Dear all,
I used the pyLSD software (http://eos.univ-reims.fr/LSD/JmnSoft/PyLSD/)
to solve the problems
of isomer generation for the C11H24 and C12H9N formula.
The similarity of the two problems in only apparent.
The 159 isomers of formula C11H24 were generated within a few seconds.
I stopped the resolution process for C12H9N after a few millions of
solutions
because it could have lasted for days, if not for weeks.
Best,
Jean-Marc Nuzillard
Le 16/06/2020 à 11:44, Joshua Meyers a écrit :
Hey Theo,
As others have mentioned, this is indeed a non-trivial problem.
One method would be to use a de novo molecular generator with the aim
of recovering these isomers.
The ability of a generator to generate isomers is actually one of the
benchmarks of a de novo method in GuacaMol.
i.e. how many of the 159 isomers of C11H24 can be recovered by a
method (that target excludes stereochemistry).
https://github.com/BenevolentAI/guacamol/blob/da0917a679f27abdf1d526ebbf84ee6792bac2a4/guacamol/standard_benchmarks.py#L15-L28
You may be able to adapt this for your use case?
Cheers,
Josh
...Incidentally, Jan's method is also implemented there :D
On Mon, 15 Jun 2020 at 12:32, theozh <the...@gmx.net
<mailto:the...@gmx.net>> wrote:
Hello Jan,
thank you very much for your effort.
It might take a while until I will have digested what you have
implemented.
So far, I don't have Jupyter Notebook installed and I'm running
still RDKit 2019.03 or older.
I'm running RDKit on Windows, but in general, it's might be a good
opportunity to start with Linux.
best,
Theo.
Am 14.06.2020 um 12:48 schrieb Jan Halborg Jensen:
> I whipped up something quick and dirty:
https://colab.research.google.com/drive/18esebASwEfPviu-zn9xIs1fwmED-7Yi3?usp=sharing
>
>
>> On 13 Jun 2020, at 10.54, theozh <the...@gmx.net
<mailto:the...@gmx.net> <mailto:the...@gmx.net
<mailto:the...@gmx.net>>> wrote:
>>
>> Dear RDKit-Community,
>>
>> is there maybe a way with RDKit to generate random (but valid)
molecules with a given chemical sumformula?
>> For example:
>> C12H9N could generate Carbazole as valid compound.
>> The output would be mol or SMILES.
>>
>> I haven't found (yet) anything in this direction in the RDKit
documentation and in the web.
>> But maybe I overlooked some modules, functions or examples
which could be the base for realizing such a random generator?
>>
>> Thank you for any hints,
>> Theo.
>>
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Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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