[Open Babel] 5-membered ring SMARTS matching problem

[mbloodforsythe <mar...@gm...>]

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>  



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