On 08/16/2017 06:14 PM, Greg Landrum wrote:

On Wed, Aug 16, 2017 at 3:55 AM, Francois BERENGER <beren...@bioreg.kyushu-u.ac.jp <mailto: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:

    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?


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