Batch Docking

Use num_poses_to_save to retain the best pose for that many top-scoring compounds, and set run_mmgbsa=True to refine those saved poses. result.refined_scores maps every input SMILES to a DockingScore for a retained compound or None otherwise.

Batch docking workflow - high-throughput molecular docking.

BatchDockingResult dataclass

BatchDockingResult(workflow_data: dict[str, Any], workflow_type: str, workflow_uuid: str, complete: bool = True)

Bases: WorkflowResult

Result from a batch-docking workflow.

scores property

scores: dict[str, float | None]

Docking scores indexed by SMILES.

refined_scores property

refined_scores: dict[str, DockingScore | None]

Saved docking results indexed by input SMILES.

submit_batch_docking_workflow

submit_batch_docking_workflow(smiles_list: list[str], protein: Protein | ProteinUUID, pocket: list[list[float]], executable: str = 'vina', scoring_function: str = 'vinardo', exhaustiveness: float = 8, num_poses_to_save: int = 0, run_mmgbsa: bool = False, name: str = 'Batch Docking Workflow', folder_uuid: str | None = None, folder: Folder | None = None, max_credits: int | None = None, webhook_url: str | None = None, is_draft: bool = False) -> Workflow[BatchDockingResult]

Submits a batch-docking workflow to the API.

Parameters:

Name	Type	Description	Default
smiles_list	list[str]	SMILES strings to dock	required
protein	Protein | ProteinUUID	protein to dock (UUID or Protein object)	required
pocket	list[list[float]]	binding pocket as [[cx, cy, cz], [sx, sy, sz]] – center (Å) and box size (Å)	required
executable	str	which docking implementation to use	'vina'
scoring_function	str	which docking scoring function to use	'vinardo'
exhaustiveness	float	docking exhaustiveness parameter	8
num_poses_to_save	int	number of top-scoring compounds whose best pose to save	0
run_mmgbsa	bool	whether to refine the saved poses with MM/GBSA. Ignored when num_poses_to_save is zero	False
name	str	name of the workflow	'Batch Docking Workflow'
folder_uuid	str | None	UUID of the folder to place the workflow in	None
folder	Folder | None	destination folder	None
max_credits	int | None	maximum number of credits to use	None
webhook_url	str | None	URL that Rowan will POST to when the workflow completes	None
is_draft	bool	save as a draft without starting execution	False

Returns:

Type	Description
Workflow[BatchDockingResult]	submitted workflow

Raises:

Type	Description
HTTPStatusError	request to the API fails