El vie, 01-07-2011 a las 10:08 +0200, Pascal Muller escribió:
> Dear Miguel,
>
>
> Hello. I posted the attached long message a couple of weeks
> ago and I
> have had no reply at all, not even a comment. Fully
> uninteresting
> subject?
>
>
> Of course not - the COD is of great interest, I think. But I never
> worked with metal-containing molecules, and don't have programming
> skills too, so I have a few other questions:
> Have you the same problem if you try to convert cif in pdb, sdf or
> mol2?
Hello. Thanks a lot for your reply. I have tested the Cu-pyridine file
with different output formats. I have seen that the output in sdf, mol2
and cml is also wrong. The result is the same for the three: aromaticity
in pyridine ring is lost, the N atom appears forming three single bonds
(metal and neighbouring carbons) and the opposite (para) C atom appears
forming three single bonds (its H and their neighbours), hence as a
spurious radical. Again, babel wants to keep valence three for N at all
costs.
PDB format is not a good test, since it does not contain bond order
information (if I have correctly understood the PDB specification for
the CONECT clause, please correct me if I am wrong!!). I have made the
test anyway and the output connectivity seems to be OK. But if I
transform this to SMILES (or to any other format containing bond order
information) the wrong output appears again. I think it is not a problem
of one format or the other, is a problem of openbabel internal way of
determining bond orders.
> Did you try other software?
No, I have not. But I doubt there is a better free choice than openbabel
for getting SMILES from CIF. But if anyone knows about another good
choice, I can test it ...
> What about cif2pdb?
As told above, PDB created by openbabel is correct but PDB does not
contain bond order information. The problem will appear again in the PDB
-> SMILES transformation. No point in testing another software that just
creates PDB.
> Is the output (e.g. smi or sdf) correct if you try to save the
> metal-containing molecule with e.g. msketch of Chemaxon?
I do not have this software installed but I understood that it is just
for making drawings of the output, isn't it? Well, I am fully sure that
the SMILES (or the SDF) is wrong just inspecting the SMILES string or
the file. If I represent the SMILES using the daylight depict web tool,
I see the same wrong thing that the SMILES represents.
As a general comment, I think that all chemical formats and most
chemical programs (free and not-free) are developed with the mind of an
organic chemist. There is a need for inorganic chemists being involved
in the cheminformatic world. In inorganic chemistry, the valence of
nitrogen is in many cases _4_ , not 3.
Thanks again. Best wishes,
Miguel Quirós
--
Miguel Quirós Olozábal
Departamento de Química Inorgánica. Facultad de Ciencias.
Universidad de Granada. 18071 Granada. SPAIN.
email: mquiros<at>ugr<dot>es
mquiros<arroba>ugr<punto>es
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