Thanks James! On Wed, 19 May 2021 at 17:40, James Davidson <j.david...@vernalis.com> wrote:
> Hi Greg, > > > > Thanks for the response (and sorry to be the bearer of bad news!). > > Issue added: https://github.com/rdkit/rdkit/issues/4155 > > > > Kind regards > > > > James > > > > *From:* Greg Landrum <greg.land...@gmail.com> > *Sent:* 19 May 2021 14:59 > *To:* James Davidson <j.david...@vernalis.com> > *Cc:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] Problem finding potential stereo-centres > in bridged bicyclics involving 4-membered rings? > > > > Hi James, > > > > I don't think that's the same bug as #3490. I think it's something > different; "yay". > > ;-) > > > > It would be great if you could file a github issue for this. > > > > Thanks, > > -greg > > > > > > On Wed, May 19, 2021 at 3:20 PM James Davidson <j.david...@vernalis.com> > wrote: > > Dear All, > > > > I’ve got a strong suspicion that what I am seeing is related to the open > issue 3490 (https://github.com/rdkit/rdkit/issues/3490), but as I can’t > seem to find a mention of a non-spiro problem then I thought I would share. > > Tested in 2020.09.4 and 2021.03.2 with the same result. > > > > smi_list = ['CC1CCC(CC1)C(N)=O', 'CC12CCC(CC1)(C2)C(N)=O', > 'CC1CC(C1)C(N)=O', 'CC12CC(C1)(CC2)C(N)=O'] > > for smi in smi_list: > > mol = Chem.MolFromSmiles(smi) > > display(show_mol(mol, size=(450, 200))) # wrapper function for new > drawing code in jupyter > > print(list(Chem.FindPotentialStereo(mol))) > > print(Chem.FindMolChiralCenters(mol, includeUnassigned=True, > useLegacyImplementation=False)) > > > > The 4 cases are: > > - Symmetrically-disubstituted 6-membered ring > - A bridged version (using a 1-atom bridge to avoid a completely > symmetrical product) > - Symmetrically-disubstituted 4-membered ring > - A bridged version (this time using a 2-atom bridge to avoid symmetry) > > > > And this is what I see: > > > > > > In the case of the bridged 4-membered ring (or bridged 5-membererd ring, > depending on your viewpoint!), FindPotentialStereo() fails to identify the > two potential stereo atoms. > > If anyone can spot if this is the same issue as 3490, or something > different, then that would be appreciated! > > > > Kind regards > > > > James > ------------------------------ > > > PLEASE READ - This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or postmas...@vernalis.com. Email is not > a secure method of communication and the Company cannot accept > responsibility for the accuracy or completeness of this message or any > attachment(s). Please check this email for virus infection for which the > Company accepts no responsibility. If verification of this email is sought > then please request a hard copy. Unless otherwise stated, any views or > opinions presented are solely those of the author and do not represent > those of the Company. > > Vernalis (R&D) Limited (no. 1985479) > Granta Park, Great Abington > Cambridge, CB21 6GB, United Kingdom > Tel: +44 (0)1223 895 555 > ------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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