Re: [Rdkit-discuss] Problem finding potential stereo-centres in bridged bicyclics involving 4-membered rings?
Thanks James! On Wed, 19 May 2021 at 17:40, James Davidson 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 > *Sent:* 19 May 2021 14:59 > *To:* James Davidson > *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 > 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) 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 > > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem finding potential stereo-centres in bridged bicyclics involving 4-membered rings?
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 Sent: 19 May 2021 14:59 To: James Davidson 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 mailto: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: [cid:image001.png@01D74CCD.B6F2A180] 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<mailto: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) 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<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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 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) 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 > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Problem finding potential stereo-centres in bridged bicyclics involving 4-membered rings?
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: [cid:image001.png@01D74CB9.B0931950] 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) 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
