public void TestMap_Map_Map()
{
IChemObjectBuilder builder = ChemObjectBuilder.Instance;
IAtom c1 = builder.NewAtom("C");
IAtom o2 = builder.NewAtom("O");
IAtom n3 = builder.NewAtom("N");
IAtom c4 = builder.NewAtom("C");
IAtom h5 = builder.NewAtom("H");
// new stereo element
ITetrahedralChirality original = new TetrahedralChirality(c1, new IAtom[] { o2, n3, c4, h5 }, TetrahedralStereo.Clockwise);
// clone the atoms and place in a map
var mapping = new CDKObjectMap();
IAtom c1clone = (IAtom)c1.Clone();
mapping.Set(c1, c1clone);
IAtom o2clone = (IAtom)o2.Clone();
mapping.Set(o2, o2clone);
IAtom n3clone = (IAtom)n3.Clone();
mapping.Set(n3, n3clone);
IAtom c4clone = (IAtom)c4.Clone();
mapping.Set(c4, c4clone);
IAtom h5clone = (IAtom)h5.Clone();
mapping.Set(h5, h5clone);
// map the existing element a new element
ITetrahedralChirality mapped = (ITetrahedralChirality)original.Clone(mapping);
Assert.AreNotSame(original.ChiralAtom, mapped.ChiralAtom, "mapped chiral atom was the same as the original");
Assert.AreSame(c1clone, mapped.ChiralAtom, "mapped chiral atom was not the clone");
var originalLigands = original.Ligands;
var mappedLigands = mapped.Ligands;
Assert.AreNotSame(originalLigands[0], mappedLigands[0], "first ligand was the same as the original");
Assert.AreSame(o2clone, mappedLigands[0], "first mapped ligand was not the clone");
Assert.AreNotSame(originalLigands[1], mappedLigands[1], "second ligand was the same as the original");
Assert.AreSame(n3clone, mappedLigands[1], "second mapped ligand was not the clone");
Assert.AreNotSame(originalLigands[2], mappedLigands[2], "third ligand was the same as the original");
Assert.AreSame(c4clone, mappedLigands[2], "third mapped ligand was not the clone");
Assert.AreNotSame(originalLigands[3], mappedLigands[3], "forth ligand was te same as the original");
Assert.AreSame(h5clone, mappedLigands[3], "forth mapped ligand was not the clone");
Assert.AreEqual(original.Stereo, mapped.Stereo, "stereo was not mapped");
}
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);
}