atomi in reactant.Atoms)
{
if (atomi.IsReactiveCenter && checkReatantAtom(reactant, atomi))
{
foreach (var bondi in reactant.GetConnectedBonds(atomi))
{
if (bondi.IsReactiveCenter && bondi.Order == BondOrder.Single)
{
IAtom atomj = bondi.GetOther(atomi);
if (atomj.IsReactiveCenter &&
(atomj.FormalCharge ?? 0) == 0 &&
!reactant.GetConnectedSingleElectrons(atomj).Any())
{
foreach (var bondj in reactant.GetConnectedBonds(atomj))
{
if (bondj.Equals(bondi))
{
continue;
}
if (bondj.IsReactiveCenter &&
bondj.Order == BondOrder.Double)
{
IAtom atomk = bondj.GetOther(atomj);
if (atomk.IsReactiveCenter &&
checkAtom(atomk) &&
!reactant.GetConnectedSingleElectrons(atomk).Any())
{
var atomList = new List <IAtom>
{
atomi,
atomj,
atomk
};
var bondList = new List <IBond>
{
bondi,
bondj
};
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, CheckReactant checkReatant, CheckReactantAtom checkReatantAtom, CheckAtom checkAtom)
{
if (checkReatant != null && !checkReatant(reactant))
{
return;
}
foreach (var atomi in reactant.Atoms)
{
if (checkReatantAtom(reactant, atomi))
{
foreach (var bondi in reactant.GetConnectedBonds(atomi))
{
if (bondi.Order == BondOrder.Single)
{
IAtom atomj = bondi.GetOther(atomi);
if ((atomj.FormalCharge ?? 0) == 0 &&
!reactant.GetConnectedSingleElectrons(atomj).Any())
{
foreach (var bondj in reactant.GetConnectedBonds(atomj))
{
if (bondj.Equals(bondi))
{
continue;
}
if (bondj.Order == BondOrder.Double)
{
IAtom atomk = bondj.GetOther(atomj);
if (checkAtom(atomk) &&
!reactant.GetConnectedSingleElectrons(atomk).Any())
{
atomi.IsReactiveCenter = true;
atomj.IsReactiveCenter = true;
atomk.IsReactiveCenter = true;
bondi.IsReactiveCenter = true;
bondj.IsReactiveCenter = true;
}
}
}
}
}
}
}
}
}