On Tue, Jun 22, 2010 at 12:05 PM, Noel O'Boyle <baoille...@gmail.com> wrote: > On 22 June 2010 09:06, Noel O'Boyle <baoille...@gmail.com> wrote: >> On 22 June 2010 03:31, Craig A. James <cja...@emolecules.com> wrote: >>> On 6/21/10 6:32 PM, Tim Vandermeersch wrote: >>>> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison >>>> <ge...@geoffhutchison.net> wrote: >>>>>> The changes are in svn trunk. The current test set (aromatics.smi, >>>>>> attype.00.smi& nci.smi) is not good though. >>>>> >>>>> By that, I assume you mean that the current test set is not sufficient >>>>> for SSSR vs. LSSR? I can probably generate a *MUCH* larger test set if >>>>> that's what you need. >>>> >>>> There are not enough cases where the SSSR is not canonical. I already >>>> added some (tetrahedron, cube, octahedron, fullerene 20& 60). While >>>> the SSSR doesn't fail the canonical test for bridged rings, having 3 >>>> rings in the LSSR (2 in SSSR) gives more intuitive results for >>>> substructure search. >>> >>> An interesting way to test various things is with the SMILES >>> "anti-canonical" option, -xC. It's amazing how many algorithms can have >>> hidden atom-order dependencies. Unfortunately, it's hard to make test >>> cases using -xC directly because the results are deliberately quasi-random. >>> >>> Craig >> >> Just a quick note, RDKit and OEChem both have something to say on the >> subject of SSSR. See for example links and discussion at >> http://ctr.wikia.com/wiki/Ring_counts_in_a_SMILES_file. > > Just to point out the four additional test failures due to recent SSSR > checkins: http://my.cdash.org/index.php?project=Open%20Babel&date=2010-06-21
It seems the SSSR -> LSSR change in kekulize.cpp is the problem. I changed it back until this is fixed. It might be that some result files need updating though. > - 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
