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:

module spider rdkit

and look for more information on a specific version with:

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:

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:

Deactivate any Python virtual environment.
```
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.

Load the module.

module load rdkit/2024.03.5 python/3.12

Check that it is visible by pip

$ pip list | grep rdkit
rdkit            2024.3.5

python -c 'import rdkit'

If no errors are raised, then everything is OK!

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.