Re: [Open Babel] obgrep error

[remy d1 <re...@gm...>]

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
>
>