Cookbook

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.

Note

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.

• Setup

  • • • Choose and Configure a Protocol

      • Protocol

        Simulation procedure for an alchemic mutation.
    • • Chemical component definition

        SDF, PDB, RDKit, OpenFF Molecule, solvent spec, etc.

      • • • Loading proteins, Defining solvents

          • SolventComponent and ProteinComponent

            Other chemical components needed to simulate the ligand.
        • • • • Loading small molecules

              • SmallMoleculeComponent

                The ligands that will be mutated.

            • • Orion/FEP+

                Network from another tool.

          • • • Planning a Ligand Network

            • • Ligand Networks by Hand

            • • Creating Ligand Networks Exported from Orion or FEP+

          • LigandNetwork

            A network of ligand transformations.

          • • • Visualizing Ligand Networks

  • Create an Alchemical Network

  • AlchemicalNetwork

    A complete simulation campaign.

• Dumping a Transformation to JSON

• Run

  • openfe quickrun

    OpenFE recommends using the openfe quickrun CLI command to execute a transformation.

• Gather

  • openfe gather

    OpenFE recommends using the openfe gather CLI command to collect the results of a transformation.

List of Cookbooks

• Loading Molecules and Chemical Systems
• Dumping a Transformation to JSON
• Using jq to inspect OpenFE JSONs
• Choose and Configure a Protocol
• Planning a Ligand Network
• Relative Free Energy Alchemical Network Planners
• Creating Ligand Networks Exported from Orion or FEP+
• Ligand Networks by Hand
• Visualizing Ligand Networks
• Create an Alchemical Network
• Assigning partial charges to an OpenFF Molecule
• BespokeFit: Using bespoke force field parameters with OpenFE protocols
• Recap