public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
var type = new RearrangementAnionReaction();
/* [C-]-C=C-C */
var setOfReactants = GetExampleReactants();
var molecule = setOfReactants[0];
/* 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);
var product = setOfReactions[0].Products[0];
Assert.AreEqual(-1, product.Atoms[2].FormalCharge.Value);
Assert.AreEqual(0, product.GetConnectedLonePairs(product.Atoms[1]).Count());
/* C=C-[C-]-C */
var molecule2 = GetExpectedProducts()[0];
var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
}
public void TestMapping()
{
var type = new RearrangementAnionReaction();
var setOfReactants = GetExampleReactants();
var molecule = setOfReactants[0];
molecule.LonePairs.Add(CDK.Builder.NewLonePair(molecule.Atoms[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);
var product = setOfReactions[0].Products[0];
Assert.AreEqual(11, setOfReactions[0].Mappings.Count);
var mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[0]);
Assert.AreEqual(mappedProductA1, product.Atoms[0]);
mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[1]);
Assert.AreEqual(mappedProductA1, product.Atoms[1]);
mappedProductA1 = (IAtom)ReactionManipulator.GetMappedChemObject(setOfReactions[0], molecule.Atoms[2]);
Assert.AreEqual(mappedProductA1, product.Atoms[2]);
}
public void TestManuallyCentreActive()
{
var type = new RearrangementAnionReaction();
var setOfReactants = GetExampleReactants();
var molecule = setOfReactants[0];
/* manually put the center active */
molecule.Atoms[0].IsReactiveCenter = true;
molecule.Bonds[0].IsReactiveCenter = true;
molecule.Atoms[1].IsReactiveCenter = true;
molecule.Bonds[1].IsReactiveCenter = true;
molecule.Atoms[2].IsReactiveCenter = true;
molecule.Bonds[2].IsReactiveCenter = true;
molecule.Atoms[3].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);
var product = setOfReactions[0].Products[0];
/* C=C-[C-]-C */
var molecule2 = GetExpectedProducts()[0];
var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
}
public void TestCDKConstants_REACTIVE_CENTER()
{
var type = new RearrangementAnionReaction();
var setOfReactants = GetExampleReactants();
var molecule = setOfReactants[0];
/* manually put the reactive center */
molecule.Atoms[0].IsReactiveCenter = true;
molecule.Atoms[1].IsReactiveCenter = true;
molecule.Atoms[2].IsReactiveCenter = true;
molecule.Bonds[0].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);
var 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.Atoms[2].IsReactiveCenter);
Assert.IsTrue(reactant.Atoms[2].IsReactiveCenter);
Assert.IsTrue(molecule.Bonds[0].IsReactiveCenter);
Assert.IsTrue(reactant.Bonds[0].IsReactiveCenter);
Assert.IsTrue(molecule.Bonds[1].IsReactiveCenter);
Assert.IsTrue(reactant.Bonds[1].IsReactiveCenter);
}
public void TestRearrangementAnionReaction()
{
var type = new RearrangementAnionReaction();
Assert.IsNotNull(type);
}
public void TestAutomaticSearchCentreActiveExample3()
{
var type = new RearrangementAnionReaction();
/* [F+]=C1-[C-]-C=C-C=C1 */
var 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.Double);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms[2].FormalCharge = -1;
molecule.LonePairs.Add(CDK.Builder.NewLonePair(molecule.Atoms[0]));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[3], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[3], molecule.Atoms[4], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[4], molecule.Atoms[5], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[5], molecule.Atoms[6], BondOrder.Double);
molecule.AddBond(molecule.Atoms[6], molecule.Atoms[1], BondOrder.Single);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
var setOfReactants = CDK.Builder.NewAtomContainerSet();
setOfReactants.Add(molecule);
/* initiate */
MakeSureAtomTypesAreRecognized(molecule);
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(2, setOfReactions.Count);
Assert.AreEqual(1, setOfReactions[0].Products.Count);
var product1 = setOfReactions[1].Products[0];
/* [F+]=C1-[C=]-C-[C-]-C=C1 */
var molecule2 = builder.NewAtomContainer();
molecule2.Atoms.Add(builder.NewAtom("F"));
molecule2.Atoms[0].FormalCharge = 1;
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[1], BondOrder.Double);
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.AddBond(molecule2.Atoms[1], molecule2.Atoms[2], BondOrder.Single);
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.AddBond(molecule2.Atoms[2], molecule2.Atoms[3], BondOrder.Double);
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.Atoms[4].FormalCharge = -1;
molecule2.AddBond(molecule2.Atoms[3], molecule2.Atoms[4], BondOrder.Single);
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.AddBond(molecule2.Atoms[4], molecule2.Atoms[5], BondOrder.Single);
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.AddBond(molecule2.Atoms[5], molecule2.Atoms[6], BondOrder.Double);
molecule2.AddBond(molecule2.Atoms[6], molecule2.Atoms[1], BondOrder.Single);
AddExplicitHydrogens(molecule2);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule2);
CDK.LonePairElectronChecker.Saturate(molecule2);
MakeSureAtomTypesAreRecognized(molecule2);
var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product1);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
//////////////////////////////////////////////////
var product2 = setOfReactions[0].Products[0];
/* F=c1ccccc1 */
var molecule3 = builder.NewAtomContainer();
molecule3.Atoms.Add(builder.NewAtom("F"));
molecule3.Atoms.Add(builder.NewAtom("C"));
molecule3.AddBond(molecule3.Atoms[0], molecule3.Atoms[1], BondOrder.Single);
molecule3.Atoms.Add(builder.NewAtom("C"));
molecule3.AddBond(molecule3.Atoms[1], molecule3.Atoms[2], BondOrder.Double);
molecule3.Atoms.Add(builder.NewAtom("C"));
molecule3.AddBond(molecule3.Atoms[2], molecule3.Atoms[3], BondOrder.Single);
molecule3.Atoms.Add(builder.NewAtom("C"));
molecule3.AddBond(molecule3.Atoms[3], molecule3.Atoms[4], BondOrder.Double);
molecule3.Atoms.Add(builder.NewAtom("C"));
molecule3.AddBond(molecule3.Atoms[4], molecule3.Atoms[5], BondOrder.Single);
molecule3.Atoms.Add(builder.NewAtom("C"));
molecule3.AddBond(molecule3.Atoms[5], molecule3.Atoms[6], BondOrder.Double);
molecule3.AddBond(molecule3.Atoms[6], molecule3.Atoms[1], BondOrder.Single);
AddExplicitHydrogens(molecule3);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule3);
CDK.LonePairElectronChecker.Saturate(molecule3);
MakeSureAtomTypesAreRecognized(molecule3);
queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product2);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule3, queryAtom));
Assert.AreEqual(12, setOfReactions[0].Mappings.Count);
}