Dear Andrew:
Thank you very much for your input.
I was able to refine and correct my approach with your suggestions.
Cheers,
Markus
On Wed, Feb 8, 2017 at 12:23 PM, Andrew Dalke <da...@dalkescientific.com>
wrote:
> On Feb 8, 2017, at 19:22, Markus Metz <metm...@gmail.com> wrote:
> > The question to you is: Is there another more elegant way of doing it?
> May be I missed something from the python API?
>
> I don't quite follow what you are looking for, though I have managed to
> condense your code somewhat, into:
>
> updatedMapping = None
> for ring in m.GetRingInfo().AtomRings():
> if set(ring).issubset(maps):
> updatedMapping = ring
>
> if updatedMapping is not None:
> updatedMapping = sorted(updatedMapping)
> for i, atom_idx in enumerate(updatedMapping, 1):
> m.GetAtomWithIdx(atom_idx).SetProp("molAtomMapNumber", str(i))
>
>
> Is it that you do not want to number the "*" atoms? In that case you can
> ask the query structure for the atoms with atomic number 0:
>
> >>> for atom in corea.GetAtoms():
> ... print(atom.GetAtomicNum())
> ...
> 0
> 6
> 6
> 6
> 6
> 6
> 6
> 0
>
> and ignore numbering the atoms at those positions.
>
> Or that you don't want to include ring atoms which aren't ring atoms in
> the query structure?
>
> In which case you can ask the query structure for its rings:
>
> >>> corea.GetRingInfo().AtomRings()
> ((1, 6, 5, 4, 3, 2),)
>
> and use that to guide which atoms should/should not be numbered.
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
>
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