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 thatpython -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'.