public override void TestInitiate_IAtomContainerSet_IAtomContainerSet() { var type = new RearrangementLonePairReaction(); var setOfReactants = GetExampleReactants(); var molecule = setOfReactants[0]; /* 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); var product = setOfReactions[0].Products[0]; Assert.AreEqual(-1, product.Atoms[2].FormalCharge.Value); Assert.AreEqual(0, product.GetConnectedLonePairs(product.Atoms[1]).Count()); var molecule2 = GetExpectedProducts()[0]; var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product); Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom)); }
public void TestMapping() { var type = new RearrangementLonePairReaction(); var setOfReactants = GetExampleReactants(); var molecule = setOfReactants[0]; molecule.LonePairs.Add(CDK.Builder.NewLonePair(molecule.Atoms[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 product = setOfReactions[0].Products[0]; Assert.AreEqual(10, setOfReactions[0].Mappings.Count); var mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[0]); Assert.AreEqual(mappedProductA1, product.Atoms[0]); 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() { var type = new RearrangementLonePairReaction(); var setOfReactants = GetExampleReactants(); var molecule = setOfReactants[0]; /* manually put the center active */ molecule.Atoms[0].IsReactiveCenter = true; molecule.Bonds[0].IsReactiveCenter = true; molecule.Atoms[1].IsReactiveCenter = true; molecule.Bonds[1].IsReactiveCenter = true; molecule.Atoms[2].IsReactiveCenter = true; molecule.Bonds[2].IsReactiveCenter = true; molecule.Atoms[3].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); var product = setOfReactions[0].Products[0]; /* C=C-[C-]-C */ var molecule2 = GetExpectedProducts()[0]; var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product); Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom)); }
public void TestCDKConstants_REACTIVE_CENTER() { var type = new RearrangementLonePairReaction(); var setOfReactants = GetExampleReactants(); var molecule = setOfReactants[0]; /* manually put the reactive center */ molecule.Atoms[0].IsReactiveCenter = true; molecule.Atoms[1].IsReactiveCenter = true; molecule.Atoms[2].IsReactiveCenter = true; molecule.Bonds[0].IsReactiveCenter = true; molecule.Bonds[1].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); var 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.Atoms[2].IsReactiveCenter); Assert.IsTrue(reactant.Atoms[2].IsReactiveCenter); Assert.IsTrue(molecule.Bonds[0].IsReactiveCenter); Assert.IsTrue(reactant.Bonds[0].IsReactiveCenter); Assert.IsTrue(molecule.Bonds[1].IsReactiveCenter); Assert.IsTrue(reactant.Bonds[1].IsReactiveCenter); }
public void TestRearrangementLonePairReaction() { var type = new RearrangementLonePairReaction(); Assert.IsNotNull(type); }
public void TestFluorobenzene() { var molecule = builder.NewAtomContainer(); molecule.Atoms.Add(builder.NewAtom("F")); 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.Double); molecule.Atoms.Add(builder.NewAtom("C")); molecule.AddBond(molecule.Atoms[2], molecule.Atoms[3], BondOrder.Single); molecule.Atoms.Add(builder.NewAtom("C")); molecule.AddBond(molecule.Atoms[3], molecule.Atoms[4], BondOrder.Double); molecule.Atoms.Add(builder.NewAtom("C")); molecule.AddBond(molecule.Atoms[4], molecule.Atoms[5], BondOrder.Single); molecule.Atoms.Add(builder.NewAtom("C")); molecule.AddBond(molecule.Atoms[5], molecule.Atoms[6], BondOrder.Double); molecule.AddBond(molecule.Atoms[6], molecule.Atoms[1], BondOrder.Single); AddExplicitHydrogens(molecule); AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule); CDK.LonePairElectronChecker.Saturate(molecule); var type = new RearrangementLonePairReaction(); var setOfReactants = CDK.Builder.NewAtomContainerSet(); 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 */ var setOfReactions = type.Initiate(setOfReactants, null); Assert.AreEqual(1, setOfReactions.Count); Assert.AreEqual(1, setOfReactions[0].Products.Count); var product1 = setOfReactions[0].Products[0]; var molecule1 = builder.NewAtomContainer(); molecule1.Atoms.Add(builder.NewAtom("F")); molecule1.Atoms[0].FormalCharge = 1; molecule1.Atoms.Add(builder.NewAtom("C")); molecule1.AddBond(molecule1.Atoms[0], molecule1.Atoms[1], BondOrder.Double); molecule1.Atoms.Add(builder.NewAtom("C")); molecule1.Atoms[2].FormalCharge = -1; molecule1.AddBond(molecule1.Atoms[1], molecule1.Atoms[2], BondOrder.Single); molecule1.Atoms.Add(builder.NewAtom("C")); molecule1.AddBond(molecule1.Atoms[2], molecule1.Atoms[3], BondOrder.Single); molecule1.Atoms.Add(builder.NewAtom("C")); molecule1.AddBond(molecule1.Atoms[3], molecule1.Atoms[4], BondOrder.Double); molecule1.Atoms.Add(builder.NewAtom("C")); molecule1.AddBond(molecule1.Atoms[4], molecule1.Atoms[5], BondOrder.Single); molecule1.Atoms.Add(builder.NewAtom("C")); molecule1.AddBond(molecule1.Atoms[5], molecule1.Atoms[6], BondOrder.Double); molecule1.AddBond(molecule1.Atoms[6], molecule1.Atoms[1], BondOrder.Single); AddExplicitHydrogens(molecule1); AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule1); CDK.LonePairElectronChecker.Saturate(molecule1); var qAC = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(molecule1); Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(product1, qAC)); }