Is this not a case of Schrodingers aromaticity? Until we know what the dummy atom is, it is both aromatic and not?
Best, Nick Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter @ICRnews ________________________________________ From: Peter Shenkin [shen...@gmail.com] Sent: 15 June 2015 17:11 To: Greg Landrum Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] SMILES: Why are rings consisting of wildcards assumed to be aromatic? On Mon, Jun 15, 2015 at 9:54 AM, Greg Landrum <greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote: On Thu, Jun 11, 2015 at 5:54 PM, Peter Shenkin <shen...@gmail.com<mailto:shen...@gmail.com>> wrote: If I canonicalize *1**1 in RDKit, I get [*]1:[*]:[*]:1. I expected [*]1[*][*]1. ... This is certainly a bug and I've put it on the list of stuff to fix: https://github.com/rdkit/rdkit/issues/518 Thanks much, Greg. That is very helpful. Pursuing another remark you made, RDKit canonicalizes C1=C*C=C1 as [*]1cccc1. This may also be unwarranted, because the wildcard could be another C, in which case the structure would not be aromatic. -P. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
