Re: [Rdkit-discuss] UFF/MMFF atom types
Hi Michal,
Ouch, it looks like I have somehow forgotten about this. I’ll have a look next
week and get back to you.
Cheers,
p.
> On 10 Aug 2018, at 19:20, Michal Krompiec wrote:
>
> Hi Paolo,
> Has anything changed (re adding new atom types to UFF or MMFF) since then?
> Best,
> Michal
>
>> On Tue, 5 Nov 2013 at 06:56, Paolo Tosco wrote:
>> 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 wrote:
>>>
>>> Hi Michal,
>>>
>>>
On Mon, Nov 4, 2013 at 11:45 AM, Michal Krompiec
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
>>>
>>
>>> --
>>> November Webinars for C, C++, Fortran Developers
>>> Accelerate application performance with scalable programming models. Explore
>>> techniques for threading, error checking, porting, and tuning. Get the most
>>> from the latest Intel processors and coprocessors. See abstracts and
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>>
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Re: [Rdkit-discuss] UFF/MMFF atom types
Hi Paolo,
Has anything changed (re adding new atom types to UFF or MMFF) since then?
Best,
Michal
On Tue, 5 Nov 2013 at 06:56, Paolo Tosco wrote:
> 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 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
>
>
> --
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models.
> Explore
> techniques for threading, error checking, porting, and tuning. Get the
> most
> from the latest Intel processors and coprocessors. See abstracts and
> register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231=/4140/ostg.clktrk
>
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>
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[Rdkit-discuss] UFF/MMFF atom types
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 Is it possible to define/modify the force field by hand? (for example, use the parametrs of S for Se) Thanks, Michal -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] UFF/MMFF atom types
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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
