public void TestBB_AutomaticSearchCentreActiveFormaldehyde()
{
IReactionProcess type = new HeterolyticCleavagePBReaction();
var setOfReactants = GetExampleReactants();
IAtomContainer molecule = setOfReactants[0];
/* automatic search of the reactive atoms and bonds */
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter();
param.IsSetParameter = false;
paramList.Add(param);
type.ParameterList = paramList;
/* initiate */
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
MakeSureAtomTypesAreRecognized(molecule);
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(1, setOfReactions.Count);
Assert.AreEqual(1, setOfReactions[0].Products.Count);
IAtomContainer product = setOfReactions[0].Products[0];
Assert.IsTrue(uiTester.IsIsomorph(GetExpectedProducts()[0], product));
}
public void TestMapping()
{
IReactionProcess type = new HeterolyticCleavagePBReaction();
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 TestOspDoubleB()
{
//CreateFromSmiles("O=C")
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("O"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[3], 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 HeterolyticCleavagePBReaction();
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);
// expected products
//CreateFromSmiles("[O-][C+]")
IAtomContainer expected1 = builder.NewAtomContainer();
expected1.Atoms.Add(builder.NewAtom("O"));
expected1.Atoms[0].FormalCharge = -1;
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.Atoms[1].FormalCharge = +1;
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[1], BondOrder.Single);
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[2], BondOrder.Single);
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[3], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected1);
CDK.LonePairElectronChecker.Saturate(expected1);
IAtomContainer product1 = setOfReactions[0].Products[0];
QueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(expected1);
Assert.IsTrue(uiTester.IsIsomorph(product1, queryAtom));
}
public void TestCDKConstants_REACTIVE_CENTER()
{
IReactionProcess type = new HeterolyticCleavagePBReaction();
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
/* C=O */
IAtomContainer molecule = builder.NewAtomContainer();//CreateFromSmiles("C=O")
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("O"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Double);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
setOfReactants.Add(molecule);
/* 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 */
MakeSureAtomTypesAreRecognized(molecule);
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(1, setOfReactions.Count);
Assert.AreEqual(1, setOfReactions[0].Products.Count);
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);
}