public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
        {
            IReactionProcess type = new RadicalSiteHrBetaReaction();

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

            IAtomContainer product   = setOfReactions[0].Products[0];
            IAtomContainer molecule2 = GetExpectedProducts()[0];

            IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);

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

            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(19, 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[6]);

            Assert.AreEqual(mappedProductA2, product.Atoms[6]);
            IAtom mappedProductA3 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0],
                                                                                   molecule.Atoms[3]);

            Assert.AreEqual(mappedProductA3, product.Atoms[3]);
        }
        public void TestCDKConstants_REACTIVE_CENTER()
        {
            IReactionProcess type = new RadicalSiteHrBetaReaction();

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

            /* manually put the reactive center */
            molecule.Atoms[3].IsReactiveCenter = true;
            molecule.Atoms[0].IsReactiveCenter = true;
            molecule.Atoms[6].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 reactant = setOfReactions[0].Reactants[0];

            Assert.IsTrue(molecule.Atoms[6].IsReactiveCenter);
            Assert.IsTrue(reactant.Atoms[6].IsReactiveCenter);
            Assert.IsTrue(molecule.Atoms[0].IsReactiveCenter);
            Assert.IsTrue(reactant.Atoms[0].IsReactiveCenter);
            Assert.IsTrue(molecule.Atoms[3].IsReactiveCenter);
            Assert.IsTrue(reactant.Atoms[3].IsReactiveCenter);
            Assert.IsTrue(molecule.Bonds[5].IsReactiveCenter);
            Assert.IsTrue(reactant.Bonds[5].IsReactiveCenter);
        }
        public void TestRadicalSiteHrBetaReaction()
        {
            IReactionProcess type = new RadicalSiteHrBetaReaction();

            Assert.IsNotNull(type);
        }