Re: [Rdkit-discuss] can't kekulize molecule

[Greg L. <gre...@gm...>]

On Wed, Aug 16, 2017 at 3:55 AM, Francois BERENGER <
ber...@bi...> wrote:

> On 08/16/2017 03:36 PM, Greg Landrum wrote:
>
>>
>> The RDKit Mol2 parser is really only validated for the atom types
>> generated by corina. I'm not surprised that the ouput from open babel would
>> not be understood. This is documented:
>> http://rdkit.org/docs/api/rdkit.Chem.rdmolfiles-module.html#
>> MolFromMol2File
>>
>
> It would be really nice if open babel MOL2 output could directly be read
> in by rdkit.
>

Adding this support is not an impossible task for someone who understands
the open babel interpretation of the Mol2 atom types. Nik's code for
dealing with the cleanup of the corina atom types is quite well documented
and creating a bunch of test cases using OpenBabel would be pretty
straightforward. It would take time and care though.

I'd guess that in the end it's easier and more straightforward to just let
open babel do the translation.


> I often find myself running
> $ obabel in.mol2 -O out.sdf
> just for that purpose.
>

The question I always end up asking here is: Why do you have open babel
mol2 files in the first place?
If you're reading those into another piece of software (the usual answer):
are you sure that the other software and open babel interpret the atom
types the same way? Really sure?

-greg