Hi all, Thanks for all your replies. I wonder what kind of logic may be put in place to fix these mistakes algorithmically. Any ways to configure the correct stereochemistry before embedding the structure?
Thanks, On Thu, 19 Jan 2023 at 17:49, Giovanni Tricarico < [email protected]> wrote: > Indeed, the only two chemically valid configurations for this molecule > seem to be: > > > > > > Impressive that rdkit can detect this kind of contradictions. > > > > G > > > > *From:* Kangway Chuang (CHUANGK4) via Rdkit-discuss < > [email protected]> > *Sent:* 19 January 2023 17:54 > *To:* Ling Chan <[email protected]>; Gianmarco Ghiandoni < > [email protected]> > *Cc:* RDKit <[email protected]> > *Subject:* Re: [Rdkit-discuss] Embedding of molecules with incorrect > stereochistry assignment > > > > Agree with Hao above. For the molecules provided, the second example is > geometrically inaccessible given the stereochemical constraints. In this > case, the expected behavior should be an unsuccessful embedding. > > > > Kangway > > > > On Thu, Jan 19, 2023 at 8:49 AM Ling Chan <[email protected]> wrote: > > Keep trying with more random seeds? > > > > On Thu., Jan. 19, 2023, 07:38 Hao, <[email protected]> wrote: > > Hi Gianmarco, > > > > In my experience, this just means that you have an impossible molecule. I > haven't found any ways around it besides trying to embed. If it fails, try > to swap the other stereoisomer. I find this particularly prevalent in large > scale datasets where data quality is not very good. > > > > Best, > > Hao > > > > On Thu, Jan 19, 2023 at 7:09 AM Gianmarco Ghiandoni <[email protected]> > wrote: > > Hi all, > > > > Anyone can help with this matter? > > > > Thanks, > > > > On Tue, 17 Jan 2023 at 13:03, Gianmarco Ghiandoni <[email protected]> > wrote: > > Hi all, > > > > I have come across an issue while embedding structures with > stereochemistry configurations that presumably lead to clashes between > atoms: > > > > from rdkit import Chem > > from rdkit.Chem import AllChem > > > > smiles="C1N[C@@H]2CO[C@H]1C2" > > m = Chem.MolFromSmiles(smiles) > > mh = Chem.AddHs(m) > > print(AllChem.EmbedMolecule(mh, randomSeed=11)) > > > > smiles="C1N[C@@H]2CO[C@@H]1C2" > > m = Chem.MolFromSmiles(smiles) > > mh = Chem.AddHs(m) > > print(AllChem.EmbedMolecule(mh, randomSeed=11)) > > > > > > Produces: > > 0 (successful embedding) > -1 (unsuccessful embedding) > > > > What is in your opinion the best way to deal with this in order to avoid > failures? > > > > Thanks, > > -- > > *Gianmarco* > > > > > -- > > *Gianmarco* > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > <https://eur05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=05%7C01%7Cgiovanni.tricarico%40glpg.com%7Cbb3a6b722ea54a755f2108dafa40bfbf%7C627f3c33bccc48bba033c0a6521f7642%7C1%7C0%7C638097453261043031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=COfMwgZqYa6%2B9RKiqKRcIE8i7C%2BqziVSS7HaZAT3N3s%3D&reserved=0> > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > <https://eur05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=05%7C01%7Cgiovanni.tricarico%40glpg.com%7Cbb3a6b722ea54a755f2108dafa40bfbf%7C627f3c33bccc48bba033c0a6521f7642%7C1%7C0%7C638097453261043031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=COfMwgZqYa6%2B9RKiqKRcIE8i7C%2BqziVSS7HaZAT3N3s%3D&reserved=0> > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > <https://eur05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=05%7C01%7Cgiovanni.tricarico%40glpg.com%7Cbb3a6b722ea54a755f2108dafa40bfbf%7C627f3c33bccc48bba033c0a6521f7642%7C1%7C0%7C638097453261043031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=COfMwgZqYa6%2B9RKiqKRcIE8i7C%2BqziVSS7HaZAT3N3s%3D&reserved=0> > > This e-mail and its attachment(s) (if any) may contain confidential and/or > proprietary information and is intended for its addressee(s) only. Any > unauthorized use of the information contained herein (including, but not > limited to, alteration, reproduction, communication, distribution or any > other form of dissemination) is strictly prohibited. If you are not the > intended addressee, please notify the originator promptly and delete this > e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor > any of its affiliates shall be liable for direct, special, indirect or > consequential damages arising from alteration of the contents of this > message (by a third party) or as a result of a virus being passed on. > -- *Gianmarco*
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