On 6/23/10 9:44 AM, Tim Vandermeersch wrote: >> Sorry to keep nagging, but the remaining test failure seems to be real >> bug: http://my.cdash.org/testDetails.php?test=2416695&build=76838 >> >> It says that babel -ismi -osmi >> '[nH]1c2ccccc2c2c3C(=O)NCc3c3c4ccccc4[nH]c3c12' gives >> '[nH]1c2CCCCc2c2c3C(=O)NCc3c3c4ccccc4[nH]c3c12'. >> >> If you look at both in Daylight Depict, you will see that aromaticity >> is lost in a phenyl ring at the end of five conjugated rings. > > The SSSR and LSSR are the same (6 rings) for this molecule. The > problem must be in Craig's new aromaticity code...
As far as I know, I didn't change the aromaticity algorithm, only the efficiency of applying it. The actual rules should be identical (and still broken as shown by this example). The solution requires a complete rewrite of the rules. We discussed this recently in the OpenSMILES discussion. The problem (IMHO) is the poor definitions of electron counts for each SMARTS. Some SMARTS are allowed zero or one electron, some are allowed one or two electrons. That's completely bogus if you ask me. It just means your SMARTS aren't specific enough. We need to nail down a clear, concise ALGORITHMIC definition of aromaticity, including the SMARTS that define the electron contributions of every possible aromatic atom and its environment. I've been nagging everyone for about two years about this, with little progress. We should stop writing code and finish writing the specification. Until we do that, we'll keep patching specific cases and arguing about it. Craig ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
