Cannot Install RDKit on Google Colab

[eereenah-fast]

• Google Colab
• Miniconda installation

Up until today I have used RDKit in Google Colab using the following Miniconda installation:

!wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
!chmod +x Miniconda3-latest-Linux-x86_64.sh
!time bash ./Miniconda3-latest-Linux-x86_64.sh -b -f -p /usr/local
!time conda install -q -y -c conda-forge rdkit

import sys
sys.path.append('/usr/local/lib/python3.7/site-packages/')

But now I keep getting the following error: ModuleNotFoundError: No module named 'rdkit'

I have tried installing RDKit with the full distribution of Anaconda as well, but no results so far. Is there any way I can fix this issue?

Thank you and apologies for the trivial question!

[bp-kelley]

I'm mildly surprised this works at all.

In any case, google collab is apparently using python 3.6.9 and miniconda is using python 3.8. I tried this out and it does seem to work:

!wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
!chmod +x Miniconda3-latest-Linux-x86_64.sh
!time bash ./Miniconda3-latest-Linux-x86_64.sh -b -f -p /usr/local
!time conda install -y python=3.6
!time conda install -q -y -c conda-forge rdkit
import sys
sys.path.append('/usr/local/lib/python3.6/site-packages/')
import rdkit
from rdkit import Chem
m = Chem.MolFromSmiles("c1ccccc1")

Note you can get the python version with

sys.version

And then just change the 3.6 above to whatever version google collab is reporting.

Obviously, this is something we can't REALLY support, but installing miniconda with the /usr/local prefix is a bit of genius I think!

[eereenah-fast]

Thanks a lot for your help!