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> 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>> > 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. > >> > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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