Carbon with 5 bonds

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Carbon with 5 bonds

Stefano Forli
I'm working with molecules containing ketones and unsaturated bonds.

When using OpenBabel with Python to add hydrogens with pH correction, the code generates
carbons with 5 bonds.
Attached there is an example with a small fragment that triggers it.

The procedure to protonate structures (unset flags, set charges, etc...) comes from
Avogadro, and I've used it a lot in the past with no major issues.

If mol.SetAutomaticFormalCharge(True) is disabled, the problem does not appear, but the pH
correction is not applied.

Is this a bug? It looks so to me.



  Stefano Forli, PhD

  Assistant Professor of ISCB
  Molecular Graphics Laboratory

  Dept. of Integrative Structural
  and Computational Biology, MB-112A
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: +1 (858)784-2055
     fax: +1 (858)784-2860
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