public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
/* Ionize(>C=O): C=CCC(=O)CC -> C=CCC(=O*)CC , 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);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
CDK.LonePairElectronChecker.Saturate(reactant);
foreach (var atom in reactant.Atoms)
{
if (reactant.GetConnectedLonePairs(atom).Count() > 0)
{
atom.IsReactiveCenter = true;
}
}
var setOfReactants = CDK.Builder.NewAtomContainerSet();
setOfReactants.Add(reactant);
/* initiate */
MakeSureAtomTypesAreRecognized(reactant);
var type = new ElectronImpactNBEReaction();
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(1, setOfReactions.Count);
Assert.AreEqual(1, setOfReactions[0].Products.Count);
var molecule = setOfReactions[0].Products[0];
Assert.AreEqual(1, molecule.Atoms[4].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[4]).Count());
Assert.IsTrue(setOfReactions[0].Mappings.Any());
}
public void TestMapping()
{
var type = new ElectronImpactNBEReaction();
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;
var setOfReactions = type.Initiate(setOfReactants, null);
var product = setOfReactions[0].Products[0];
Assert.AreEqual(4, setOfReactions[0].Mappings.Count);
var mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0],
molecule.Atoms[1]);
Assert.AreEqual(mappedProductA1, product.Atoms[1]);
}
public void TestCDKConstants_REACTIVE_CENTER()
{
var type = new ElectronImpactNBEReaction();
var setOfReactants = GetExampleReactants();
var molecule = setOfReactants[0];
/* manually put the reactive center */
molecule.Atoms[1].IsReactiveCenter = true;
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter
{
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);
var reactant = setOfReactions[0].Reactants[0];
Assert.IsTrue(molecule.Atoms[1].IsReactiveCenter);
Assert.IsTrue(reactant.Atoms[1].IsReactiveCenter);
}
public void TestAutomatic_Set_Active_Atom()
{
// Ionize(>C=O): C=CCC(=O)CC -> C=CCC(=O*)CC, without setting 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);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
CDK.LonePairElectronChecker.Saturate(reactant);
var setOfReactants = CDK.Builder.NewAtomContainerSet();
setOfReactants.Add(reactant);
/* initiate */
MakeSureAtomTypesAreRecognized(reactant);
var type = new ElectronImpactNBEReaction();
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(1, setOfReactions.Count);
Assert.AreEqual(1, setOfReactions[0].Products.Count);
var molecule = setOfReactions[0].Products[0];
Assert.AreEqual(1, molecule.Atoms[4].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[4]).Count());
}
public void TestFspSingleB()
{
//CreateFromSmiles("FC")
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("F"));
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.AddBond(molecule.Atoms[1], 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);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
molecule.Atoms[0].IsReactiveCenter = true;
var setOfReactants = CDK.Builder.NewAtomContainerSet();
setOfReactants.Add(molecule);
var type = new ElectronImpactNBEReaction();
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter
{
IsSetParameter = true
};
paramList.Add(param);
type.ParameterList = paramList;
/* initiate */
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(1, setOfReactions.Count);
// expected products
//CreateFromSmiles("[F*+]C")
var expected1 = builder.NewAtomContainer();
expected1.Atoms.Add(builder.NewAtom("F"));
expected1.Atoms[0].FormalCharge = 1;
expected1.SingleElectrons.Add(builder.NewSingleElectron(expected1.Atoms[0]));
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[1], BondOrder.Single);
expected1.Atoms.Add(builder.NewAtom("H"));
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);
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[4], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected1);
CDK.LonePairElectronChecker.Saturate(expected1);
var product1 = setOfReactions[0].Products[0];
var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(expected1);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(product1, queryAtom));
}