Hi Craig, On Mon, Jan 25, 2010 at 7:00 PM, Craig James <[email protected]> wrote: > 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.
Incomplete specification is indeed a common problem I encounter too. > 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. I cannot speak for OpenBabel. The CDK, however, aromaticity is based on strong atom typing, where for each atom it is explicitly defined how many electrons are donated to the (potentially) aromatic system. > 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. You lost me here. Is this OpenBabel specific? Where does SMARTS come in? Would the question not need to be: "Can you identify an aromatic atom where the number of electrons it donates is ambiguous, and there is no reasonable SMILES that can separate the two cases?" ? > (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 That is not something I can say at this moment. BTW, do you refer in your question to atoms or elements? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
