openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] SMILES, SMARTS, and PDB
I think you need custom code. For python, you could use pybel. There are three
lines that do what you want
(http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall).
You only miss
.
-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
*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
@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
On 05/07/2013 17:54, Brett T. Hannigan wrote:
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
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
On 05/07/2013 17:54, Brett T. Hannigan wrote:
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
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