Hi Paul,
On Mon, Nov 1, 2010 at 3:54 PM, Paul Emsley <paul.ems...@bioch.ox.ac.uk> wrote:
>
> For the record, I would like to describe how I proceeded in the light of
> your reply.
>
> My starting point to construct an RWMol is an mmCIF restraints file. As
> well as containing description of the bonds and angles (etc.) this file
> describes the atoms, part of the description of which is the
> "type_energy". Pyrrole and carbazole Ns (for example) have the type
> "NR15"(energy types are listed in energy_lib.cif [1]) so now when I see
> an atom of that type [2], I add an extra H bonded to the N and
> everything is then peachy.
What you are describing sounds correct. One possible, minor,
optimization if you are building the molecule atom by atom (as opposed
to reading it from a mol block): you don't actually need to put the H
in the graph. You can instead do something like the following:
[6]>>> m = Chem.MolFromSmiles('c1cccn1',sanitize=False)
[7]>>> m.GetAtomWithIdx(4).SetNumExplicitHs(1)
[8]>>> Chem.SanitizeMol(m)
[9]>>> print Chem.MolToSmiles(m)
-----> print(Chem.MolToSmiles(m))
c1cc[nH]c1
>
> Thanks again,
you're welcome!
Best Regards,
-greg
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