/// <summary>
/// set the active center for this molecule.
/// The active center will be those which correspond with X=Y.
/// </summary>
/// <param name="reactant">The molecule to set the activity</param>
private static void SetActiveCenters(IAtomContainer reactant)
{
if (AtomContainerManipulator.GetTotalCharge(reactant) != 0)
{
return;
}
foreach (var bondi in reactant.Bonds)
{
if (((bondi.Order == BondOrder.Double) || (bondi.Order == BondOrder.Triple)))
{
int chargeAtom0 = bondi.Begin.FormalCharge ?? 0;
int chargeAtom1 = bondi.End.FormalCharge ?? 0;
if (chargeAtom0 >= 0 && chargeAtom1 >= 0 &&
!reactant.GetConnectedSingleElectrons(bondi.Begin).Any() &&
!reactant.GetConnectedSingleElectrons(bondi.End).Any() &&
!reactant.GetConnectedLonePairs(bondi.Begin).Any() &&
!reactant.GetConnectedLonePairs(bondi.End).Any())
{
bondi.IsReactiveCenter = true;
bondi.Begin.IsReactiveCenter = true;
bondi.End.IsReactiveCenter = true;
}
}
}
}
internal IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents, string atomSymbol)
{
CheckInitiateParams(reactants, agents);
IReactionSet setOfReactions = reactants.Builder.NewReactionSet();
IAtomContainer reactant = reactants[0];
IParameterReaction ipr = base.GetParameterClass(typeof(SetReactionCenter));
if (ipr != null && !ipr.IsSetParameter)
{
SetActiveCenters(reactant);
}
if (AtomContainerManipulator.GetTotalCharge(reactant) > 0)
{
return(setOfReactions);
}
foreach (var atomi in reactant.Atoms)
{
if (atomi.IsReactiveCenter &&
(atomi.FormalCharge ?? 0) <= 0 &&
reactant.GetConnectedLonePairs(atomi).Any() &&
!reactant.GetConnectedSingleElectrons(atomi).Any())
{
var atomList = new List <IAtom> {
atomi
};
IAtom atomH = reactant.Builder.NewAtom(atomSymbol);
atomH.FormalCharge = 1;
atomList.Add(atomH);
var moleculeSet = reactant.Builder.NewAtomContainerSet();
moleculeSet.Add(reactant);
IAtomContainer adduct = reactant.Builder.NewAtomContainer();
adduct.Atoms.Add(atomH);
moleculeSet.Add(adduct);
IReaction reaction = Mechanism.Initiate(moleculeSet, atomList, null);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
return(setOfReactions);
}
private static void SetActiveCenters(IAtomContainer reactant)
{
if (AtomContainerManipulator.GetTotalCharge(reactant) > 0)
{
return;
}
foreach (var atomi in reactant.Atoms)
{
if ((atomi.FormalCharge ?? 0) <= 0 &&
reactant.GetConnectedLonePairs(atomi).Any() &&
!reactant.GetConnectedSingleElectrons(atomi).Any())
{
atomi.IsReactiveCenter = true;
}
}
}
/// <summary>
/// Initiate process.
/// It is needed to call the addExplicitHydrogensToSatisfyValency
/// from the class tools.HydrogenAdder.
/// </summary>
/// <exception cref="CDKException"> Description of the Exception</exception>
/// <param name="reactants">reactants of the reaction</param>
/// <param name="agents">agents of the reaction (Must be in this case null)</param>
public IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents)
{
Debug.WriteLine($"initiate reaction: {GetType().Name}");
if (reactants.Count != 1)
{
throw new CDKException($"{GetType().Name} only expects one reactant");
}
if (agents != null)
{
throw new CDKException($"{GetType().Name} don't expects agents");
}
var setOfReactions = reactants.Builder.NewReactionSet();
var 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);
}
if (AtomContainerManipulator.GetTotalCharge(reactant) != 0)
{
return(setOfReactions);
}
foreach (var bondi in reactant.Bonds)
{
if (bondi.IsReactiveCenter &&
((bondi.Order == BondOrder.Double) || (bondi.Order == BondOrder.Triple)) &&
bondi.Begin.IsReactiveCenter &&
bondi.End.IsReactiveCenter)
{
int chargeAtom0 = bondi.Begin.FormalCharge ?? 0;
int chargeAtom1 = bondi.End.FormalCharge ?? 0;
if (chargeAtom0 >= 0 && chargeAtom1 >= 0 &&
!reactant.GetConnectedSingleElectrons(bondi.Begin).Any() &&
!reactant.GetConnectedSingleElectrons(bondi.End).Any() &&
!reactant.GetConnectedLonePairs(bondi.Begin).Any() &&
!reactant.GetConnectedLonePairs(bondi.End).Any())
{
for (int j = 0; j < 2; j++)
{
var atomList = new List <IAtom>();
if (j == 0)
{
atomList.Add(bondi.Begin);
atomList.Add(bondi.End);
}
else
{
atomList.Add(bondi.End);
atomList.Add(bondi.Begin);
}
var atomH = reactant.Builder.NewAtom("H");
atomH.FormalCharge = 1;
atomList.Add(atomH);
var bondList = new List <IBond> {
bondi
};
var moleculeSet = reactant.Builder.NewAtomContainerSet();
moleculeSet.Add(reactant);
var adduct = reactant.Builder.NewAtomContainer();
adduct.Atoms.Add(atomH);
moleculeSet.Add(adduct);
var reaction = Mechanism.Initiate(moleculeSet, atomList, bondList);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
}
}
return(setOfReactions);
}