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]);
}
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));
}
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);
}
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));
}
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));
}
public void TestHyperconjugationReaction()
{
var type = new HyperconjugationReaction();
Assert.IsNotNull(type);
}
public void TestHyperconjugationReaction()
{
IReactionProcess type = new HyperconjugationReaction();
Assert.IsNotNull(type);
}