Skip to content

Create a Complex

This document describes how to create a Complex object, that can be used to run Docking, ABFE and RBFE.

From a directory

from deeporigin.drug_discovery import Complex

# here, we're using the example data directory
sim = Complex.from_dir(EXAMPLE_DATA_DIR)

The directory should contain:

  • exactly one PDB file for the protein
  • one or more SDF files for the ligands. Each SDF file can contain one or more molecules.

From Protein and Ligand objects

A Complex object can be also be constructed using Protein and Ligand objects. 

from deeporigin.drug_discovery import Complex

sim = Complex(protein=protein, ligands=ligands)

Modifying a Complex

You can modify a Complex object by adding or replacing ligands. The Complex's hash will automatically update when ligands are modified.

# Create a complex with just the protein
complex = Complex(protein=protein, ligands=[])

# Add a single ligand
new_ligand = Ligand.from_sdf("ligand.sdf")
complex.ligands = complex.ligands + [new_ligand]

# Add multiple ligands
more_ligands = Ligand.from_sdf("multiple_ligands.sdf")  # Returns a list if file contains multiple molecules
complex.ligands = complex.ligands + more_ligands

# Replace all ligands
complex.ligands = [new_ligand]  # Replace with a single ligand
Constructing Ligands

To see how to construct Ligands, see this

Constructing the Protein

To see how to construct the Protein, see this