Thanks Noel.
It's good news to know that at least the problem is on the radars.
If it can help, I will be happy to provide examples and practical applications.
On the other hand, about the MCS, I looked back at the old thread in the mailing list and
I fund that there was already a C++ implementation from Igor Filippov:
http://forums.openbabel.org/Maximum-common-substructure-MCS-with-OpenBabel-td4657949.html
which happens to be also in the contributed section of the OB code:
https://github.com/openbabel/contributed/tree/master/c%2B%2B/mcs-cliquer
If a significant part of that can be reused and adapted to get into the main code, it
could simplify the implementation of SMIRKS transformations, too.
S
On 02/03/2018 01:40 PM, Noel O'Boyle wrote:
Ok - I understand now, and your comments are definitely taken on board. It's certainly
true that OBChemTsfm is missing many features of a SMIRKS transformer, and it would be
great to have more in there. I don't really know how difficult that would be; I'll add it
to my list, but I'd definitely encourage anyone who's interested to see whether they could
improve on it. We're putting out calls for Google Summer of Code at the moment; maybe this
is a possible project for a student.
On 1 February 2018 at 18:27, Stefano Forli <fo...@scripps.edu <mailto:fo...@scripps.edu>>
wrote:
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> <mailto: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>
<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/>
<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>>
<mailto: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>>
<mailto: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>>
<mailto: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>>
<mailto: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>>
<mailto: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>>
<mailto: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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Stefano Forli, PhD
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
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Stefano Forli, PhD
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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 <mailto:fo...@scripps.edu>
http://www.scripps.edu/~forli/
--
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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
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