Thanks Markus, but I'm still confused. After following your steps, I activate the my-rdkit-env conda environment from the Anaconda command prompt, then launch jupyter notebook from there, and then I see three conda environments there, and one of those is my-rdkit-env. However, when I go to files/new/notebook I only see Python [root] and Python [py27] as environments and if I create a notebook and run my rdkit code I get the ImportError: No module named rdkit.
Any help on how to set the conda environment in jupyter to be able to run rdkit stuff? Sorry, I'm not very familiar with conda. I really appreciate all the help received so far. Thanks in advance Gonzalo On Mon, Sep 26, 2016 at 10:27 PM, Markus Sitzmann <[email protected] > wrote: > 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 > > and then activate "give-your-enviroment-whatever-name-you-want" > > Your error message above just says that you are trying to create a > environment with the same name again > > Markus > > On Mon, Sep 26, 2016 at 2:11 PM, Gonzalo Colmenarejo < > [email protected]> wrote: > >> 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 < >> [email protected]> wrote: >> >>> Hi Gonzalo, >>> You need to activate your environment: >>> activate my-rdkit-env >>> >>> See: http://conda.pydata.org/docs/using/envs.html#change-environm >>> ents-activate-deactivate >>> >>> Best, >>> Marta >>> >>> >>> 2016-09-26 13:45 GMT+02:00 Gonzalo Colmenarejo < >>> [email protected]>: >>> > 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 9:06 PM, Greg Landrum <[email protected]> >>> > wrote: >>> >> >>> >> I think anaconda is fine, but it looks like either the RDKit isn't >>> >> installed correctly or you aren't running the anaconda Python. >>> >> >>> >> Please check that the python you are running is the one from anaconda >>> and >>> >> that the RDKit is installed (that last one is "conda list") >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> On Fri, Sep 23, 2016 at 8:31 PM +0200, "Gonzalo Colmenarejo" >>> >> <[email protected]> wrote: >>> >> >>> >>> Hi Greg, >>> >>> >>> >>> It shows: >>> >>> >>> >>> ImportError: No module named rdkit >>> >>> >>> >>> Should I reinstall anaconda? >>> >>> >>> >>> Thanks >>> >>> >>> >>> Gonzalo >>> >>> >>> >>> On Fri, Sep 23, 2016 at 2:54 PM, Greg Landrum < >>> [email protected]> >>> >>> wrote: >>> >>>> >>> >>>> Hi Gonzalo, >>> >>>> >>> >>>> Are you sure that the jupyter you are running is the same one that >>> came >>> >>>> with your conda installation? >>> >>>> Can you do, from the command line: >>> >>>> python -c "from rdkit import Chem" >>> >>>> >>> >>>> On Fri, Sep 23, 2016 at 10:49 AM, Gonzalo Colmenarejo >>> >>>> <[email protected]> wrote: >>> >>>>> >>> >>>>> Hi, >>> >>>>> I had a previous release of RDKit (2015_03_1) in my Windows 8 PC >>> >>>>> installed in the old fashioned mode and it worked OK. I renamed the >>> >>>>> corresponding folder and installed the latest version of RDKit >>> through >>> >>>>> conda. Now I get the following error message when trying to run my >>> previous >>> >>>>> code in Jupyter: ImportError: No module named rdkit >>> >>>>> >>> >>>>> Any advice on how to fix this would be appreciated. >>> >>>>> >>> >>>>> Thanks a lot >>> >>>>> >>> >>>>> Gonzalo >>> >>>>> >>> >>>>> >>> >>>>> ------------------------------------------------------------ >>> ------------------ >>> >>>>> >>> >>>>> _______________________________________________ >>> >>>>> Rdkit-discuss mailing list >>> >>>>> [email protected] >>> >>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >>>>> >>> >>>> >>> >>> >>> > >>> > >>> > ------------------------------------------------------------ >>> ------------------ >>> > >>> > _______________________________________________ >>> > Rdkit-discuss mailing list >>> > [email protected] >>> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> > >>> >> >> >> ------------------------------------------------------------ >> ------------------ >> >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >
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