Hello,
You can "convert" from PDB to PDB using filter option (
http://openbabel.org/wiki/--filter_option)
obabel input.pdb -O output.pdb --filter "s='CN'"
If your database is really large, or you want to search multiple times,
then I'd suggest using FastSearch for performance reasons. For further
lecture: http://openbabel.org/wiki/FastSearch
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/7/5 Brett T. Hannigan <bret...@mail.med.upenn.edu>
> I have a database of molecules in pdb files. I'd like to go through each
> molecule and see if it has certain substructures, and if they do identify
> which atoms are part of that substructure. So it's easy enough to read the
> pdb file in, convert it to SMILES representation, and then do a SMARTS
> query to look for my substructures. However, if the SMARTS query reports
> that the substructure is present in the molecule, I'm not sure how to
> identify the atoms in the pdb file which make up the match. Any ideas?
>
> --
> ******************************************
> Brett T. Hannigan
> 8011 Ardleigh St.
> Philadelphia, PA 19118
> brett.hanni...@gmail.com
> ******************************************
>
>
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