RDKit

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

Available versions

rdkit C++ libraries and Python bindings are available as a module.

You can find available versions with:

[name@server ~]$ module spider rdkit

and look for more information on a specific version with:

[name@server ~]$ module spider rdkit/X.Y.Z

where X.Y.Z is the exact desired version, for instance 2024.03.5.

Python bindings

The module contains bindings for multiple Python versions. To discover which are the compatible Python versions, run:

[name@server ~]$ module spider rdkit/X.Y.Z

where X.Y.Z represents the desired version.

rdkit as a Python package dependency

When rdkit is a dependency of another package, the dependency needs to be fulfilled:

1. Deactivate any Python virtual environment.

[name@server ~]$ test $VIRTUAL_ENV && deactivate

Note: If you had a virtual environment activated, it is important to deactivate it first, then load the module, before reactivating your virtual environment.

2. Load the module.

[name@server ~]$ module load rdkit/2024.03.5 python/3.12

3. Check that it is visible by pip

[name@server ~]$ pip list | grep rdkit
rdkit            2024.3.5

[name@server ~]$ python -c 'import rdkit'

If no errors are raised, then everything is OK!

4. Create a virtual environment and install your packages.

Troubleshooting

ModuleNotFoundError: No module named 'rdkit'

If rdkit is not accessible, you may get the following error when importing it: ModuleNotFoundError: No module named 'rdkit'

Possible solutions:

• check which Python versions are compatible with your loaded RDKit module using module spider rdkit/X.Y.Z. Once a compatible Python module is loaded, check that python -c 'import rdkit' works.
• load the module before activating your virtual environment: please see the rdkit as a package dependency section above.

See also ModuleNotFoundError: No module named 'X'.