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
