public override void TestInitiate_IAtomContainerSet_IAtomContainerSet() { IReactionProcess type = new SharingChargeDBReaction(); var setOfReactants = GetExampleReactants(); IAtomContainer molecule = setOfReactants[0]; /* initiate */ var paramList = new List <IParameterReaction>(); var param = new SetReactionCenter { IsSetParameter = false }; paramList.Add(param); type.ParameterList = paramList; var setOfReactions = type.Initiate(setOfReactants, null); Assert.AreEqual(1, setOfReactions.Count); Assert.AreEqual(1, setOfReactions[0].Products.Count); IAtomContainer product = setOfReactions[0].Products[0]; Assert.AreEqual(1, product.Atoms[1].FormalCharge.Value); Assert.AreEqual(0, product.GetConnectedLonePairs(product.Atoms[1]).Count()); /* C[C+]O| */ IAtomContainer molecule2 = GetExpectedProducts()[0]; IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product); Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom)); }
public void TestCDKConstants_REACTIVE_CENTER() { IReactionProcess type = new SharingChargeDBReaction(); var setOfReactants = GetExampleReactants(); IAtomContainer molecule = setOfReactants[0]; /* manually put the reactive center */ molecule.Atoms[1].IsReactiveCenter = true; molecule.Atoms[2].IsReactiveCenter = true; molecule.Bonds[1].IsReactiveCenter = true; var paramList = new List <IParameterReaction>(); var param = new SetReactionCenter { IsSetParameter = true }; paramList.Add(param); type.ParameterList = paramList; /* initiate */ var setOfReactions = type.Initiate(setOfReactants, null); IAtomContainer reactant = setOfReactions[0].Reactants[0]; Assert.IsTrue(molecule.Atoms[1].IsReactiveCenter); Assert.IsTrue(reactant.Atoms[1].IsReactiveCenter); Assert.IsTrue(molecule.Atoms[2].IsReactiveCenter); Assert.IsTrue(reactant.Atoms[2].IsReactiveCenter); Assert.IsTrue(molecule.Bonds[1].IsReactiveCenter); Assert.IsTrue(reactant.Bonds[1].IsReactiveCenter); }
public void TestMapping() { IReactionProcess type = new SharingChargeDBReaction(); var setOfReactants = GetExampleReactants(); IAtomContainer molecule = setOfReactants[0]; /* automatic search of the center active */ var paramList = new List <IParameterReaction>(); var param = new SetReactionCenter { IsSetParameter = false }; paramList.Add(param); type.ParameterList = paramList; /* initiate */ var setOfReactions = type.Initiate(setOfReactants, null); IAtomContainer product = setOfReactions[0].Products[0]; Assert.AreEqual(8, setOfReactions[0].Mappings.Count); IAtom mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[1]); Assert.AreEqual(mappedProductA1, product.Atoms[1]); mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[2]); Assert.AreEqual(mappedProductA1, product.Atoms[2]); }
public void TestManuallyCentreActive() { IReactionProcess type = new SharingChargeDBReaction(); var setOfReactants = GetExampleReactants(); IAtomContainer molecule = setOfReactants[0]; /* manually put the center active */ molecule.Atoms[1].IsReactiveCenter = true; molecule.Atoms[2].IsReactiveCenter = true; molecule.Bonds[1].IsReactiveCenter = true; var paramList = new List <IParameterReaction>(); var param = new SetReactionCenter { IsSetParameter = true }; paramList.Add(param); type.ParameterList = paramList; /* initiate */ var setOfReactions = type.Initiate(setOfReactants, null); Assert.AreEqual(1, setOfReactions.Count); Assert.AreEqual(1, setOfReactions[0].Products.Count); IAtomContainer product = setOfReactions[0].Products[0]; /* C-[C+]O| */ IAtomContainer molecule2 = GetExpectedProducts()[0]; IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product); Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom)); }