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.
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.