Does 'r' just use rings present in the SSSR? Are you familiar with the shortcomings of SSSR e.g. for cubane? (see http://www.ics.uci.edu/~dock/manuals/oechem/cplusprog/node127.html for example)
I'm not sure that this answers your question, but it may be the cause of what you're seeing. - Noel On 21 March 2013 20:50, mbloodforsythe <martin.bloodforsy...@gmail.com> wrote: > I have been encountering some problems with OpenBabel SMARTS matching using > both PyBel and from within Avogadro (example file attached below). When I > search for "[r5]" OpenBabel correctly identifies all 45 atoms that are part > of of 5-membered rings, indicating that it has correctly processed the > connectivity data (visually Avogadro also shows the correct bonds). > However, when I search for "[r5]1[r5][r5][r5][r5]1" or "[r5][r5]", one of > the bonds (C62-C63) is not recognized so only 11 pentagon rings are found > out of the possible 12. > > Any thoughts on this issue? I have encountered similar issues in many > different .pdb files for fullerene molecules, so I think that this problem > is slightly more general. > > c68_1108.pdb <http://forums.openbabel.org/file/n4656088/c68_1108.pdb> > > > > -- > View this message in context: > http://forums.openbabel.org/5-membered-ring-SMARTS-matching-problem-tp4656088.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
