Complex

This document describes how to create a Complex object, that can be used to run Docking, ABFE, and historically RBFE (the Complex.rbfe helper is removed).

Deprecated: Complex

The Complex class is deprecated. Prefer Docking, ABFE, PocketFinder, and SystemPrep for new projects. The legacy RBFE helper is removed. This how-to remains for legacy notebooks.

Creating a Complex¶

From a directory¶

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

sim = Complex.from_dir(BRD_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, BRD_DATA_DIR, Protein, Ligand

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

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

From `LigandSet` objects¶

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

from deeporigin.drug_discovery import Complex, BRD_DATA_DIR, Protein, LigandSet

protein = Protein.from_file(BRD_DATA_DIR / "brd.pdb")
ligands = LigandSet.from_dir(BRD_DATA_DIR)

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

Modifying a Complex¶

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

from deeporigin.drug_discovery import Complex, Protein, Ligand, BRD_DATA_DIR
protein = Protein.from_file(BRD_DATA_DIR / "brd.pdb")
ligand = Ligand.from_sdf(BRD_DATA_DIR / "brd-2.sdf")
ligand3 = Ligand.from_sdf(BRD_DATA_DIR / "brd-3.sdf")

# Create a complex with just the protein
sim = Complex(protein=protein)

# Add a single ligand
sim.ligands = ligand3

# Add another ligand
ligand4 = Ligand.from_sdf(BRD_DATA_DIR / "brd-4.sdf")
sim.ligands = sim.ligands + ligand4

# Replace all ligands
ligand5 = Ligand.from_sdf(BRD_DATA_DIR / "brd-5.sdf")
sim.ligands = ligand5  # Replace with a single ligand

Constructing Ligands

To see how to construct Ligands, see Ligands

Constructing the Protein

To see how to construct the Protein, see Proteins

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.

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

result = sim.prepare(sim.ligands[0])
result.prepared_systems[0].show()

result is a FunctionResult that wraps the API response. The prepared proteins are available as a list on result.prepared_systems.

When preparing all ligands at once, the result aggregates costs and systems:

result = sim.prepare()
result.prepared_systems  # list of Protein objects, one per ligand
result.cost              # total cost across all preparations

You should see something like:

which shows you the prepared system.

Estimating cost¶

To get a cost estimate without running system preparation, use quote=True:

result = sim.prepare(sim.ligands[0], quote=True)
result.estimate  # estimated cost in dollars
result.cost      # None (function was not executed)

System preparation parameters

Look at the reference documentation to understand parameters for system preparation.

Specifying a Client¶

A Complex can be configured with a DeepOriginClient explicitly, using:

sim = Complex.from_dir(..., client=client)

You do not typically need to do this. If no client is specified, it is automatically configured using saved tokens and config.

Reference¶

Complex