public void TestCNSPcore()
{
var filename = "NCDK.Data.MDL.cnssmarts.sdf";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new EnumerableSDFReader(ins, CDK.Builder);
var query = new PharmacophoreQuery();
var arom = new PharmacophoreQueryAtom("A", "c1ccccc1");
var n1 = new PharmacophoreQueryAtom("BasicAmine", "[NX3;h2,h1,H1,H2;!$(NC=O)]");
var b1 = new PharmacophoreQueryBond(arom, n1, 5.0, 7.0);
query.Atoms.Add(arom);
query.Atoms.Add(n1);
query.Bonds.Add(b1);
var mol = reader.First();
reader.Close();
var matcher = new PharmacophoreMatcher(query);
var status = matcher.Matches(mol);
Assert.IsTrue(status);
var pmatches = matcher.GetMatchingPharmacophoreAtoms();
Assert.AreEqual(1, pmatches.Count);
var upmatches = matcher.GetUniqueMatchingPharmacophoreAtoms();
Assert.AreEqual(1, upmatches.Count);
}
public void TestMatchingBonds()
{
var filename = "NCDK.Data.MDL.cnssmarts.sdf";
var ins = ResourceLoader.GetAsStream(filename);
EnumerableSDFReader reader = new EnumerableSDFReader(ins, CDK.Builder);
PharmacophoreQuery query = new PharmacophoreQuery();
PharmacophoreQueryAtom arom = new PharmacophoreQueryAtom("A", "c1ccccc1");
PharmacophoreQueryAtom n1 = new PharmacophoreQueryAtom("BasicAmine", "[NX3;h2,h1,H1,H2;!$(NC=O)]");
PharmacophoreQueryBond b1 = new PharmacophoreQueryBond(arom, n1, 5.0, 7.0);
query.Atoms.Add(arom);
query.Atoms.Add(n1);
query.Bonds.Add(b1);
IAtomContainer mol = (IAtomContainer)reader.First();
reader.Close();
PharmacophoreMatcher matcher = new PharmacophoreMatcher(query);
bool status = matcher.Matches(mol);
Assert.IsTrue(status);
var pmatches = matcher.GetMatchingPharmacophoreAtoms();
Assert.AreEqual(1, pmatches.Count);
var upmatches = matcher.GetUniqueMatchingPharmacophoreAtoms();
Assert.AreEqual(1, upmatches.Count);
var bmatches = matcher.GetMatchingPharmacophoreBonds();
Assert.AreEqual(1, bmatches.Count);
var bmatch = bmatches[0];
Assert.AreEqual(1, bmatch.Count);
PharmacophoreBond pbond = (PharmacophoreBond)BondRef.Deref(bmatch[0]);
Assert.AreEqual(5.63, pbond.BondLength, 0.01);
}
public void TestMatchedAtoms()
{
Assert.IsNotNull(conformers);
// make a query
var query = new PharmacophoreQuery();
var o = new PharmacophoreQueryAtom("D", "[OX1]");
var n1 = new PharmacophoreQueryAtom("A", "[N]");
var n2 = new PharmacophoreQueryAtom("A", "[N]");
query.Atoms.Add(o);
query.Atoms.Add(n1);
query.Atoms.Add(n2);
var b1 = new PharmacophoreQueryBond(o, n1, 4.0, 4.5);
var b2 = new PharmacophoreQueryBond(o, n2, 4.0, 5.0);
var b3 = new PharmacophoreQueryBond(n1, n2, 5.4, 5.8);
query.Bonds.Add(b1);
query.Bonds.Add(b2);
query.Bonds.Add(b3);
var conf1 = conformers[0];
var matcher = new PharmacophoreMatcher(query);
bool status = matcher.Matches(conf1);
Assert.IsTrue(status);
var pmatches = matcher.GetMatchingPharmacophoreAtoms();
Assert.AreEqual(2, pmatches.Count);
var upmatches = matcher.GetUniqueMatchingPharmacophoreAtoms();
Assert.AreEqual(1, upmatches.Count);
}