On 31/10/10 14:18, Greg Landrum wrote:
> Hi Paul,
>
> On Sun, Oct 31, 2010 at 12:09 PM, Paul Emsley
> <paul.ems...@bioch.ox.ac.uk> wrote:
>
>>
>> I'm running into problems when I try to kekulize carbazole.
>>
>> The description I start with is that all the bonds are marked as
>> Bond::AROMATIC and I do setIsAromatic(true) on all the atoms (which are
>> all non-hydrogens). The explicitValence() for the N is 3.
>>
>> MolOps::Kekulize() fails in that case, "Can't kekulize mol".
>>
>> If I add single bonds to hydrogens (including a hydrogens on the N) then
>> MolOps::Kekulize() works.
>>
>> So my question is, how should I adjust the molecule description in the
>> first case so that MolOps::Kekulize() works without hydrogens too?
>>
> The problem is probably the lack of an explicit H on the nitrogen
> atom. It's easily demonstrated with pyrrole:
>
> [2]>>> m=Chem.MolFromSmiles('c1cccn1')
> [15:10:05] Can't kekulize mol
>
> You can fix this by letting the RDKit know that there's an H on the N atom:
> [3]>>> m=Chem.MolFromSmiles('c1ccc[nH]1')
> [4]>>>
>
> Carbazole is the same story:
> [4]>>> m=Chem.MolFromSmiles('c1ccc2c(c1)[nH]c1ccccc21')
> [5]>>>
>
> Note that in either case if you provide the structure in its Kekule
> form this doesn't happen, here's the illustration for pyrrole:
> [5]>>> m=Chem.MolFromSmiles('C1=CC=CN1')
> [6]>>> Chem.MolToSmiles(m)
> Out[6] 'c1cc[nH]c1'
>
> There's an argument to be made that the Kekulization code could be
> made more robust with respect to this particular edge case, but to
> this point the effort involved has not seem justified by the payoff:
> most of the time the H is present in the SMILES, so this problem
> doesn't occur.
>
>
Hi Greg,
Thanks for your informative and speedy reply.
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.
Thanks again,
Paul.
[1]
http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/lib/data/monomers/ener_lib.cif
[2] there are other cases that I need to handle
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