Filter outputs of Docking

This document describes how to filter the outputs of Docking based on various properties.

Here we assume that you have constructed a Complex object and successfully run Docking. Following convention, we assume that the Complex object is called sim.

Fetch Docking results

First, we get the results of Docking in a pandas DataFrame using:

df = sim.docking.get_results()

Fetch combined SDF

We can generate a single SDF file with all the poses using:

sim.docking.get_poses("poses.sdf")

Filter results

We can now filter this dataframe using any criteria we want. For example, we can only retain ligands that have a pose_score greater than 0.9 using:

df = df[df["pose_score"] > 0.9]

The filtered dataframe now only has ligands that matches the required criterion.

Filter SDF by SMILES strings

We can create a new SDF file with only these ligands using:

from deeporigin.drug_discovery import chemistry

chemistry.filter_sdf_by_smiles(
    input_sdf_file="poses.sdf",
    output_sdf_file="filtered_ligands.sdf",
    keep_only_smiles=df["SMILES"],
)

We can visualize these ligands using:

from deeporigin.drug_discovery import chemistry

chemistry.show_molecules_in_sdf_file("filtered_ligands.sdf")

A visualization similar to the following will be shown: