Thanks Geoffrey,
So the bit I'm confused about and forgive me cause I'm not a chemist, is
given that it uses the capital N in N^2 rather than lowercase or the
generic form this means it's explicitly aliphatic, but pyrrole is aromatic,
surely it shouldn't match even if it is sp2?
Eva
On 23 January 2015 at 18:19, Geoffrey Hutchison <geoff.hutchi...@gmail.com>
wrote:
> > I'm having some difficulty understanding how Pyrrole matches with the
> SMARTS string N^2 given that it's aromatic.
>
> The ^ pattern is an extension to SMARTS. It indicates matching a
> particular hybridization (i.e., sp2 here). Certainly pyrrole has an sp2
> nitrogen.
>
> What happens is that hybridization must be assigned, so a whole new set of
> SMARTS are run to assign hybridizations. There have been some efforts to
> write implicit valence rules without SMARTS.
>
> -Geoff
------------------------------------------------------------------------------
New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
