Hi Paolo,
thanks for your help! I'll have a look at SMARTS.
Regards
Stefan
Am 2021-10-24 22:26, schrieb Paolo Tosco:
Hi Stefan,
The RDKit MMFF94 code assigns one of the 99 atom types, which is what
is
required to assign correct force field parameters to each atom.
If you need the specific atom sub-type you will need to use SMARTS
patterns
or similar to identify the specific sub-environment of a certain MMFF94
atom type.
Alternatively, you may use a piece of software that I wrote ~10 years
ago:that assigns numeric sub-types, that you may then relate to the
respective symbolic atom type:
http://sdf2xyz2sdf.sourceforge.net/
Hope this helps, cheers
p.
On Fri, Oct 22, 2021 at 7:22 PM Hiemer, Stefan <stefan.hie...@fau.de>
wrote:
Dear Omar,
I already know this thread. The problem is, that I do not know, how to
come from the GetMMFFAtomType returned unsigned integer to the string
representation. The unsigned integer code is not unique to a specific
symbolic atom type. Look for example at entry 2-4 of this file
https://github.com/openbabel/openbabel/blob/master/data/mmffdef.par:
C=C 2 2 2 1 0 VINYLIC
* CSP2 2 2 2 1 0 GENERIC CSP2
* CGD 2 2 2 1 0 GUANIDINE CARBON
There you have the same numerical MMFF type (second column) for three
different symbolic atom types. So my question is: Since the numerical
MMFF is not unique to the symbolic atom type how can I get the
symbolic
ones from rdkit? I need the symbolic types in order as the before
mentioned MC code takes them as input.
Regards
Stefan
Am 2021-10-22 06:40, schrieb Omar H94:
> Dear stefan,
>
> I had a similar issue, and based on answer by Paolo Tosco, you can find
> MMFF Symbols/Definitions here :
> https://github.com/openbabel/openbabel/blob/master/data/mmffdef.par
> The thread: https://sourceforge.net/p/rdkit/mailman/message/36949170/
>
> I hope this helps,
> Omar.
>
> On Fri, Oct 22, 2021 at 7:12 AM Hiemer, Stefan <stefan.hie...@fau.de>
> wrote:
>
>> Hello everyone,
>>
>> I need to find the symbolic atom types of the Merck force field in
>> order
>> to create inputs for a Monte Carlo code
>> (http://towhee.sourceforge.net/)
>> as indicated in this example
>> (
>>
https://sourceforge.net/p/towhee/code/HEAD/tree/Examples/Isobaric_Isothermal_Ensemble/MMFF94_Ethyleneoxide/towhee_input
).
>>
>> As far as I can see, rdkit currently only provides the numerical MMFF
>> atom type via GetMMFFAtomType for each atom. Is there a convenient way
>> to get the symbolic ones (as the MC code requires them)?
>>
>> Thanks and Regards
>> Stefan
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
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