Hello Geoff, thank you for your answer. Please see my comments which are
inline with yours comments below
2017-05-23 12:38 GMT-03:00 Geoffrey Hutchison <geoff.hutchi...@gmail.com>:
> > For now we are interested in consistency before "accuracy", which is
> another subject. As a related note, we have tested several atom typing
> programs (Knodle, I-interpret, Unicon and also Open Babel) and the
> perception of the number of aromatic atoms typically differ in 10-20 % when
> analyzing a 3600 structures in the PDBbind database.
>
This is hardly surprising. For one, if I take 10 organic chemists in a room
> and ask them to identify aromatic rings, I’ll get at least 10-20% variation.
>
> More specifically, there is not one uniform cheminformatics model for
> aromaticity - because there is no well-defined chemical definition. That’s
> omitting the hard cases, even given a specific aromatic model. I’d guess we
> get 5-10 bug reports per year on specific cases for OB aromaticity
> detection.
>
>
That was exactly the point implied in this comment. Open Babel seems as
good as any other program at detecting aromaticity.
> But your question is how do you get uniform atom types, regardless of the
> input file format. This is probably impossible. If you have data in format
> X with correct bond and formal charge assignments (e.g., SDF) and data in
> XYZ format with atoms and no bonds or formal charges, you have to assume
> that all the bond perception is perfect. I don’t have a good metric for
> OB’s implementation, but I’d guess somewhere in the ~90-95% range.
>
>
Well, as long as coordinates and atomic numbers are provided in a file, it
should be possible to always come up with the same atom typing, regardless
the format. Indeed you will have to loose information for the sake of
consistency.
> In short, please don’t throw away good data. Stick to file formats that
> retain as much information as possible.
>
I agree with you in principle, but consider the following not uncommon
scenario. We are working on docking (autodock vina) whose score depends on
atom typing. As you know the ligands come in different formats, usually
pdb, mol2 or sdf. We would expect to obtain the same docking result
regardless the input format.
-Marcos.
> -Geoff
--
Marcos Villarreal
Dpto de Química Teórica y Computacional
Facultad de Ciencias Químicas
Universidad Nacional de Cordoba
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