/// <summary>
/// Checks whether the query angle constraint matches a target distance.
/// <para>
/// This method checks whether a query constraint is satisfied by an observed
/// angle (represented by a <see cref="PharmacophoreAngleBond"/> in the target molecule.
/// </para>
/// </summary>
/// <remarks>
/// Note that angles are compared upto 2 decimal places.
/// </remarks>
/// <param name="bond">The angle relationship in a target molecule</param>
/// <returns>true if the target angle lies within the range of the query constraint</returns>
public bool Matches(IBond bond)
{
bond = BondRef.Deref(bond);
if (bond is PharmacophoreAngleBond pbond)
{
double bondLength = Round(pbond.BondLength, 2);
return(bondLength >= lower && bondLength <= upper);
}
else
{
return(false);
}
}
public void TestMatchedBonds()
{
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 bMatches = matcher.GetMatchingPharmacophoreBonds();
Assert.AreEqual(2, bMatches.Count); // 2 since we haven't gotten a unique set
Assert.AreEqual(3, bMatches[0].Count);
var pbond = (PharmacophoreBond)BondRef.Deref(bMatches[0][0]);
var patom1 = (PharmacophoreAtom)AtomRef.Deref(pbond.Begin);
var patom2 = (PharmacophoreAtom)AtomRef.Deref(pbond.End);
Assert.AreEqual("D", patom1.Symbol);
Assert.AreEqual("A", patom2.Symbol);
var bondMap = matcher.GetTargetQueryBondMappings();
Assert.AreEqual(2, bondMap.Count);
var mapping = bondMap[0];
// get the 'BondRef' for lookup
var value = mapping[bMatches[0][0]];
Assert.AreEqual(b1, value);
}
public void TestMatchingBonds()
{
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);
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);
var pbond = (PharmacophoreBond)BondRef.Deref(bmatch[0]);
Assert.AreEqual(5.63, pbond.BondLength, 0.01);
}
private static Expr GetBondExpr(IBond bond)
{
return(((QueryBond)BondRef.Deref(bond)).Expression);
}
public static IAtomContainer SuppressQueryHydrogens(IAtomContainer mol)
{
// pre-checks
foreach (var atom in mol.Atoms)
{
if (!(AtomRef.Deref(atom) is QueryAtom))
{
throw new ArgumentException("Non-query atoms found!", nameof(mol));
}
}
foreach (var bond in mol.Bonds)
{
if (!(BondRef.Deref(bond) is QueryBond))
{
throw new ArgumentException("Non-query bonds found!", nameof(mol));
}
}
var plainHydrogens = new CDKObjectMap();
foreach (var atom in mol.Atoms)
{
int hcnt = 0;
foreach (var nbor in mol.GetConnectedAtoms(atom))
{
var qnbor = (QueryAtom)AtomRef.Deref(nbor);
if (mol.GetConnectedBonds(nbor).Count() == 1 &&
IsSimpleHydrogen(qnbor.Expression))
{
hcnt++;
plainHydrogens.Set(nbor, atom);
}
}
if (hcnt > 0)
{
var qatom = (QueryAtom)AtomRef.Deref(atom);
var e = qatom.Expression;
var hexpr = new Expr();
for (int i = 0; i < hcnt; i++)
{
hexpr.And(new Expr(ExprType.TotalHCount, i).Negate());
}
e.And(hexpr);
}
}
// nothing to do
if (!plainHydrogens.Any())
{
return(mol);
}
var res = new QueryAtomContainer();
foreach (var atom in mol.Atoms)
{
if (!plainHydrogens.ContainsKey(atom))
{
res.Atoms.Add(atom);
}
}
foreach (var bond in mol.Bonds)
{
if (!plainHydrogens.ContainsKey(bond.Begin) &&
!plainHydrogens.ContainsKey(bond.End))
{
res.Bonds.Add(bond);
}
}
foreach (var se in mol.StereoElements)
{
res.StereoElements.Add((IStereoElement <IChemObject, IChemObject>)se.Clone(plainHydrogens));
}
return(res);
}
