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pythonpython-3.xubuntu-20.04rdkit
SEBASTIAN
SEBASTIAN

Reputation: 75

Problems installing RDKit in python 3.8 Ubuntu 20.04 LTS

I have had a lot of trouble trying to install RDKit using python3 and Ubuntu 20.04 LTS Tried to install rdkit this way:

sudo apt-get install python3-rdkit

But then when I try to import it using python3 it doesn't work. It installed indeed, but it is not in the package-list. Neither I can import it after using for example:

from rdkit import Chem

The official web (https://www.rdkit.org/docs/Install.html) site does have the following installation sentence, but it didn't work:

sudo apt-get install python-rdkit librdkit1 rdkit-data

I will appreciate any help!

Upvotes: 5

Views: 4391

Answers (3)

artran
artran

Reputation: 320

When apt installs python3-rdkit it puts the packages in /usr/lib/python3/dist-packages/rdkit, which Python doesn't seem to pick up. I symlinked that folder to the site-packages folder with:

cd /usr/local/lib/python3.9/site-packages/
ln -s /usr/lib/python3/dist-packages/rdkit .

and then I could import rdkit in python.

Note: running apt show python3-rdkit shows that the package is currently for Python 3.9

Upvotes: 0

Brndn
Brndn

Reputation: 846

After you've created and activated your conda environment, run:

conda install -c conda-forge rdkit

Ref: https://anaconda.org/conda-forge/rdkit

Upvotes: 3

beginner_
beginner_

Reputation: 7622

I'm not sure rdkit is actually compatible with python 3.8 yet. For example there are no python 3.8 build on conda channel.

Upvotes: 0

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