Alchemical Networks: Creation

In the previous section we detail the theory of AlchemicalNetwork objects and what they contain. Here we explain how you can go about creating a AlchemicalNetwork by combining its various components.

Python API

You can manually create a AlchemicalNetwork by creating a list of Transformation objects. The cookbook on creating alchemical networks demonstrates how to do this.

Alchemical Network Planners

OpenFE provides convenience classes for creating AlchemicalNetwork. These currently include;

• RBFEAlchemicalNetworkPlanner: creating relative binding free energy networks using the RelativeHybridTopologyProtocol

• RHFEAlchemicalNetworkPlanner: creating relative hydration free energy networks using the RelativeHybridTopologyProtocol

The Relative Alchemical Network Planners cookbook demonstrates how to use these.

Note

The Network Planners are provided for user convenience. Whilst they cover majority of use cases, they may not currently offer the complete range of options available through the Python API.

Command-line interface

The Alchemical Network Planners can be used directly through the command line interface.

For example, you can create a relative binding free energy (RBFE) network using:

$ openfe plan-rbfe-network -p protein.pdb -M dir_with_sdfs/

Similarly you can create a relative hydration free energy (RHFE) network using:

$ openfe plan-rhfe network -M dir_with_sdfs/

Please see the RBFE CLI tutorial for an example on how to use the CLI to run an RBFE campaign.