Dear OpenBabel developers,
I have prepared one more patch (attached) against the latest SVN
OpenBabel. With this patch the mighty OpenBabel can correctly assign
MMFF94 types of ALL of the 761 structures of the CCL.NET MMFF validation
suite starting from the original .mol2 file! Before this patch I had to
use a MOL/SDF file translated from the MOL2 file with some manual fixes.
I will briefly comment those patches in the following:
- there was a bug preventing elements such as Ca and Cu written in
uppercase to be correctly recognized (ttab.SetToType missing)
- added a couple of lines to allow later correct MMFF94 typing of
Cu(I)/Cu(II) and Fe(II)/Fe(III)
- added a few lines of code to allow correct typing of Cu(I)/Cu(II) and
- partial charges must be preserved for the previous patches to work;
without looking at the original partial charges read from the mol2 file
or the formal charges read from the mol/sdf file it would be impossible
to distinguish between different oxidation states of Cu/Fe, and in fact
the original code did not attempt to do that. In the absence of charges
(e.g. because a pdb was imported), Cu(II) and Fe(III) are assigned by
Thanks once again for all your work and collaboration.
Paolo Tosco, Ph.D. Phone: +39 011 6707680
Dipartimento di Scienza Fax: +39 011 6707687
e Tecnologia del Farmaco Mob: +39 348 5537206
Via Pietro Giuria, 9 E-mail: paolo.tosco@...