public void TestFindMatchingAtomType_IAtomContainer_IAtom()
{
var matcher = SybylAtomTypeMatcher.GetInstance();
Assert.IsNotNull(matcher);
var ethane = TestMoleculeFactory.MakeAlkane(2);
var expectedTypes = new[] { "C.3", "C.3" };
AssertAtomTypes(testedAtomTypes, expectedTypes, ethane);
}
public void TestNonExistingType()
{
var mol = builder.NewAtomContainer();
var atom = builder.NewAtom();
mol.Atoms.Add(atom);
var matcher = SybylAtomTypeMatcher.GetInstance();
var type = matcher.FindMatchingAtomType(mol, atom);
Assert.IsNotNull(type);
Assert.AreEqual("X", type.AtomTypeName);
}
public void TestAdenine()
{
var mol = TestMoleculeFactory.MakeAdenine();
var expectedTypes = new[] { "C.ar", "C.ar", "C.ar", "N.ar", "N.ar", "N.ar", "N.ar", "N.3", "C.ar", "C.ar" };
var matcher = SybylAtomTypeMatcher.GetInstance();
var types = matcher.FindMatchingAtomTypes(mol).ToReadOnlyList();
for (int i = 0; i < expectedTypes.Length; i++)
{
AssertAtomType(testedAtomTypes, $"Incorrect perception for atom {i}", expectedTypes[i], types[i]);
}
}
public void TestBenzene_AtomContainer()
{
var benzene = TestMoleculeFactory.MakeBenzene();
// test if the perceived atom types match that
var matcher = SybylAtomTypeMatcher.GetInstance();
var types = matcher.FindMatchingAtomTypes(benzene);
foreach (var type in types)
{
Assert.AreEqual("C.ar", type.AtomTypeName);
}
}
private static void PercieveAtomTypesAndConfigureAtoms(IAtomContainer container)
{
var matcher = SybylAtomTypeMatcher.GetInstance();
var atoms = container.Atoms.GetEnumerator();
while (atoms.MoveNext())
{
var atom = atoms.Current;
atom.AtomTypeName = null;
var matched = matcher.FindMatchingAtomType(container, atom);
if (matched != null)
{
AtomTypeManipulator.Configure(atom, matched);
}
}
}
public void TestFindMatchingAtomType_IAtomContainer()
{
var filename = "NCDK.Data.Mol2.atomtyping.mol2";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new Mol2Reader(ins);
var mol = reader.Read(builder.NewAtomContainer());
// just check consistency; other methods do perception testing
var matcher = SybylAtomTypeMatcher.GetInstance();
var types = matcher.FindMatchingAtomTypes(mol).ToReadOnlyList();
for (int i = 0; i < types.Count; i++)
{
IAtomType type = matcher.FindMatchingAtomType(mol, mol.Atoms[i]);
Assert.AreEqual(type.AtomTypeName, types[i].AtomTypeName);
}
}
public void TestAniline()
{
var benzene = TestMoleculeFactory.MakeBenzene();
var nitrogen = benzene.Builder.NewAtom("N");
benzene.Atoms.Add(nitrogen);
benzene.Bonds.Add(benzene.Builder.NewBond(benzene.Atoms[0], nitrogen, BondOrder.Single));
// test if the perceived atom types match that
var matcher = SybylAtomTypeMatcher.GetInstance();
var types = matcher.FindMatchingAtomTypes(benzene).ToReadOnlyList();
for (int i = 0; i < 6; i++)
{
AssertAtomType(testedAtomTypes, "Incorrect perception for atom " + i, "C.ar", types[i]);
}
AssertAtomType(testedAtomTypes, "Incorrect perception for atom " + 6, "N.3", types[6]);
}
public override IAtomTypeMatcher GetAtomTypeMatcher(IChemObjectBuilder builder)
{
return(SybylAtomTypeMatcher.GetInstance());
}
public void TestGetInstance_IChemObjectBuilder()
{
var matcher = SybylAtomTypeMatcher.GetInstance();
Assert.IsNotNull(matcher);
}