Runtime error "No module named rdkit" when Launching on Colab

[sneumann]

Describe the bug

When launching the Notebook on Colab, I get

ModuleNotFoundError                       Traceback (most recent call last)

[/tmp/ipython-input-3916824123.py](https://localhost:8080/#) in <cell line: 0>()
----> 1 from rdkit import Chem
      2 from rdkit.Chem import Draw

ModuleNotFoundError: No module named 'rdkit'

To Reproduce

Steps to reproduce the behaviour

1. Click on 'https://colab.research.google.com/github/IUPAC/WFChemCookbook/blob/main/book/manipulations/computing_inchis.ipynb'

Expected behaviour

The Colab should execute the Notebook

Yours,
Steffen

[stuchalk]

@sneumann I have been working on this and have no useful solution. I am going to try this notebook in the new version of Jupyter book that is touted as much better. I will let you know what I find. (this may also fix the other issue you reported)

[DunklesArchipel]

I don't think that it is possible to run the notebook with all dependencies evoked upon opening the notebook in colab. There is a set of modules, which ship with Colab. Any other dependencies must be installed manually.

The straight forward fix is to add a cell at the top of the notebook in colab and run shell commands with a preceeding !

!pip install rdkit

or evoke the installation using the jupyter magic command via %

%pip install rdkit

[stuchalk]

Yes, I have been trying to the the Jupyter magic to work. Let me try again now considering the timely comment. Thanks @DunklesArchipel

[nap84]

Adding !pip install rdkit worked for me as well.

A similar problem occurs on Colab further down in the notebook when importing open babel. Adding a cell that uses apt-get to install it seems to be the easiest solution:

!apt-get update -qq
!apt-get install -y openbabel
!pip install openbabel-wheel

(I saw another notebook where conda was used, however, this crashed the kernel when I gave it a shot.)

[stuchalk]

I have tried the suggestions above and neither work. I have no more time to work on this. I am thinking that the CookBook needs to be migrated to Jupyter Book v2 which is built using Node and nominally supports running code in the book not necessarily on Colab or Binder. This is a major lift so for now I have assigned 'no fix' as if I am going to work on this more I need time/funding to do it.