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
On Mon, Mar 19, 2012 at 2:58 AM, Fredrik Wallner fred...@wallner.nu wrote:
No, Geoff is right. Taken from the Daylight manual at
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
All SMILES expressions are also valid SMARTS expressions, but the
semantics changes because SMILES
I think it's the other way around while SMARTS are SMILES one can treat
them as such but since SMARTS are more specific and contain information
more detailed, one cannot treat SMILES (canonical or not) as SMARTS.
Pybel/openbabel seems to agree with me as i get this error message with
SMILES but
No, Geoff is right. Taken from the Daylight manual at
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
All SMILES expressions are also valid SMARTS expressions, but the semantics
changes because SMILES describes molecules whereas SMARTS describes patterns.
The molecule
Hello everybody,
I am currently trying to generate SMARTS Patterns from an 'mol' or 'sdf'
file using pybel. So far I haven't been able to succeed.
Is it possible to convert Canonical-SMILES (which is possible) into SMARTS?
Or can I use Canonical-SMILES with the pybel.smarts() module?
I look
I am currently trying to generate SMARTS Patterns from an 'mol' or 'sdf' file
using pybel. So far I haven't been able to succeed.
Is it possible to convert Canonical-SMILES (which is possible) into SMARTS?
Or can I use Canonical-SMILES with the pybel.smarts() module?
I look forward to your
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