On Wed, Jun 23, 2010 at 6:02 PM, Noel O'Boyle <baoille...@gmail.com> wrote: > On 23 June 2010 01:37, Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote: >> On Tue, Jun 22, 2010 at 11:08 PM, Tim Vandermeersch >> <tim.vandermeer...@gmail.com> wrote: >>> On Tue, Jun 22, 2010 at 9:59 PM, Greg Landrum <greg.land...@gmail.com> >>> wrote: >>>> Hi Tim, >>>> >>>> On Tue, Jun 22, 2010 at 9:34 PM, Tim Vandermeersch >>>> <tim.vandermeer...@gmail.com> wrote: >>>>> >>>>> On the openbabel devel mainling list there was discussion about the >>>>> Largest Set of Smallest Rings (LSSR). RDKit calls this symmetric SSSR >>>>> I think. Craig proposed an algorithm to directly select this LSSR from >>>>> the found rings. This doesn't work for all cases though >>>>> >>>>> Most of these extensions (e.g. ESSR, RDKit, ...) to the SSSR start >>>>> from the SSSR itself. I know how to compute this LSSR from the SSSR >>>>> but is it possible to compute this LSSR without the SSSR? >>>> >>>> we do it from the SSSR, since that's also useful information to have. >>> >>> Yes, since the number of rings in the SSSR is known, you can exit >>> quickly and you could also avoid searching for larger rings etc. >>> >>>> I suspect, though I haven't done more than sketch something on a piece >>>> of paper just now, that it's possible to find the LSSR using a BFS >>>> where, unlike usual BFS algorithms, you keep track of the predecessor >>>> at each node. >>>> >>>> Maybe I'll play around with this a bit tomorrow. >>> >>> At first I thought it was possible but I have tried various "settings" >>> and there always remain problematic cases. You don't have to try >>> anything if you don't have time. I was just wondering if this was a >>> conscious choice in RDKit. >>> >>> Do you have any references for the implementation in RDKit? I'm >>> currently using these papers: >>> >>> Berger et.al., Counterexamples in Chemical Ring Perception, 2008 >>> http://en.scientificcommons.org/43518654 (pdf: >>> http://www.bioinf.uni-leipzig.de/Publications/PREPRINTS/03-012.pdf) >>> >>> Vismara, Union of all the minimum cycle bases of a graph, 1996 >>> http://www.emis.de/journals/EJC/Volume_4/PostScriptfiles/v4i1r9.ps >>> (GPLv2+ source code: http://www.tbi.univie.ac.at/~pmg/cycdeco/ ) >>> >>> The first gives a good overview and references the second paper as the >>> simplest canonical ring set. Still have to go through the details to >>> see how this might compare to what is done in RDKit. >> >> There is now a working version (at least for all structures I've >> tested) in svn trunk. It is based on lemma 1 from the Vismara paper. >> There is also a proof so I'm hopeful :-) >> >> The rings we now have in the LSSR are known as the relevant cycles. >> The Berger paper also uses this terminology (relevant cycles of graph >> G = R(G) ) and lists this ring set as one of the 3 best (canonical, >> ...) candidates. R(G) can be used for general graphs (<-> planar >> graphs). >> >> Another candidate is the Extended SSR (ESSR) but this only works for >> planar graphs. The final candidate are the beta-rings but I can't say >> much about it. > > 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... > - Noel > ------------------------------------------------------------------------------ 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
