コード例 #1
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        public void TestMapping()
        {
            var type = new HyperconjugationReaction();

            var setOfReactants = GetExampleReactants();
            var molecule       = setOfReactants[0];

            /* automatic search of the center active */
            var paramList = new List <IParameterReaction>();
            var param     = new SetReactionCenter();

            param.IsSetParameter = false;
            paramList.Add(param);
            type.ParameterList = paramList;

            /* initiate */
            var setOfReactions = type.Initiate(setOfReactants, null);

            var product1 = setOfReactions[0].Products[0];
            var product2 = setOfReactions[0].Products[1];

            Assert.AreEqual(3, setOfReactions.Count);
            Assert.AreEqual(2, setOfReactions[0].Products.Count);

            // if these assertions fail the atom order may have changed
            var mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[1]);

            Assert.AreEqual(mappedProductA1, product1.Atoms[1]);
            mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[2]);
            Assert.AreEqual(mappedProductA1, product1.Atoms[2]);
            mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[6]);
            Assert.AreEqual(mappedProductA1, product2.Atoms[0]);
        }
コード例 #2
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        public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
        {
            var type           = new HyperconjugationReaction();
            var setOfReactants = CDK.Builder.NewAtomContainerSet();

            /* [C+]CC */
            var molecule = builder.NewAtomContainer();

            molecule.Atoms.Add(builder.NewAtom("C"));
            molecule.Atoms[0].FormalCharge = 1;
            molecule.Atoms.Add(builder.NewAtom("C"));
            molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
            molecule.Atoms.Add(builder.NewAtom("C"));
            molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Single);
            AddExplicitHydrogens(molecule);

            setOfReactants.Add(molecule);

            /* automatic search of the center active */
            var paramList = new List <IParameterReaction>();
            var param     = new SetReactionCenter();

            param.IsSetParameter = false;
            paramList.Add(param);
            type.ParameterList = paramList;

            /* initiate */
            MakeSureAtomTypesAreRecognized(molecule);

            var setOfReactions = type.Initiate(setOfReactants, null);

            Assert.AreEqual(2, setOfReactions.Count);
            Assert.AreEqual(2, setOfReactions[0].Products.Count);

            var product = setOfReactions[0].Products[0];
            /* C=CC */
            var molecule2 = builder.NewAtomContainer();

            molecule2.Atoms.Add(builder.NewAtom("C"));
            molecule2.Atoms.Add(builder.NewAtom("C"));
            molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[1], BondOrder.Double);
            molecule2.Atoms.Add(builder.NewAtom("C"));
            molecule2.AddBond(molecule2.Atoms[1], molecule2.Atoms[2], BondOrder.Single);
            AddExplicitHydrogens(molecule2);

            Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, product));

            product = setOfReactions[0].Products[1];
            /* [H+] */
            molecule2 = builder.NewAtomContainer();
            molecule2.Atoms.Add(builder.NewAtom("H"));
            molecule2.Atoms[0].FormalCharge = 1;

            Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, product));
        }
コード例 #3
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        public void TestCDKConstants_REACTIVE_CENTER()
        {
            var type = new HyperconjugationReaction();

            var setOfReactants = GetExampleReactants();
            var molecule       = setOfReactants[0];

            /* manually put the reactive center */
            molecule.Atoms[1].IsReactiveCenter = true;
            molecule.Atoms[2].IsReactiveCenter = true;
            molecule.Atoms[6].IsReactiveCenter = true;
            molecule.Bonds[1].IsReactiveCenter = true;
            molecule.Bonds[5].IsReactiveCenter = true;

            var paramList = new List <IParameterReaction>();
            var param     = new SetReactionCenter();

            param.IsSetParameter = true;
            paramList.Add(param);
            type.ParameterList = paramList;

            /* initiate */
            var setOfReactions = type.Initiate(setOfReactants, null);

            IAtomContainer reactant1 = setOfReactions[0].Reactants[0];

            Assert.IsTrue(molecule.Atoms[1].IsReactiveCenter);
            Assert.IsTrue(reactant1.Atoms[1].IsReactiveCenter);
            Assert.IsTrue(molecule.Atoms[2].IsReactiveCenter);
            Assert.IsTrue(reactant1.Atoms[2].IsReactiveCenter);
            Assert.IsTrue(molecule.Atoms[6].IsReactiveCenter);
            Assert.IsTrue(reactant1.Atoms[6].IsReactiveCenter);
            Assert.IsTrue(molecule.Bonds[1].IsReactiveCenter);
            Assert.IsTrue(reactant1.Bonds[1].IsReactiveCenter);
            Assert.IsTrue(molecule.Bonds[5].IsReactiveCenter);
            Assert.IsTrue(reactant1.Bonds[5].IsReactiveCenter);
        }
コード例 #4
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        public void TestWithNegativeCharge()
        {
            var type = new HyperconjugationReaction();

            var setOfReactants = GetExampleReactants();

            /* automatic search of the center active */
            var paramList = new List <IParameterReaction>();
            var param     = new SetReactionCenter();

            param.IsSetParameter = false;
            paramList.Add(param);
            type.ParameterList = paramList;

            /* initiate */
            var setOfReactions = type.Initiate(setOfReactants, null);

            Assert.AreEqual(3, setOfReactions.Count);
            Assert.AreEqual(2, setOfReactions[0].Products.Count);

            var product = setOfReactions[0].Products[0];

            var molecule2 = GetExpectedProducts()[0];

            var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(molecule2);

            Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(product, queryAtom));

            product = setOfReactions[0].Products[1];

            molecule2 = builder.NewAtomContainer();
            molecule2.Atoms.Add(builder.NewAtom("H"));
            molecule2.Atoms[0].FormalCharge = 1;

            queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);
            Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
        }
コード例 #5
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        public void TestManuallyCentreActive()
        {
            var type = new HyperconjugationReaction();

            var setOfReactants = GetExampleReactants();
            var molecule       = setOfReactants[0];

            /* manually put the center active */
            molecule.Atoms[1].IsReactiveCenter = true;
            molecule.Atoms[2].IsReactiveCenter = true;
            molecule.Atoms[6].IsReactiveCenter = true;
            molecule.Bonds[1].IsReactiveCenter = true;
            molecule.Bonds[5].IsReactiveCenter = true;

            var paramList = new List <IParameterReaction>();
            var param     = new SetReactionCenter();

            param.IsSetParameter = true;
            paramList.Add(param);
            type.ParameterList = paramList;

            /* initiate */

            var setOfReactions = type.Initiate(setOfReactants, null);

            Assert.AreEqual(1, setOfReactions.Count);
            Assert.AreEqual(2, setOfReactions[0].Products.Count);

            var product = setOfReactions[0].Products[0];

            var molecule2 = GetExpectedProducts()[0];

            var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);

            Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
        }
コード例 #6
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        public void TestHyperconjugationReaction()
        {
            var type = new HyperconjugationReaction();

            Assert.IsNotNull(type);
        }
コード例 #7
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        public void TestHyperconjugationReaction()
        {
            IReactionProcess type = new HyperconjugationReaction();

            Assert.IsNotNull(type);
        }