private static IAtomContainer RecomputeHydrogens(IAtomContainer mol, IAtomContainer atomContainer, List <IAtom> remove, CDKObjectMap map)
{
// Recompute hydrogen counts of neighbours of removed Hydrogens.
foreach (var aRemove in remove)
{
// Process neighbours.
foreach (var iAtom in atomContainer.GetConnectedAtoms(aRemove))
{
if (!map.TryGetValue(iAtom, out IAtom neighb))
{
continue; // since for the case of H2, neight H has atom heavy atom neighbor
}
//Added by Asad
if (!(neighb is IPseudoAtom))
{
neighb.ImplicitHydrogenCount = (neighb.ImplicitHydrogenCount ?? 0) + 1;
}
else
{
neighb.ImplicitHydrogenCount = 0;
}
}
}
return(mol);
}
public override ICDKObject Clone(CDKObjectMap map)
{
if (map == null)
{
throw new ArgumentNullException(nameof(map));
}
if (map.TryGetValue(this, out IAtom clone))
{
return(clone);
}
clone = (Atom)base.Clone(map);
map.Add(this, clone);
return(clone);
}
public override ICDKObject Clone(CDKObjectMap map)
{
if (map == null)
{
throw new ArgumentNullException(nameof(map));
}
if (map.TryGetValue(this, out IBond iclone))
{
return(iclone);
}
var clone = (Bond)base.Clone(map);
// clone all the Atoms
if (atoms != null)
{
clone.InitAtoms(atoms.Select(n => (IAtom)n?.Clone(map)));
}
map.Add(this, clone);
return(clone);
}