Re: [Open Babel] obgrep error

[Geoffrey H. <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