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Work with a Complex

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

Creating a Complex

From a directory

# here, we're using the example data directory
from deeporigin.drug_discovery import Complex, EXAMPLE_DATA_DIR

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, EXAMPLE_DATA_DIR, Protein, Ligand

protein = Protein.from_file(EXAMPLE_DATA_DIR / "brd.pdb")
ligand = Ligand.from_sdf(EXAMPLE_DATA_DIR / "brd-2.sdf")

sim = Complex(protein=protein, ligands=[ligand])

Modifying a Complex

You can modify a Complex object by adding or replacing ligands. 

from deeporigin.drug_discovery import Complex, Protein, Ligand
protein = Protein.from_file(EXAMPLE_DATA_DIR / "brd.pdb")
ligand = Ligand.from_sdf(EXAMPLE_DATA_DIR / "brd-2.sdf")

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

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

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

# Replace all ligands
sim.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

Preparing a complex

To prepare a protein-ligand complex for simulation or further analysis, use the Complex.prepare() method. This method runs system preparation on a given ligand in the context of the complex's protein, handling tasks such as protonation, water retention, and box padding.

Usage

sim.prepare(ligand)

Typically, you would call this method using a ligand in the complex:

sim.prepare(sim.ligands[0])

Arguments

  • ligand (Ligand): The ligand to prepare. This should be an instance of the Ligand class associated with your complex.
  • padding (float, optional): Padding (in angstroms) to add around the system. Default is 1.0.
  • keep_waters (bool, optional): Whether to keep water molecules in the prepared system. Default is False.
  • is_lig_protonated (bool, optional): Whether the ligand is already protonated. Default is True.
  • is_protein_protonated (bool, optional): Whether the protein is already protonated. Default is True.

You can override any of these defaults as needed:

sim.prepare(
    ligand,
    padding=2.0,
    keep_waters=True,
    is_lig_protonated=False,
    is_protein_protonated=False,
)

What happens during preparation?

  • The method calls the system preparation backend, which processes the protein and ligand files.
  • The prepared complex is saved to a cache for efficiency.
  • The resulting structure can be visualized or used for downstream workflows.

After preparation, the prepared complex structure will be shown automatically.