Use outputs of Docking for FEP

This document describes how to use the outputs of Docking as inputs to FEP tools.

Assumptions

We assume that you have

1. created a Complex object
2. run Docking
3. Generated a SDF file with docked poses

Split Docking outputs SDF file

Docking generates a single SDF file with all the ligands in it. FEP tools (ABFE and RBFE) require SDF files with individual molecules in their own SDF file. To get here, we use a utility function as follows:

from deeporigin.drug_discovery import chemistry

sdf_files = chemistry.split_sdf_file(
    input_sdf_path="filtered_ligands.sdf", 
)

sdf_files contains a list of paths to the generated SDF files.

We can use this to generate a new list of Ligands and modify the Complex

from deeporigin.drug_discovery import Ligand

sim.ligands = [Ligand(file) for file in files]

This object can be used to run ABFE or RBFE.