public void TestAngleMatch2()
{
var filename = "NCDK.Data.MDL.cnssmarts.sdf";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new EnumerableSDFReader(ins, CDK.Builder);
var query = new PharmacophoreQuery();
var n1 = new PharmacophoreQueryAtom("BasicAmine", "[NX3;h2,h1,H1,H2;!$(NC=O)]");
var n2 = new PharmacophoreQueryAtom("BasicAmine", "[NX3;h2,h1,H1,H2;!$(NC=O)]");
var n3 = new PharmacophoreQueryAtom("BasicAmine", "[NX3;h2,h1,H1,H2;!$(NC=O)]");
var b1 = new PharmacophoreQueryAngleBond(n1, n2, n3, 89.14);
query.Atoms.Add(n1);
query.Atoms.Add(n2);
query.Atoms.Add(n3);
query.Bonds.Add(b1);
var mol = reader.First();
reader.Close();
var matcher = new PharmacophoreMatcher(query);
var status = matcher.Matches(mol);
Assert.IsTrue(status);
}
public void TestAngleMatch3()
{
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 PharmacophoreQueryAngleBond(o, n1, n2, 43, 47);
query.Bonds.Add(b1);
var matcher = new PharmacophoreMatcher(query);
bool firstTime = true;
int i = 0;
var statuses = new bool[100];
foreach (var conf in conformers)
{
if (firstTime)
{
statuses[i] = matcher.Matches(conf, true);
firstTime = false;
}
else
{
statuses[i] = matcher.Matches(conf, false);
}
i++;
}
Assert.AreEqual(100, statuses.Length);
var hits = new int[9];
int idx = 0;
for (i = 0; i < statuses.Length; i++)
{
if (statuses[i])
{
hits[idx++] = i;
}
}
int[] expected = { 0, 6, 32, 33, 48, 54, 60, 62, 69 };
for (i = 0; i < expected.Length; i++)
{
Assert.AreEqual(expected[i], hits[i], $"Hit {i} didn't match");
}
}
public void TestToString()
{
PharmacophoreQueryAtom qatom1 = new PharmacophoreQueryAtom("Amine", "[CX2]N");
PharmacophoreQueryAtom qatom2 = new PharmacophoreQueryAtom("aromatic", "c1ccccc1");
PharmacophoreQueryAtom qatom3 = new PharmacophoreQueryAtom("blah", "C");
PharmacophoreQueryAngleBond qbond1 = new PharmacophoreQueryAngleBond(qatom1, qatom2, qatom3, 54.735);
string repr = qbond1.ToString();
Assert.AreEqual(repr, "AC::Amine [[CX2]N]::aromatic [c1ccccc1]::blah [C]::[54.74 - 54.74] ");
}
public void TestLower()
{
PharmacophoreQueryAtom qatom1 = new PharmacophoreQueryAtom("Amine", "[CX2]N");
PharmacophoreQueryAtom qatom2 = new PharmacophoreQueryAtom("aromatic", "c1ccccc1");
PharmacophoreQueryAtom qatom3 = new PharmacophoreQueryAtom("blah", "C");
PharmacophoreQueryAngleBond qbond1 = new PharmacophoreQueryAngleBond(qatom1, qatom2, qatom3, 54.735);
PharmacophoreQueryAngleBond qbond2 = new PharmacophoreQueryAngleBond(qatom1, qatom2, qatom3, 50, 60);
Assert.AreEqual(54.74, qbond1.GetLower(), 0.01);
Assert.AreEqual(50.00, qbond2.GetLower(), 0.01);
}
public void TestMatches()
{
PharmacophoreAtom patom1 = new PharmacophoreAtom("[CX2]N", "Amine", new Vector3(1, 1, 1));
PharmacophoreAtom patom2 = new PharmacophoreAtom("c1ccccc1", "Aromatic", Vector3.Zero);
PharmacophoreAtom patom3 = new PharmacophoreAtom("C", "Blah", new Vector3(1, 0, 0));
PharmacophoreAngleBond pbond = new PharmacophoreAngleBond(patom1, patom2, patom3);
PharmacophoreQueryAtom qatom1 = new PharmacophoreQueryAtom("Amine", "[CX2]N");
PharmacophoreQueryAtom qatom2 = new PharmacophoreQueryAtom("aromatic", "c1ccccc1");
PharmacophoreQueryAtom qatom3 = new PharmacophoreQueryAtom("blah", "C");
PharmacophoreQueryAngleBond qbond1 = new PharmacophoreQueryAngleBond(qatom1, qatom2, qatom3, 54.735);
PharmacophoreQueryAngleBond qbond2 = new PharmacophoreQueryAngleBond(qatom1, qatom2, qatom3, 50, 60);
PharmacophoreQueryAngleBond qbond3 = new PharmacophoreQueryAngleBond(qatom1, qatom2, qatom3, 60, 80);
PharmacophoreQueryBond qbond4 = new PharmacophoreQueryBond(qatom1, qatom2, 1, 2);
Assert.IsTrue(qbond1.Matches(pbond));
Assert.IsTrue(qbond2.Matches(pbond));
Assert.IsFalse(qbond3.Matches(pbond));
Assert.IsFalse(qbond4.Matches(pbond));
}
