On 23 June 2010 18:43, Craig A. James <cja...@emolecules.com> wrote: > 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).
To be clear, this test passed on Sunday evening, but not since then. > 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 > ------------------------------------------------------------------------------ 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
