You should install jupyter (and all other packages you need) in the same
environment as rdkit. Also, you need to activate the environment in order
to use it. Try running the following commands (assuming that you've already
created my-rdkit-env):

$ source activate my-rdkit-env
$ conda install jupyter notebook matplotlib    # rdkit.Chem.Draw needs
matplotlib
$ jupyter notebook --ip foo_ip --port foo_port


2017-10-29 19:24 GMT+01:00 Germano Massullo <germano.massu...@gmail.com>:

> Hi there, I am having a problem with rdkit in Anaconda3/Jupyter
> environment. This is the complete procedure I followed to install the
> packages on a Fedora 26 installation.
>
> I downloaded Anaconda3-5.0.1-Linux-x86_64.sh
> so I runned
> # sh Anaconda3-5.0.1-Linux-x86_64.sh
> I installed it into /opt/anaconda3
> # chmod -R 777 /opt/anaconda3
> then as user
> $ conda create -c rdkit -n my-rdkit-env rdkit
> $ jupyter-notebook --ip foo_ip --port foo_port
>
> then in the notebook
>
> =========
> import rdkit
> from rdkit import Chem
> from rdkit.Chem import Draw
> from rdkit.Chem.Draw import SimilarityMaps
> =========
>
> and I get the error
>
> =========
> ModuleNotFoundError                       Traceback (most recent call last)
> <ipython-input-2-4537b9d3a7ad> in <module>()
> ----> 1 from rdkit import Chem
>       2 from rdkit.Chem import Draw
>       3 from rdkit.Chem.Draw import SimilarityMaps
>
> ModuleNotFoundError: No module named 'rdkit'
> =========
>
>
> $ conda info:
>
> Current conda install:
>
>               platform : linux-64
>          conda version : 4.3.30
>       conda is private : False
>      conda-env version : 4.3.30
>    conda-build version : 3.0.27
>         python version : 3.6.3.final.0
>       requests version : 2.18.4
>       root environment : /opt/anaconda3  (writable)
>    default environment : /opt/anaconda3
>       envs directories : /opt/anaconda3/envs
>                          /home/user/.conda/envs
>          package cache : /opt/anaconda3/pkgs
>                          /home/user/.conda/pkgs
>           channel URLs : https://repo.continuum.io/pkgs/main/linux-64
>                          https://repo.continuum.io/pkgs/main/noarch
>                          https://repo.continuum.io/pkgs/free/linux-64
>                          https://repo.continuum.io/pkgs/free/noarch
>                          https://repo.continuum.io/pkgs/r/linux-64
>                          https://repo.continuum.io/pkgs/r/noarch
>                          https://repo.continuum.io/pkgs/pro/linux-64
>                          https://repo.continuum.io/pkgs/pro/noarch
>            config file : None
>             netrc file : None
>           offline mode : False
>             user-agent : conda/4.3.30 requests/2.18.4 CPython/3.6.3
> Linux/4.13.5-200.fc26.x86_64 Fedora/26 glibc/2.25
>                UID:GID : 1001:1001
>
> $ conda list —show-channel-urls:
>
> # packages in environment at /opt/anaconda3:
> #
>
>
>
> What can I do?
> Thank you very much
>
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