`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 ¶

Bases: WorkflowStep

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

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

Functions¶

get_poses ¶

get_poses() -> list[str] | None

return a list of paths to SDF files that contain the poses of all ligands after docking

get_results ¶

get_results() -> DataFrame | None

return a list of paths to CSV files that contain the results from docking

run ¶

run(
    *,
    pocket: Optional[Pocket] = None,
    box_size: Optional[
        tuple[Number, Number, Number]
    ] = None,
    pocket_center: Optional[
        tuple[Number, Number, Number]
    ] = None,
    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	`None`
`pocket_center`	`tuple[float, float, float]`	pocket center	`None`
`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_results ¶

show_results()

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

deeporigin.drug_discovery.docking¶