Dear all,
I use OpenBabel to determine chemical informations like bond orders and
formal charges. Therefore I convert a molecule in xyz-format, in which
only topology and atom positions are known, into cml-format. From
cml-format I can extract the needed informations: bond orders, formal
charges, aromaticity. This is working very well for neutral molecules,
but unfortunately not for charged heterocycles, e.g.
Pyridinium c1cc[nH+]cc1
Protonated imidazole c1c[nH+]c[nH]1
Pyrylium c1cc[o+]cc1
Phenoxide anion [O-]c1ccccc1
They all should be aromatic, but they aren't. I think the problem is
caused by the fact that aromaticity is determined before formal charges
are assigned, discussed by Geoff long time ago:
http://forums.openbabel.org/openbabel-Bugs-2888510-Formal-Charge-Assignment-before-Aromaticity-td960439.html
Unlike him I think this is still a problem. I can't switch to SDF or
SMILES, because they have already included bond informations, which I
even try to determine. Since I didn't have found a suitable solution
yet, I ask for your help. If there is no easy solution I hope a active
developer of OpenBabel can help, perhaps with the aid of a financial
recompense. It's very important for our company to fix this problem as
soon as possible.
Regards,
Bernd
--
Dr Bernd Doser
Scientific Software Developer
Avant-garde Materials Simulation
Merzhauser Strasse 177
79100 Freiburg im Breisgau, Germany
Phone: +49 761 479984-23
Homepage: http://www.avmatsim.de
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://ad.doubleclick.net/clk;258768047;13503038;j?
http://info.appdynamics.com/FreeJavaPerformanceDownload.html
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
