public void TestRecursive29_cdkAromaticModel()
{
SMARTSQueryTool sqt = CreateFromSmarts("[NX3;H2,H1;!$(NC=O)]");
IAtomContainer smi = CreateFromSmiles("Cc1cc(=O)c(c[nH]1)C(=O)NC(c1ccc(cc1)O)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)CSc1nnnn1C");
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder));
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(smi);
int[] result = SMARTSSearchTest.Match(sqt, smi);
Assert.AreEqual(1, result[0]);
Assert.AreEqual(1, result[1]);
}
public void TestRecursiveSmarts27_cdkAromaticModel()
{
SMARTSQueryTool sqt = CreateFromSmarts("[NX3;H2,H1;!$(NC=O)]");
IAtomContainer smi = CreateFromSmiles("CCCc1nc(c2n1[nH]c(nc2=O)c1cc(ccc1OCC)S(=O)(=O)N1CCN(CC1)CC)C");
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder));
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(smi);
int[] result = SMARTSSearchTest.Match(sqt, smi);
Assert.AreEqual(1, result[0]);
Assert.AreEqual(1, result[1]);
}
public void TestBasicAmineOnDrugs_cdkAromaticModel()
{
var filename = "drugs.smi";
var ins = ResourceLoader.GetAsStream(GetType(), filename);
using (EnumerableSMILESReader reader = new EnumerableSMILESReader(ins, ChemObjectBuilder.Instance))
{
SMARTSQueryTool sqt = new SMARTSQueryTool("[NX3;H2,H1;!$(NC=O)]", ChemObjectBuilder.Instance);
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder));
int nmatch = 0;
int nmol = 0;
foreach (var container in reader)
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
// skip un-typed atoms, they can't be run through the CDK aromatic
// model
foreach (var atom in container.Atoms)
{
if (atom.AtomTypeName == null)
{
goto continue_READ;
}
}
if (sqt.Matches(container))
{
nmatch++;
}
nmol++;
continue_READ:
;
}
Assert.AreEqual(141, nmol);
Assert.AreEqual(4, nmatch);
}
}