Could it be that you have forgotten to "conda install jupyter" in the
environment where the RDKit is installed?
On Fri, Sep 30, 2016 at 9:32 AM, Gonzalo Colmenarejo <
[email protected]> wrote:
> 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
>>>> >>>>>
>>>> >>>>
>>>> >>>
>>>> >
>>>> >
>>>> > ------------------------------------------------------------
>>>> ------------------
>>>> >
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>>>> >
>>>>
>>>
>>>
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>>>
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>>
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