On Tue, Oct 09, 2012 at 09:01:08AM +0200, David van der Spoel wrote: > On 2012-10-08 21:08, Reinis Danne wrote: > > On Mon, Oct 08, 2012 at 07:40:51PM +0200, David van der Spoel wrote: > >> On 2012-10-08 19:11, Reinis Danne wrote: > >>> On Mon, Oct 08, 2012 at 03:00:30PM +0200, David van der Spoel wrote: > >>>>> > >>>>> It adds TWO H for InChi output, not for SDF output, but it only produces > >>>>> two double bonds (out of three). I guess these are related? > >>> > >>> Yes, they are. It is bond order perception fail (together with > >>> kekulization). More about it below. > >>> > >> Fulvene works with this patch, both pdb and gaussian. > >> For Azulene and Tetracene pdb input work but not gaussian (double bonds > >> in the wrong place). > > > > In wrong place? I saw just respectively one or two separate Cs, > > so I think it didn't find optimal matching and ended up with one > > less double bond. Tough I still have to check if it really was > > the case. I have a new kekulization implementation (it is not > > yet really in usable state) and it finds correct double bonds > > for azulene and tetracene so I think there might be kekulization > > at fault. Tough it still doesn't explain why now PDB works while > > Gaussian output doesn't. > > I would be happy to test it, have > 1500 small molecules that I need > bondorders for. If I compare the sdf from the old and the new algorithm > I can manually check those that are different.
First I have to make it to pass OB internal tests, at the moment it works only on simple aromatic systems (C and H), but fails badly on more complicated ones. And I have to add some sanity checks since it manages to crash OB in different ways. Reinis ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
