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
--
Hi Siavoush,
I've tried a few times with OpenBabel, but since there is no support for actual chemical
reactions, its essentially impossible to do.
At least for me, the best way to handle the problem is to use the RXN format, which can be
used to describe any chemical reactions. For that you m
Hi Siavoush,
To my understanding, in OBChemTsfm::Init (phmodel.cpp, around line 208),
there's only options to delete atoms, change the atomic number or charge,
or modify bonds.
If your combinations have very simple rules, you might be able to use a
workaround in Open Babel to get around these lim
Yes - absolutely. Can you provide a specific example? The SMILES syntax "&"
is intended for this use. I'm not sure whether that code is in good shape,
but this would be a good chance to test it out and get it working if not.
- Noel
On 30 January 2018 at 15:25, Siavoush Dastmalchi via OpenBabel-di
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 b
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
