Re: [Rdkit-discuss] OCEAN: Our Target Prediction Paper (including Source Code)

2016-09-26 Thread Axel Pahl
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

[Rdkit-discuss] OCEAN: Our Target Prediction Paper (including Source Code)

2016-09-26 Thread Paul Czodrowski
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

Re: [Rdkit-discuss] drawing code take 3

2016-09-26 Thread Peter S. Shenkin
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

Re: [Rdkit-discuss] drawing code take 3

2016-09-26 Thread Dimitri Maziuk
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

Re: [Rdkit-discuss] drawing code take 3

2016-09-26 Thread Peter S. Shenkin
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

[Rdkit-discuss] drawing code take 3

2016-09-26 Thread Dimitri Maziuk
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-

Re: [Rdkit-discuss] Conda installation of RDKit on W8

2016-09-26 Thread Markus Sitzmann
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

Re: [Rdkit-discuss] Conda installation of RDKit on W8

2016-09-26 Thread Marta Stępniewska-Dziubińska
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

Re: [Rdkit-discuss] Conda installation of RDKit on W8

2016-09-26 Thread Gonzalo Colmenarejo
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

Re: [Rdkit-discuss] Conda installation of RDKit on W8

2016-09-26 Thread Gonzalo Colmenarejo
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