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); }