public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
IReactionProcess type = new SharingChargeSBReaction();
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(2, setOfReactions[0].Products.Count);
IAtomContainer product1 = setOfReactions[1].Products[0];
IAtomContainer molecule1 = GetExpectedProducts()[0];
IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product1);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule1, queryAtom));
IAtomContainer product2 = setOfReactions[0].Products[1];
IAtomContainer expected2 = GetExpectedProducts()[0];
queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(expected2);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(product2, queryAtom));
}
public void TestMapping()
{
IReactionProcess type = new SharingChargeSBReaction();
var setOfReactants = GetExampleReactants();
IAtomContainer molecule = setOfReactants[0];
/* manually put the reactive center */
molecule.Atoms[1].IsReactiveCenter = true;
molecule.Atoms[2].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);
IAtomContainer product1 = setOfReactions[0].Products[0];
IAtomContainer product2 = setOfReactions[0].Products[1];
Assert.AreEqual(10, setOfReactions[0].Mappings.Count);
IAtom 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, product2.Atoms[0]);
}
public void TestCDKConstants_REACTIVE_CENTER()
{
IReactionProcess type = new SharingChargeSBReaction();
var setOfReactants = GetExampleReactants();
IAtomContainer molecule = setOfReactants[0];
/* manually put the reactive center */
molecule.Atoms[1].IsReactiveCenter = true;
molecule.Atoms[2].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);
IAtomContainer reactant = setOfReactions[0].Reactants[0];
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[1].IsReactiveCenter);
Assert.IsTrue(reactant.Bonds[1].IsReactiveCenter);
}
public void TestManuallyCentreActive()
{
IReactionProcess type = new SharingChargeSBReaction();
var setOfReactants = GetExampleReactants();
IAtomContainer molecule = setOfReactants[0];
/* manually put the center active */
molecule.Atoms[1].IsReactiveCenter = true;
molecule.Atoms[2].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);
Assert.AreEqual(1, setOfReactions.Count);
Assert.AreEqual(2, setOfReactions[0].Products.Count);
IAtomContainer product1 = setOfReactions[0].Products[0];
IAtomContainer molecule1 = GetExpectedProducts()[0];
IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product1);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule1, queryAtom));
IAtomContainer product2 = setOfReactions[0].Products[1];
IAtomContainer expected2 = GetExpectedProducts()[1];
queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(expected2);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(product2, queryAtom));
}
public void TestFspChargeSingleB()
{
//CreateFromSmiles("[F+]C")
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("F"));
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("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[2], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[3], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[4], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[5], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
molecule.Atoms[0].IsReactiveCenter = true;
molecule.Atoms[1].IsReactiveCenter = true;
molecule.Bonds[0].IsReactiveCenter = true;
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
setOfReactants.Add(molecule);
IReactionProcess type = new SharingChargeSBReaction();
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);
//CreateFromSmiles("FH")
IAtomContainer expected1 = builder.NewAtomContainer();
expected1.Atoms.Add(builder.NewAtom("F"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[1], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected1);
CDK.LonePairElectronChecker.Saturate(expected1);
IAtomContainer product1 = setOfReactions[0].Products[0];
QueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(expected1);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(product1, queryAtom));
//CreateFromSmiles("[C+]")
IAtomContainer expected2 = builder.NewAtomContainer();
expected2.Atoms.Add(builder.NewAtom("C"));
expected2.Atoms[0].FormalCharge = +1;
expected2.Atoms.Add(builder.NewAtom("H"));
expected2.Atoms.Add(builder.NewAtom("H"));
expected2.Atoms.Add(builder.NewAtom("H"));
expected2.AddBond(expected2.Atoms[0], expected2.Atoms[1], BondOrder.Single);
expected2.AddBond(expected2.Atoms[0], expected2.Atoms[2], BondOrder.Single);
expected2.AddBond(expected2.Atoms[0], expected2.Atoms[3], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected2);
IAtomContainer product2 = setOfReactions[0].Products[1];
queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(expected2);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(product2, queryAtom));
}
public void TestSharingChargeSBReaction()
{
IReactionProcess type = new SharingChargeSBReaction();
Assert.IsNotNull(type);
}
