> You are right, using a correct SMILES string type assignment is perfect. Are
> you aware of a 3D-coordinate format from which OpenBabel could be able to
> extract formal charge information in order to assign types properly while
> retaining 3D coordinates rather than rebuilding them as startin
> downloaded through SVN (20 July 2010), fails to assign correct atom
> types to pyridinium ion; namely, aromaticity is not perceived, and all
In what form are you importing the molecule? SMILES? PDB? If there is no
assigned formal charge to the pyridinium nitrogen, then there is no guaranteed
Dear OpenBabel developers,
I noticed that obenergy, as of the current development version
downloaded through SVN (20 July 2010), fails to assign correct atom
types to pyridinium ion; namely, aromaticity is not perceived, and all
atoms are assigned aliphatic atom types (2 for carbon, 8 for nitro
