deeporigin.drug_discovery.docking

This module encapsulates methods to run docking and show docking results on Deep Origin

Attributes

Number module-attribute

Number = float | int

Classes

Docking

class to handle Docking-related tasks within the Complex class.

Objects instantiated here are meant to be used within the Complex class.

Attributes

parent instance-attribute

parent = parent

Functions

get_poses

get_poses(output_sdf_file: str) -> None

generate a single SDF file containing all the poses of all ligands docked to the protein

Parameters:

Name	Type	Description	Default
output_sdf_file	str	path to output SDF file. All poses will be written to a SDF file in this location.	required

get_results

get_results() -> DataFrame

Get docking results from Deep Origin

run

run(
    *,
    box_size: tuple[Number, Number, Number],
    pocket_center: tuple[Number, Number, Number],
    batch_size: Optional[int] = 32,
    n_workers: Optional[int] = None
)

Run bulk docking on Deep Origin. Ligands will be split into batches based on the batch_size argument, and will run in parallel on Deep Origin clusters.

Parameters:

Name	Type	Description	Default
box_size	tuple[float, float, float]	box size	required
pocket_center	tuple[float, float, float]	pocket center	required
batch_size	int	batch size. Defaults to 30.	32
n_workers	int	number of workers. Defaults to None.	None

show_poses

show_poses()

show docked ligands with protein in 3D

show_progress

show_progress()

show progress of bulk Docking run

show_results

show_results()

show results of bulk Docking run in a table, rendering 2D structures of molecules