On Tue, Jun 22, 2010 at 10:06 AM, 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.
Our approach is similar to RDKit. When I have time, I'll check how Greg handles this. > ------------------------------------------------------------------------------ > 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
