Hi Marcos,
There is no straightforward way to do it OpenBabel, I've recentrly
developed such fingerprint (Protein-Ligand Extended Connectivity FP) and
presented it on RDKit UGM
https://github.com/rdkit/UGM_2017/blob/master/Posters/Wojcikowski-PLEC_fingerprint.pdf
PLEC Basically is what you've suggested - a collection of hashed contacts
in the complex. There is an OpenBabel and RDKit's implementation of PLEC in
ODDT, see
https://oddt.readthedocs.io/en/latest/rst/oddt.html#oddt.fingerprints.PLEC
and here https://github.com/oddt/oddt/blob/master/oddt/fingerprints.py#L616
If you wish to experiment with the function that you've asked for there it
is (_ECFP_atom_hash):
https://github.com/oddt/oddt/blob/master/oddt/fingerprints.py#L358
There is Noel's blog with ECFP that you can play with (
https://baoilleach.blogspot.com/2008/07/calculate-circular-fingerprints-with.html)
although OBMolAtomBFSIter is buggy and does not work correctly with
disconnected molecular parts, which will happen with proteins (
https://github.com/openbabel/openbabel/issues/1639).
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-10-16 15:27 GMT+02:00 Marcos Vinicius Da Silva Santana <
marcossant...@id.uff.br>:
> Is it possible to calculate circular fingerprints around a predefined
> atom/atom-pair?
>
> For example, I'm using a PDB file containing a ligand (LIG) showing a
> nitrogen atom (e.g. N) that interacts with an oxygen atom of a serine
> residue (let's call it OG).
> What I want is to generate a circular fingerprint around this atom pair
> (N-OG), while ignoring other ligand atoms. This would be similar to
> protein-ligand interaction fingerprints.
> Is it possible with OpenBabel?
>
> Best wishes,
>
> Marcos Vinicius Santana
> M.Sc
> Farmacêutico
> Universidade Federal Fluminense
> Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular
> (LABiEMol)
> Niterói, RJ - Brazil
>
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