> I am doing substructure search with Pybel, but the results were somehow > different from what I expected.
You're searching with SMARTS on a quasi-aromatic fragment. The SMILES you used indicates explicit double bonds. That may not match if aromaticity is detected in the ring system. I don't have time for a quick check, but I'd guess that part of the fused ring is detected as aromatic and the third Si-ring is not. My suggestion would be something like this: [#14r5]@[#6r5]@[#6r5]@[#6r5]@[#6r5] # silicon in a 5-membered ring with 5 carbons http://www.daylight.com/dayhtml_tutorials/languages/smarts/ Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
