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 nitrogen),
while all formal charges are set to zero. On the contrary, correct atom
typing is observed for pyridine.
Paolo Tosco, Ph.D. Phone: +39 011 6707680
Dipartimento di Scienza Fax: +39 011 6707687
e Tecnologia del Farmaco Mob: +39 348 5537206
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Italy http://www.open3dqsar.org ================================================================
> 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 starting from a SMILES string?