This section describes common tasks involving the OpenFE Python API.

The OpenFE CLI provides a simple way to perform the most common procedures for free energy calculations, but does not provide much flexibility for fine-tuning your approach or combining OpenFE with other tools. The Python API allows that flexibility, but using it is more complex. This cookbook breaks down common steps that would be implemented in Python to help navigate that complexity.


This section is a work-in-progress.

The Basic Workflow#

The typical way to use the Python API is to load a number of molecules you want to calculate free energies of, construct a LigandNetwork connecting them in an efficient way, and then combine that with information for how each ligand should be simulated to construct an AlchemicalNetwork, which specifies the entire simulation campaign. This provides a lot of flexibility in how molecules are specified, mapped, connected, and simulated, without exposing a great deal of complexity. OpenFE recommends this workflow for most users.

List of Cookbooks#