Hi Greg,
Thanks a lot for your reply! It makes sense to me. I wonder if there is a
plan for rdkit to generate the mol2 file directly from the rdkit molecule
object?
Thanks,
Shuai
On Wed, Aug 16, 2017 at 5:14 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
>
>
> On Wed, Aug 16, 2017 at 3:55 AM, Francois BERENGER <
> beren...@bioreg.kyushu-u.ac.jp> 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
>
>
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