The OpenSMILES aromaticity challenge... I think I've identified a fundamental problem with all of the OpenSMILES aromaticity discussions so far. People keep sending examples where a particular atom "donates 1 or 2 electrons," or "can donate 1 electron." I think that's completely bogus. If you don't know whether it's 0, 1 or 2, then you haven't specified the atom's environment well enough.
A perfect example of this is OpenBabel itself. The original aromaticity rules have a *range* of electrons that can be donated by the atom matched by a particular SMARTS. And in every case, if you do a bit of investigation, you can split the rule into two new rules, each with a more specific SMARTS, where there's no ambiguity any more. So here is the challenge: Can you identify an aromatic atom where the number of electrons it donates is ambiguous, and there is no reasonable SMARTS that can separate the two cases? I'm going to claim that there are *no* situations where we don't know exactly the number of electrons each atom will donate, if we specify a precise enough SMARTS. (This is trivially true in the sense that you could write the SMARTS of every possible aromatic ring system, but I'm not talking about that. I'm talking about a sensible SMARTS that defines one atom's immediate environment, in most cases its nearest neighbors but in a few cases perhaps you need to go two neighbors out.) The OpenSMILES page has an enumeration of atoms that could be aromatic that you might use as a starting point. Are there others? http://www.opensmiles.org/spec/open-smiles-3-input.html#3.5.3 I'm sending a copy of this email to the OpenBabel list too. I'll wait a week or so for replies and then post a summary to the BlueObelisk-SMILES discussion. Craig ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
