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,
https://sourceforge.net/projects/opengrowth/
Nicolas
2018-01-30 20:53 GMT+01:00 Chris Swain <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> wrote:
Message: 1
Date: Tue, 30 Jan 2018 15:25:38 +0000 (UTC)
From: Siavoush Dastmalchi <siavous...@yahoo.com
<mailto:siavous...@yahoo.com>>
To: "openbabel-disc...@lists.sf.net <mailto:openbabel-disc...@lists.sf.net>"
<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>>
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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