public void TestSingleAtomMismatching()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C");
var query = sp.ParseSmiles("N");
var tester = new UniversalIsomorphismTester();
Assert.IsFalse(tester.IsIsomorph(target, query), "Single carbon and nitrogen should not match");
Assert.IsFalse(tester.IsIsomorph(query, target), "Single nitrogen and carbon should not match");
}
public void TestSingleAtomMatching()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C");
var query = sp.ParseSmiles("C");
var tester = new UniversalIsomorphismTester();
Assert.IsTrue(tester.IsIsomorph(target, query));
Assert.IsTrue(tester.IsIsomorph(query, target));
}
public void TestIsIsomorphIAtomContainerIAtomContainer()
{
var ac1 = builder.NewAtomContainer();
ac1.Atoms.Add(builder.NewAtom("C"));
var ac2 = builder.NewAtomContainer();
ac2.Atoms.Add(builder.NewAtom("C"));
Assert.IsTrue(uiTester.IsIsomorph(ac1, ac2));
Assert.IsTrue(uiTester.IsSubgraph(ac1, ac2));
}
public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
var type = new AdductionProtonLPReaction();
/* initiate */
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter();
param.IsSetParameter = false;
paramList.Add(param);
type.ParameterList = paramList;
var setOfReactions = type.Initiate(GetExampleReactants(), null);
Assert.AreEqual(1, setOfReactions.Count);
Assert.AreEqual(1, setOfReactions[0].Products.Count);
var product = setOfReactions[0].Products[0];
var molecule2 = GetExpectedProducts()[0];
var queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);
Assert.IsTrue(uiTester.IsIsomorph(molecule2, queryAtom));
}
/// <summary>
/// Perform a full structure search
/// </summary>
/// <param name="query"></param>
/// <param name="target"></param>
/// <param name="switches"></param>
/// <returns></returns>
public bool FullStructureMatch(
INativeMolMx query,
INativeMolMx target,
string FullStructureSearchType = null)
{
if (query == null || target == null)
{
return(false);
}
CdkMol q = query as CdkMol;
q.UpdateNativeMolecule(); // be sure up to date
if (q?.NativeMol == null)
{
return(false);
}
CdkMol t = target as CdkMol;
t.UpdateNativeMolecule();
if (t?.NativeMol == null)
{
return(false);
}
var fs = new UniversalIsomorphismTester();
if (fs.IsIsomorph(q.NativeMol, t.NativeMol))
{
return(true);
}
else
{
return(false);
}
}
public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
//CreateFromSmiles("CC=C")
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Double);
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.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[3], BondOrder.Single);
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[4], BondOrder.Single);
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[5], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[6], BondOrder.Single);
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[7], BondOrder.Single);
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[8], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
molecule.Atoms[1].IsReactiveCenter = true;
molecule.Atoms[2].IsReactiveCenter = true;
molecule.Bonds[1].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(2, setOfReactions.Count);
// expected products
//CreateFromSmiles("C[C+][C-]")
IAtomContainer expected1 = builder.NewAtomContainer();
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.Atoms[1].FormalCharge = +1;
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.Atoms[2].FormalCharge = -1;
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[1], BondOrder.Single);
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[2], BondOrder.Single);
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[3], BondOrder.Single);
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[4], BondOrder.Single);
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[5], BondOrder.Single);
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[6], BondOrder.Single);
expected1.AddBond(expected1.Atoms[2], expected1.Atoms[7], BondOrder.Single);
expected1.AddBond(expected1.Atoms[2], expected1.Atoms[8], 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));
//CreateFromSmiles("C[C-][C+]")
expected1.Atoms[1].FormalCharge = -1;
expected1.Atoms[2].FormalCharge = +1;
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected1);
CDK.LonePairElectronChecker.Saturate(expected1);
product1 = setOfReactions[1].Products[0];
queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(expected1);
Assert.IsTrue(uiTester.IsIsomorph(product1, queryAtom));
}
