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

[Francois B. <ber...@bi...>]

On 08/16/2017 06:14 PM, Greg Landrum wrote:
> 
> On Wed, Aug 16, 2017 at 3:55 AM, Francois BERENGER 
> <ber...@bi... <mailto: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
>         <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.

Can you point out that code?

I may have a look one day.

> 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
>