Hi both,
now I realize that yesterday I replied to Michal and not to the list; sorry
about that. Adding the option to force an atom type replacement wouldn't be too
much work, but would not be ideal because in cause of selenium you would get,
for instance, the same VdW radius and equilibrium bond distances as for sulfur,
which would both be too short. That could also be handled upstream the atom
typing by replacing Se with S and putting back Se downstream as I suggested
yesterday to Michal, but again a bit of a hack. Probably a better solution
would be to allow the user to provide some new parameters (as for UFF, adding
Python support) and fall back to a related atom type (sulfur, in this case) for
the missing ones. I'll look into that during the next days and let you know.
Best,
p.
--
==========================================================
Paolo Tosco, Ph.D.
Department of Drug Science and Technology
Via Pietro Giuria, 9 - 10125 Torino (Italy)
Tel: +39 011 670 7680 | Mob: +39 348 5537206
Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it
http://open3dqsar.org | http://open3dalign.org
==========================================================
> On 5 Nov 2013, at 07:20, Greg Landrum <greg.land...@gmail.com> wrote:
>
> Hi Michal,
>
>
>> On Mon, Nov 4, 2013 at 11:45 AM, Michal Krompiec <michal.kromp...@gmail.com>
>> wrote:
>> Hello,
>> Is Se defined in UFF and/or MMFF94? Apparently, molecules with
>> selenophene moieties don't optimize in RDKit, and a warning appears in
>> the log: UFFTYPER: Unrecognized atom type: Se2+2
>
> Right. UFF Parameters are there for sp3 Se ("Se3+2"), but not for the sp2
> version.
>
> There are no MMFF94 parameters for Se.
>
>> Is it possible to define/modify the force field by hand? (for example,
>> use the parametrs of S for Se)
>
> If you are working from C++, you can provide UFF parameters when you build
> the force field, but it's not currently possible to do so from Python. It's
> probably possible to add an option to the python UFF code to allow you to
> provide a new atom type (or to over-ride parameters for an existing atom
> type); I'd have to look into that.
> In the meantime, the quickest thing you could do would be to modify
> $RDBASE/Code/ForceField/UFF/Params.cpp to add the atom type you want and then
> to rebuild the RDKit.
>
> I guess that adding new atom types to MMFF94S is considerably more complex.
> Here one could imagine providing an interface to explicitly set the type of
> an atom to another existing atom type. Paolo would have to let us know how
> much work that is.
>
> -greg
>
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