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 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 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 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 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));
}