Carbon with 5 bonds

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Carbon with 5 bonds

Stefano Forli
Hi,
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.

Thanks,

S
--

  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
     email: [hidden email]
     http://www.scripps.edu/~forli/

------------------------------------------------------------------------------

_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel

unsaturated.py (838 bytes) Download Attachment
Loading...