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);
}
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, 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);
}
/// <summary>
/// Initiate process.
/// It is needed to call the addExplicitHydrogensToSatisfyValency
/// from the class tools.HydrogenAdder.
/// </summary>
/// <param name="reactants">Reactants of the reaction</param>
/// <param name="agents">Agents of the reaction (Must be in this case null)</param>
/// <exception cref="CDKException"> Description of the Exception</exception>
public IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents)
{
Debug.WriteLine("initiate reaction: ElectronImpactNBEReaction");
if (reactants.Count != 1)
{
throw new CDKException("ElectronImpactNBEReaction only expects one reactant");
}
if (agents != null)
{
throw new CDKException("ElectronImpactNBEReaction don't expects 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);
}
foreach (var atom in reactant.Atoms)
{
if (atom.IsReactiveCenter && reactant.GetConnectedLonePairs(atom).Any() &&
!reactant.GetConnectedSingleElectrons(atom).Any())
{
var atomList = new List <IAtom>
{
atom
};
IChemObjectSet <IAtomContainer> moleculeSet = reactant.Builder.NewAtomContainerSet();
moleculeSet.Add(reactant);
IReaction reaction = Mechanism.Initiate(moleculeSet, atomList, null);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
return(setOfReactions);
}
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);
}
/// <summary>
/// Initiate process.
/// It is needed to call the addExplicitHydrogensToSatisfyValency
/// from the class tools.HydrogenAdder.
/// </summary>
/// <param name="reactants">reactants of the reaction.</param>
/// <param name="agents">agents of the reaction (Must be in this case null).</param>
/// <exception cref="CDKException"> Description of the Exception</exception>
public IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents)
{
Debug.WriteLine("initiate reaction: SharingChargeDBReaction");
if (reactants.Count != 1)
{
throw new CDKException("SharingChargeDBReaction only expects one reactant");
}
if (agents != null)
{
throw new CDKException("SharingChargeDBReaction don't expects 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);
}
foreach (var atomi in reactant.Atoms)
{
if (atomi.IsReactiveCenter && atomi.FormalCharge == 1)
{
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)
{
if (!reactant.GetConnectedSingleElectrons(atomj).Any())
{
var atomList = new List <IAtom>
{
atomj,
atomi
};
var bondList = new List <IBond>
{
bondi
};
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);
}
/// <summary>
/// Initiate process.
/// It is needed to call the addExplicitHydrogensToSatisfyValency
/// from the class tools.HydrogenAdder.
/// </summary>
/// <exception cref="CDKException"></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)
{
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);
}
foreach (var atomi in reactant.Atoms)
{
if (atomi.IsReactiveCenter &&
atomi.FormalCharge == 1)
{
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.Single)
{
IAtom atomk = bondj.GetOther(atomj);
if (atomk.IsReactiveCenter &&
(atomk.FormalCharge ?? 0) == 0 &&
!reactant.GetConnectedSingleElectrons(atomk).Any() &&
atomk.AtomicNumber.Equals(AtomicNumbers.H)
)
{
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);
}
internal IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents, string atomSymbol, int charge)
{
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, atomSymbol, charge);
}
foreach (var atomi in reactants[0].Atoms)
{
if (atomi.IsReactiveCenter && reactant.GetConnectedSingleElectrons(atomi).Count() == 1 &&
atomi.FormalCharge == charge)
{
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)
{
foreach (var bondj in reactant.GetConnectedBonds(atomj))
{
if (bondj.Equals(bondi))
{
continue;
}
if (bondj.IsReactiveCenter &&
bondj.Order == BondOrder.Single)
{
IAtom atomk = bondj.GetOther(atomj);
if (atomk.IsReactiveCenter && atomk.Symbol.Equals(atomSymbol, StringComparison.Ordinal) &&
atomk.FormalCharge == 0)
{
var atomList = new List <IAtom>
{
atomi,
atomj,
atomk
};
var bondList = new List <IBond>
{
bondi,
bondj
};
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);
}
/// <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);
}