Installing rdkit

Just for the record, I am working on a cloud GPU instance and want to install rdkit for molecular compuatations.

But this isn’t so easy as one can see here: Installation — The RDKit 2023.03.1 documentation

I can’t install it via

pip install rdkit

and there’s no conda available (which I could install afaik know), but even the Ubuntu packages are not available on my instance server:

$ sudo apt-get install python-rdkit librdkit1 rdkit-data

Any ideas?

It’s not too hard to build RDKit from source pulled from github, and then add it to a venv. The RDKit build instructions are pretty decent, and only requires specifying the “alternate” build/install locations e.g. cmake -D PYTHON_LIBRARY=/usr/lib/python3.6/config/libpython3.6.a -D PYTHON_INCLUDE_DIR=/usr/include/python3.6/ -D PYTHON_EXECUTABLE=/usr/bin/python3 ..

I had to go through a couple iterations, but in the end I had it working in an otherwise pip-controlled environment without headache.

Thank you, I’ll try that next time.

Why don’t you just install conda/miniconda in your lambda workstation and then rdkit in a conda environment?

I needed a quick solution back then and outsourced all rdkit parts to my laptop. This was possible as there were only pre- and post processing steps using rdkit.

Thanks for the suggestion though.