Dear all,
This message is only relevant to people who get the mailing list in digest
format.
Someone who is subscribed to get the mailing list as a digest reported
yesterday that they were getting multiple digests per day, each with a
small number of messages. Since that's not the intent, I just
Wearing my "admin for Open Chemistry" hat for the moment.. As a community,
we've been very lucky to get a lot of good open source chemistry development
done over the last few years.
Moreover, many of these students are now exposed to RDKit, cheminformatics, and
good coding. (In other words,
Thank you Dr. Schuffenhauer. This makes sense.
--
Best,
Ganesh
On Wed, Apr 1, 2020 at 5:36 PM Schuffenhauer, Ansgar <
ansgar.schuffenha...@novartis.com> wrote:
> Hi Ganesh
>
> Chemical motives of fragments are not adding simply up. The linkage of two
> fragments creates new motives at the
IF you want to use some other python install you could try pointing your
PYTHONPATH at the directory in your conda environment where the RDKit is
installed and make sure that LD_LIBRARY_PATH is pointing to the appropriate
lib directory in that conda environment. IF that doesn't work, we likely
Any suggestions on how to get it to work? I tried to get rid of the need
for an environment in RDKit installation using conda-forge on remote
machine but I need access beyond a user. For packages with pip
installation available, *pip install --user* does the job.
Navid
On Wed, Apr 1, 2020 at
Hi Ganesh
Chemical motives of fragments are not adding simply up. The linkage of two
fragments creates new motives at the fragment linkage points not present in
either of the fragments, and the circular substructures of the once terminal
atoms are disappearing.
Depending on the type of
That isn’t the python that comes from your conda environment
On Wed, 1 Apr 2020 at 16:58, Navid Shervani-Tabar wrote:
> Here are the outputs:
>
> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]which
> python3
>
>
Here are the outputs:
(Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]which
python3
/afs/crc.nd.edu/x86_64_linux/p/pytorch/1.0.0/build-new/bin/python3
(Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]python3
-c "from rdkit import
Are you sure that you get the python from your environment when you do
"python3 main.py"?
Please try these two commands:
which python3
python3 -c "from rdkit import Chem;print(Chem.__file__)"
On Tue, Mar 31, 2020 at 11:17 PM Navid Shervani-Tabar
wrote:
> Hello RDKiters,
>
> I have been
Hi Ganesh,
To delve a bit deeper into this, if I recall correctly, SA score is calculated
based on both:
1. The prevalence of your molecule’s chemical motifs in a virtual library of
synthesizable compounds.
2. A set of logarithmic formulas that take as parameters molecular features
Hi Alan,
Thank you for pointing that out. Somehow I missed the part about the
logarithms while going through the article and your explanation makes much
more sense now.
--
Best,
Ganesh
On Wed, Apr 1, 2020 at 11:59 AM Alan Kerstjens Medina <
alankerstj...@hotmail.com> wrote:
> Hi Ganesh,
>
>
>
Hi Nils and Axel,
Thank you very much for your response.
I am trying to develop a de-novo drug design framework that uses fragments
as building blocks to assemble a molecule inside a target protein active
site.
The algorithm that I am using assembles fragments into molecules such that
the
Hi Ganesh,
I would like to challenge your premise. Why do you think that synthetic
accessibility should add up like that?
Theoretically, I would expect that the combination of A,B and C to ABC will
require some synthetic effort - so should be SA(A) + SA(B) + SA(C) <
SA(ABC).
Technically, the
Hi Ganesh,
I guess the synthesis of a fragment can be quite different from the
synthesis of a whole molecule containing that fragment, so I don't know
if it is a valid assumtion that the SA scores of the fragments have to
add up to the SA score of the whiole molecule.
Kind regards,
Axel
On
Hi Axel,
Thank you for your response.
Yes, I tried to implement the aforementioned script. It works very well on
whole molecules.
However, I am trying to implement the script on fragments. For example, if
I have fragments: A, B and C that makes up a whole molecule "ABC", then the
sum of SA
Thanks Paolo, that fixed it.
On 30/03/2020 15:05, Paolo Tosco wrote:
Hi Tim,
try rm -rf External/CoordGen/coordgen* External/CoordGen/maeparser*
you might have some outdated coordgen libs. Deleting those and
re-running cmake will download them afresh.
Cheers,
p.
On 30/03/2020 14:51, Tim
Dear all,
Yesterday was the last day for potential students to submit applications
for Google Summer of Code and we got proposals for the following five
projects:
1) RDKit integration with MongoDB. Python based
2) Implement a generalized file reader and a multi-threaded file reader.
C++ based
3)
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