Unfortunately, I don't think that's quite what I need. The obabel filter
command will look at the given pdb and then output the entire pdb if it matches
the given SMARTS query, right? What I would like to do is only get the atoms
that match the SMARTS query.
For example, let's say I have a pdb with a single phospho-serine residue. What
I would like to do is get only the phosphate atoms from the pdb, and not get
the rest of the residue atoms.
Really what I am going for here is I'd like specify some groups that I find
interesting, say a phosphate group, a phenyl group, etc. And then I have a
database of protein + ligand pdbs. I'd like to loop through those pdbs and
look for my groups that I am interested in. Rather than just identify the pdbs
that have the sub-structure I am interested in (i.e. identify all pdbs with
phosphates), I want to know which atoms in the pdb constitute the interesting
sub-structure. That way I could then align all phosphate groups and look at
the residues surrounding the phophates to see if I see common modes of binding
etc. Phosphate would just be one example, you can imagine identifying many
other interesting sub-structures.
-Brett
________________________________
From: Maciek Wójcikowski <mac...@wojcikowski.pl>
To: Brett T. Hannigan <bret...@mail.med.upenn.edu>
Cc: openbabel-discuss@lists.sourceforge.net
Sent: Saturday, July 6, 2013 6:21 AM
Subject: Re: [Open Babel] SMILES, SMARTS, and PDB
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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