public void TestMapping()
{
var type = new ElectronImpactPDBReaction();
var setOfReactants = GetExampleReactants();
var molecule = setOfReactants[0];
/* automatic search of the center active */
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter
{
IsSetParameter = false
};
paramList.Add(param);
type.ParameterList = paramList;
/* initiate */
var setOfReactions = type.Initiate(setOfReactants, null);
var product = setOfReactions[0].Products[0];
Assert.AreEqual(9, setOfReactions[0].Mappings.Count);
var mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[0]);
Assert.AreEqual(mappedProductA1, product.Atoms[0]);
var mappedProductA2 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[1]);
Assert.AreEqual(mappedProductA2, product.Atoms[1]);
}
public void TestAutomatic_Set_Active_Bond()
{
/* ionize all possible double bonds */
IAtomContainer reactant = builder.NewAtomContainer();//Miles("C=CC")
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.AddBond(reactant.Atoms[0], reactant.Atoms[1], BondOrder.Double);
reactant.AddBond(reactant.Atoms[1], reactant.Atoms[2], BondOrder.Single);
AddExplicitHydrogens(reactant);
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
setOfReactants.Add(reactant);
/* initiate */
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
MakeSureAtomTypesAreRecognized(reactant);
IReactionProcess type = new ElectronImpactPDBReaction();
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(2, setOfReactions.Count);
IAtomContainer molecule = setOfReactions[0].Products[0];
Assert.AreEqual(1, molecule.Atoms[0].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[1]).Count());
molecule = setOfReactions[1].Products[0];
Assert.AreEqual(1, molecule.Atoms[1].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[0]).Count());
}
public void TestAutomatic_Set_Active_Bond2()
{
/* ionize >C=C< , set the reactive center */
IAtomContainer reactant = builder.NewAtomContainer();//CreateFromSmiles("C=CCC(=O)CC")
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("O"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.AddBond(reactant.Atoms[0], reactant.Atoms[1], BondOrder.Double);
reactant.AddBond(reactant.Atoms[1], reactant.Atoms[2], BondOrder.Single);
reactant.AddBond(reactant.Atoms[2], reactant.Atoms[3], BondOrder.Single);
reactant.AddBond(reactant.Atoms[3], reactant.Atoms[4], BondOrder.Double);
reactant.AddBond(reactant.Atoms[3], reactant.Atoms[5], BondOrder.Single);
reactant.AddBond(reactant.Atoms[5], reactant.Atoms[6], BondOrder.Single);
AddExplicitHydrogens(reactant);
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
setOfReactants.Add(reactant);
/* initiate */
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
MakeSureAtomTypesAreRecognized(reactant);
var type = new ElectronImpactPDBReaction();
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter
{
IsSetParameter = false
};
paramList.Add(param);
type.ParameterList = paramList;
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(3, setOfReactions.Count);
IAtomContainer molecule = setOfReactions[0].Products[0];
Assert.AreEqual(1, molecule.Atoms[0].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[1]).Count());
molecule = setOfReactions[1].Products[0];
Assert.AreEqual(1, molecule.Atoms[1].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[0]).Count());
Assert.AreEqual(17, setOfReactions[0].Mappings.Count);
}
public void TestCDKConstants_REACTIVE_CENTER()
{
IReactionProcess type = new ElectronImpactPDBReaction();
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
{
IsSetParameter = true
};
paramList.Add(param);
type.ParameterList = paramList;
/* initiate */
MakeSureAtomTypesAreRecognized(molecule);
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(2, 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);
}
public void TestElectronImpactPDBReaction()
{
IReactionProcess type = new ElectronImpactPDBReaction();
Assert.IsNotNull(type);
}
public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
/* ionize >C=C< , set the reactive center */
var reactant = builder.NewAtomContainer();//CreateFromSmiles("C=CCC(=O)CC")
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("O"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.AddBond(reactant.Atoms[0], reactant.Atoms[1], BondOrder.Double);
reactant.AddBond(reactant.Atoms[1], reactant.Atoms[2], BondOrder.Single);
reactant.AddBond(reactant.Atoms[2], reactant.Atoms[3], BondOrder.Single);
reactant.AddBond(reactant.Atoms[3], reactant.Atoms[4], BondOrder.Double);
reactant.AddBond(reactant.Atoms[3], reactant.Atoms[5], BondOrder.Single);
reactant.AddBond(reactant.Atoms[5], reactant.Atoms[6], BondOrder.Single);
AddExplicitHydrogens(reactant);
foreach (var bond in reactant.Bonds)
{
var atom1 = bond.Atoms[0];
var atom2 = bond.Atoms[1];
if (bond.Order == BondOrder.Double && atom1.Symbol.Equals("C") && atom2.Symbol.Equals("C"))
{
bond.IsReactiveCenter = true;
atom1.IsReactiveCenter = true;
atom2.IsReactiveCenter = true;
}
}
var setOfReactants = CDK.Builder.NewAtomContainerSet();
setOfReactants.Add(reactant);
/* initiate */
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
MakeSureAtomTypesAreRecognized(reactant);
var type = new ElectronImpactPDBReaction();
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter
{
IsSetParameter = true
};
paramList.Add(param);
type.ParameterList = paramList;
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(2, setOfReactions.Count);
var molecule = setOfReactions[0].Products[0];
Assert.AreEqual(1, molecule.Atoms[0].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[1]).Count());
Assert.AreEqual(1, molecule.SingleElectrons.Count);
molecule = setOfReactions[1].Products[0];
Assert.AreEqual(1, molecule.Atoms[1].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[0]).Count());
Assert.AreEqual(1, molecule.SingleElectrons.Count);
Assert.AreEqual(17, setOfReactions[0].Mappings.Count);
}
