I am absolutely convinced that specifying the aromatic/lowercase form as preferred output style is a really, really bad decision.
Reconstructing a proper Kekule form from complex multi-ring structures with multiple N in mixed pyridine/pyrrole roles in combination with implicit hydrogen quickly becomes a pretty hard problem. Determining aromaticity using whatever model from a Kekule form is much easier. Also, the lowercase form implicitly encodes a specific aromaticity model, which can easily lead to a mismatch when another batch of structures that was encoded with another aromaticity model. is merged into a dataset Nobody uses canonic SMILES for structure identity checks because there are so many canonicalization variants, and much more robust methods exist, so the argument about having to choose an exact location of single and double bonds and thus introducing ambiguity has no real merit. On Fri, Dec 14, 2012 at 6:25 PM, Craig James <cja...@emolecules.com> wrote: > Thanks to Tim, there is a new version of the OpenSMILES specification, in > both HTML and PDF formats: > > http://www.opensmiles.org > > Tim did a great deal of reformating with nice style sheets, and there is a > whole new section on stereo centers. > > I'm leaving on vacation so I haven't had time to review it, but I invite > everyone to read it and make comments. > > This message is cross-posted to several mailing lists. If you're on the > BlueObelisk-SMILES list, please reply to that list. If you're not on that > list but have comments, post them where you can; perhaps someone can > cross-post them to the BO-SMILES list. > > Craig > > > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > -- Wolf-D. Ihlenfeldt - Xemistry GmbH - w...@xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh – Geschäftsführer/Managing Director: Dr. W. D. Ihlenfeldt Address: Hainholzweg 11, D-61462 Königstein, Germany HR Königstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
