public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
        {
            IReactionProcess type = new SharingAnionReaction();
            var setOfReactants    = GetExampleReactants();

            /* initiate */

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

            param.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];
            /* C=[O+] */
            IAtomContainer molecule2 = GetExpectedProducts()[0];

            IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);

            Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
        }
        public void TestManuallyCentreActive()
        {
            IReactionProcess type = new SharingAnionReaction();

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

            /* manually put the center active */
            molecule.Atoms[0].IsReactiveCenter = true;
            molecule.Atoms[1].IsReactiveCenter = true;
            molecule.Bonds[0].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(1, setOfReactions[0].Products.Count);

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

            /* C=[O+] */
            IAtomContainer molecule2 = GetExpectedProducts()[0];

            IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);

            Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
        }
        public void TestMapping()
        {
            IReactionProcess type = new SharingAnionReaction();

            var            setOfReactants = GetExampleReactants();
            IAtomContainer 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);

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

            Assert.AreEqual(4, setOfReactions[0].Mappings.Count);

            IAtom mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0],
                                                                                   molecule.Atoms[0]);

            Assert.AreEqual(mappedProductA1, product.Atoms[0]);
            IAtom mappedProductA2 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0],
                                                                                   molecule.Atoms[1]);

            Assert.AreEqual(mappedProductA2, product.Atoms[1]);
        }
        public void TestCDKConstants_REACTIVE_CENTER()
        {
            IReactionProcess type = new SharingAnionReaction();

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

            /* manually put the reactive center */
            molecule.Atoms[0].IsReactiveCenter = true;
            molecule.Atoms[1].IsReactiveCenter = true;
            molecule.Bonds[0].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 reactant = setOfReactions[0].Reactants[0];

            Assert.IsTrue(molecule.Atoms[0].IsReactiveCenter);
            Assert.IsTrue(reactant.Atoms[0].IsReactiveCenter);
            Assert.IsTrue(molecule.Atoms[1].IsReactiveCenter);
            Assert.IsTrue(reactant.Atoms[1].IsReactiveCenter);
            Assert.IsTrue(molecule.Bonds[0].IsReactiveCenter);
            Assert.IsTrue(reactant.Bonds[0].IsReactiveCenter);
        }
        public void TestCarbons()
        {
            IReactionProcess type     = new SharingAnionReaction();
            IAtomContainer   molecule = builder.NewAtomContainer();

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

            AddExplicitHydrogens(molecule);
            AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);

            CDK.LonePairElectronChecker.Saturate(molecule);

            var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();

            setOfReactants.Add(molecule);

            /* initiate */

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

            param.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];
            IAtomContainer 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);

            AddExplicitHydrogens(molecule2);
            AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule2);
            CDK.LonePairElectronChecker.Saturate(molecule2);

            IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);

            Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
        }
        public void TestSharingAnionReaction()
        {
            IReactionProcess type = new SharingAnionReaction();

            Assert.IsNotNull(type);
        }
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        public void TestSharingAnionReaction()
        {
            var type = new SharingAnionReaction();

            Assert.IsNotNull(type);
        }