Hi Peter, On Wed, Jul 6, 2011 at 7:35 PM, Peter Schellenberg <peter.schellenb...@fisica.uminho.pt> wrote: > I wonder how Avogadro recognizes double bonds. The concrete problem is > as follows: I loaded gaussian log files (results from DFT geometry > opt.) of molecules with conjugated bonds into avogadro for > visualization, and some of the double bonds did not show up or were > misplaced leading to obscure depictions such as 3-valence C or 2-valence > N. The structure is fine and corresponds to the presence of double > bonds. Of course I am aware that gaussian does not 'think' in terms of > bond orders, but from the total nr. of electrons and the valences, it > should have been obvious where to place double bonds. Of course manual > redrawing is possible.....
I'm sure one of the others who know the bond perception code will chime in soon, but in the meantime, could you provide a sample geometry file that shows this behavior? Avogadro should display these bonds correctly, and having an example to reproduce the behavior will make it easier to track down the bug. I'm cc'ing this to the openbabel developers list, as the actual bond perception takes place in their library, they may know more. Thanks, Dave > Many thanks in advance Peter > > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > _______________________________________________ > Avogadro-Discuss mailing list > avogadro-disc...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
