Hi Paul,
very interesting, thanks a lot for sharing!
Looking forward to the presentation at the UGM!
Kind regards,
Axel
On 27.09.2016 06:13, Paul Czodrowski wrote:
Dear RDKitters,
Our target prediction method – fully based on RDKit – has become online:
OCEAN: *O*ptimized *C*ross r*EA*ctivit
Dear RDKitters,
Our target prediction method - fully based on RDKit - has become online:
OCEAN: Optimized Cross rEActivity estimatioN
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00067
The source code can be found here:
https://github.com/rdkit/OCEAN
We will give a talk as well an hands-on wor
2D drawing code is tough. The 90/10 rule applies: the last 10% of
correctness takes 90% of the effort.
I like Dmitri Agrafiotis's method, but IIRC it's patented; also, though
it's good for rough work, it doesn't produce "beautiful" structural
diagrams.
Some of the 2D drawing methods that do produ
On 09/26/2016 04:42 PM, Peter S. Shenkin wrote:
> Also, the C attached to H44 has an extra H (its own or someone else's?)
> superimposed upon it.
I wonder if 2D drawing code should really work the same way as the 3D
conformer generation: generate a bunch of candidate layouts and pick the
one(s) wi
Also, the C attached to H44 has an extra H (its own or someone else's?)
superimposed upon it.
-P.
On Mon, Sep 26, 2016 at 5:38 PM, Dimitri Maziuk
wrote:
>
> On the plus side, when drawing PubChem CID 5057 from a 3D SDF before and
> after our canonicalization, RDKit draws a mirror image, but oth
On the plus side, when drawing PubChem CID 5057 from a 3D SDF before and
after our canonicalization, RDKit draws a mirror image, but otherwise
the same 2D structure. OB's "after" version is attached: enjoy the
7-bond carbon in the ring.
;)
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-
Hi Gonzalo,
after you activated my-rdkit-env, try to install rdkit by
conda install -c https://conda.anaconda.org/rdkit rdkit
Alternatively, if you go a step back, you can also start with
conda create -c https://conda.anaconda.org/rdkit -n
give-your-environment-whatever-name-you-want rdkit
Hi Gonzalo,
You need to activate your environment:
activate my-rdkit-env
See:
http://conda.pydata.org/docs/using/envs.html#change-environments-activate-deactivate
Best,
Marta
2016-09-26 13:45 GMT+02:00 Gonzalo Colmenarejo :
> rdkit is not shown within the package list. However, if I run conda c
Thanks a lot, Marta. Still, after activating the environment, I get in
jupyter the "ImportError: No module named rdkit".
This is confusing...
On Mon, Sep 26, 2016 at 1:56 PM, Marta Stępniewska-Dziubińska <
mart...@ibb.waw.pl> wrote:
> Hi Gonzalo,
> You need to activate your environment:
> activ
rdkit is not shown within the package list. However, if I run conda create
-c https://conda.anaconda.org/rdkit -n my-rdkit-env rdkit I get this
message:
Error: prefix already exists: C:\Users\Dell\Anaconda\envs\my-rdkit-env
Any idea on how this could be fixed?
Thanks
On Fri, Sep 23, 2016 at 9:0
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