private static void SetActiveCenters(IAtomContainer reactant, BondCheck bondChecker)
{
foreach (var bondi in reactant.Bonds)
{
IAtom atom1 = bondi.Begin;
IAtom atom2 = bondi.End;
if (bondChecker(bondi) &&
(atom1.FormalCharge ?? 0) == 0 &&
(atom2.FormalCharge ?? 0) == 0 &&
!reactant.GetConnectedSingleElectrons(atom1).Any() &&
!reactant.GetConnectedSingleElectrons(atom2).Any())
{
bondi.IsReactiveCenter = true;
atom1.IsReactiveCenter = true;
atom2.IsReactiveCenter = true;
}
}
}
private static void SetActiveCenters(IAtomContainer reactant, BondCheck bondCheck)
{
foreach (var bond in reactant.Bonds)
{
var atom1 = bond.Begin;
var atom2 = bond.End;
if ((bondCheck == null || bondCheck(bond)) &&
(atom1.FormalCharge ?? 0) == 0 &&
(atom2.FormalCharge ?? 0) == 0 &&
!reactant.GetConnectedSingleElectrons(atom1).Any() &&
!reactant.GetConnectedSingleElectrons(atom2).Any())
{
atom1.IsReactiveCenter = true;
atom2.IsReactiveCenter = true;
bond.IsReactiveCenter = true;
}
}
}
internal IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents, BondCheck bondChecker)
{
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, bondChecker);
}
foreach (var bondi in reactant.Bonds)
{
IAtom atom1 = bondi.Begin;
IAtom atom2 = bondi.End;
if (bondi.IsReactiveCenter &&
bondChecker(bondi) &&
atom1.IsReactiveCenter && atom2.IsReactiveCenter &&
(atom1.FormalCharge ?? 0) == 0 &&
(atom2.FormalCharge ?? 0) == 0 &&
!reactant.GetConnectedSingleElectrons(atom1).Any() &&
!reactant.GetConnectedSingleElectrons(atom2).Any())
{
for (int j = 0; j < 2; j++)
{
var atomList = new List <IAtom>();
if (j == 0)
{
atomList.Add(atom1);
atomList.Add(atom2);
}
else
{
atomList.Add(atom2);
atomList.Add(atom1);
}
var bondList = new List <IBond>
{
bondi
};
IChemObjectSet <IAtomContainer> moleculeSet = reactant.Builder.NewAtomContainerSet();
moleculeSet.Add(reactant);
IReaction reaction = Mechanism.Initiate(moleculeSet, atomList, bondList);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
}
return(setOfReactions);
}