Thanks for the clarification.
On 02/01/2018 12:43 AM, Noel O'Boyle wrote:
Actually, I think that this particular is most easily solved as Chris has suggested, using
regular ring closure digits. The deferred ring closures (&) are currently not accepted by
OB, and I guess aren't really needed in any case. We should get them working though. They
are a feature of SMILES that is not very well documented.
We have support for RXN, but the question is not about representing reactions but
generating molecules.
You are right, I was not clear on the matter.
The RXN file format is supported, but not the information contained in it: in other words,
you can't use a RXN file to instruct an OB class (OBChemTsfm?) to perform a chemical reaction.
With that in place, I found that it would be extremely easy to generate large virtual
libraries in this way:
- tag fragment breaking points/attachments with unusual elements, i.e., W, Re, Os, Ir,
etc. I use each element to tag different kinds of fragments, so W can be aromatic rings,
Re heterocycles, Os aliphatic chains, etc.
- sketch a RXN file with a simple reaction such as: frag1-W + frag2-Re ->
frag1-frag2
In both Indigo and RDKit, loading and performing the reaction can be done in a few lines
of Python, and for me it did the trick.
I have just written up a proposal to change how we handle reactions in Open Babel. If/when
this is in place, it would be worth revisiting support for reaction transformations. In
the meanwhile, if you are aware of any problems with OBChemTsfm, we'd appreciate if you
could file an issue.
I already discussed the issues in the mailing list a while back (2014, maybe?), but you
suggested that without atom-mapping of reactions, OBChemTsfm does not work reliably.
If it can be helpful to get an idea about the issue, my example was the
following:
import pybel
ob = pybel.ob
start = '[O:1]=[C:2]-[C:3]=[C:4]'
end = '[O:1]=[C:2]-[C:3]-[C:4]-[S:5][C:6]'
transformer = ob.OBChemTsfm()
transformer.Init(start, end)
org = 'C=CC(=O)Nc1ccccc1'
mol = pybel.readstring('can', org)
transformer.Apply(mol.OBMol)
print "Original :", org
print "Modified :", mol.write('can')
Essentially, adding atoms to a molecule with OBChemTsfm is not possible. I've tried adding
one atom at the time exploiting explicit hydrogens in the reaction, but that doesn't work
either.
I believe that mapping reactions would be possible once there would be some support for
identifying MCSS, and I tried tackling the problem, back then. Although, the effort was
beyond my time budget, so I had to give up (and use other toolkits, alas).
S
p.s. apologies for the repeated emails on the subject, but our spam filter was making a
mess and I couldn't see my own posts to the list
Regards,
- Noel
On 1 February 2018 at 00:16, Stefano Forli <fo...@scripps.edu <mailto:fo...@scripps.edu>>
wrote:
My experience with simulating reactions with OpenBabel was mostly
unsuccessful.
I've tried using OBChemTsfm to atoms, but I couldn't have it to work even
by adding
one atom at the time.
The most straightforward way to deal with a library enumeration would be to
have
support for the RXN format, which can be used to describe any arbitrary
reaction. For
that, I've found pretty easy to work with Indigo and RDKit.
On the other hand, I'm not familiar with the "&" notation Noel is referring
to.
If there's some documentation on the matter, please let me know!
Thanks,
S
On 01/30/2018 11:59 AM, Nicolas Cheron wrote:
Please allow me to do shameless self-promotion. I have developped an
open-source
program (using OpenBabel) that aims at creating de novo ligands by
directly
growing them in the active site of a target protein. You can also use
it without
the protein (I have called it FOG2) : you can define a core molecule
(so-called
seed), choose from which atom you will grow new molecules, and the
program will
create new molecules by adding fragments to the seed in a "rational"
way. If you
want more details, let me know, I can explain it.
The links: http://pubs.acs.org/doi/10.1021/acs.jmedchem.5b00886
<http://pubs.acs.org/doi/10.1021/acs.jmedchem.5b00886>,
https://sourceforge.net/projects/opengrowth/
<https://sourceforge.net/projects/opengrowth/>
Nicolas
2018-01-30 20:53 GMT+01:00 Chris Swain <sw...@mac.com
<mailto:sw...@mac.com>
<mailto:sw...@mac.com <mailto:sw...@mac.com>>>:
Hi,
It depends on the transformations you want to undertake. I did a
very quick
library
build about 20 years ago using SMILES strings. Just have dummy
atoms with unique
letters where you want to add functional groups then just do a
text find and
replace
with the desired SMILES of the building block you want to add
(which can of
course
contain dummy atoms). Then run through OpenBabel to generate
canonical SMILES. I
generated a 10 million molecule library doing this.
Cheers,
Chris
On 30 Jan 2018, at 19:45,
openbabel-discuss-requ...@lists.sourceforge.net
<mailto:openbabel-discuss-requ...@lists.sourceforge.net>
<mailto:openbabel-discuss-requ...@lists.sourceforge.net
<mailto:openbabel-discuss-requ...@lists.sourceforge.net>> wrote:
Message: 1
Date: Tue, 30 Jan 2018 15:25:38 +0000 (UTC)
From: Siavoush Dastmalchi <siavous...@yahoo.com
<mailto:siavous...@yahoo.com> <mailto:siavous...@yahoo.com
<mailto:siavous...@yahoo.com>>>
To: "openbabel-disc...@lists.sf.net
<mailto:openbabel-disc...@lists.sf.net>
<mailto:openbabel-disc...@lists.sf.net
<mailto:openbabel-disc...@lists.sf.net>>"
<openbabel-disc...@lists.sf.net
<mailto:openbabel-disc...@lists.sf.net>
<mailto:openbabel-disc...@lists.sf.net
<mailto:openbabel-disc...@lists.sf.net>>>
Subject: [Open Babel] using Open Babel for virtual library
generation
Message-ID: <1885905137.1937075.1517325938...@mail.yahoo.com
<mailto:1885905137.1937075.1517325938...@mail.yahoo.com>
<mailto:1885905137.1937075.1517325938...@mail.yahoo.com
<mailto:1885905137.1937075.1517325938...@mail.yahoo.com>>>
Content-Type: text/plain; charset="utf-8"
Dear List,
I was wondering if it is possible to use OB for virtual library
generation. For
example adding building blocks in a file to different sites of
a core
structure in a
combinatorial manner.
Many thanks in advance for you help.
Cheers,Siavoush
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Assistant Professor
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and Computational Biology, MB-112A
The Scripps Research Institute
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--
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Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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