Hi Jason, This gist explains why you are seeing an unexpected result:
https://gist.github.com/ptosco/20b06985cd8830d5e549165f6b9fc969 I think that, independently from the aromaticity model, tautomers with exocyclic double bonds should be penalised compared to tautomers with endocyclic double bonds. Thanks for reporting this, cheers p. On Tue, Sep 22, 2020 at 7:02 PM Gao, Zhenxiang <zhenxiang....@uconn.edu> wrote: > Thank you very much for your help. > > Most of smiles can be processed by Tautomer Canonicalization code. > However, some smiles can not be processed, such as: > > Cc1ccc(NC(=O)N=c2[nH]c(C)cn2C)nc1 > > > > CCCCC(=O)N=c1nc(C)c2ncn(C)c2[nH]1 > > > > I would appreciate it if you could give me some advice about two examples. > > > > > > Best, > > Jason Gao > > > > *From: *Markus Metz <metm...@gmail.com> > *Date: *Sunday, September 20, 2020 at 00:17 > *To: *"Gao, Zhenxiang" <zhenxiang....@uconn.edu> > *Cc: *"rdkit-discuss@lists.sourceforge.net" < > rdkit-discuss@lists.sourceforge.net> > *Subject: *Re: [Rdkit-discuss] A question of molecule structure > > > > *Message sent from a system outside of UConn.* > > > > Dear Gao: > > Your question is a tautomer related issue. > > May be this might help you: > > https://rdkit.blogspot.com/2020/01/trying-out-new-tautomer.html > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdkit.blogspot.com%2F2020%2F01%2Ftrying-out-new-tautomer.html&data=02%7C01%7Czhenxiang.gao%40uconn.edu%7Cfc72af7ef6b344ffd36b08d85d1c0f67%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C637361722399141883&sdata=WW0lnQEK4LahRwEtgEZ2oaaCDfFcERBzWsId4GoOXb8%3D&reserved=0> > > https://github.com/rdkit/rdkit/issues/2908 > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frdkit%2Frdkit%2Fissues%2F2908&data=02%7C01%7Czhenxiang.gao%40uconn.edu%7Cfc72af7ef6b344ffd36b08d85d1c0f67%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C637361722399151877&sdata=Z%2Fq33g%2FP4J7hLsvpLanS1WwguyzMNK5ZqDrLSgyQ4Pw%3D&reserved=0> > > Best, > > Markus > > > > > > On Sep 19, 2020, at 9:03 AM, Gao, Zhenxiang <zhenxiang....@uconn.edu> > wrote: > > > > Hi folks, > > > > I have a simple question. Two double bonds in the following molecule are > outsides the two rings. Does Rdkit has some functions to move two double > bonds back to the rings? > > > > SMILES : Cc1ccc(=NC(=O)N=c2[nH]c(C)cn2C)[nH]c1 > > <image001.jpg> > > > > Thanks, > > Jason Gao > > _______________________________________________ > 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 >
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