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From: remy d1 <re...@gm...> - 2011-04-22 08:02:53
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Hello Thank you very much, Geoffrey. Your message is very helpfull. Regards, Remy. 2011/4/21 Geoffrey Hutchison <ge...@ge...> > > On Apr 21, 2011, at 10:00 AM, remy d1 wrote: > > > obgrep -c 'Cc1nnc(C)[nH]1' sdf-1-3500-match-triazole-result1.sdf > > 0 > > The main problem is the use of the explicit 'H' in the pattern. In your > structure, the "lone" nitrogen (i.e., not the nn motif) has a carbon bond. A > SMARTS pattern with an "H" requests that there be an explicit hydrogen on > that atom. Of course there isn't one. > > obgrep -c 'Cc1nnc(C)n1' triazole.sdf > 1 > > > Moreover, on debian linux, I have seen that openbabel 2.2.3 includes > libopenbabel.so.3 but obgrep needs libopenbabel.so.4 > > obgrep should be included in your Open Babel package. But in any case, > libopenbabel.so.4 corresponds to v2.3.0, which you must have installed from > another source. So you should have libopenbabel.so.4 if you have an obgrep > which links to it. > > (In any case, we strongly recommend the most recent release -- it has many > fixes over 2.2.x, including both stereochemistry and aromaticity > improvements.) > > Hope that helps, > -Geoff > > |