The Setup Module

The openfe.setup submodule is designed to contain all the tools you will require to create a free energy calculation.

Network planning

Network planning refers to the process of creating routes between the ligands that you wish to calculate free energy values for. This results in a graph, where nodes are ligands and edges are the alchemical state we must simulate along to determine their relative energy.

Loading your data

Loading files.

Creating your Network

Simple radial network.

Saving your data.

Components of the Network creation process

The Network

LigandAtomMapper

We need a cartographer.

Scorer

How good is this?

Network Strategy.

How to use these pieces of info.

System setup

With a Network defined, we can now move onto creating an alchemical system for each edge on the Network.