Analogue Docking

Analogue docking workflow - dock analogues using a template ligand.

AnalogueDockingResult `dataclass`

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

Bases: WorkflowResult

Result from an analogue-docking workflow.

analogue_scores `property`

analogue_scores: dict[str, list[DockingScore]]

Docking scores for each analogue SMILES.

best_poses `property`

best_poses: dict[str, Molecule]

Best docked pose per analogue, keyed by SMILES.

Fetches the final geometry from each analogue's top-scoring pose. Analogues with no successful poses are excluded. When analogue_names were supplied at submission, each pose's name is set to the analogue name, so poses can be re-keyed by name (e.g. {p.name: p for p in ...}).

Returns:

Type	Description
`dict[str, Molecule]`	Dictionary mapping SMILES to docked `Molecule` with 3D coordinates.

get_pose

get_pose(smiles: str, index: int = 0) -> Calculation

Fetch a docked ligand pose as a calculation with 3D coordinates.

Parameters:

Name	Type	Description	Default
`smiles`	`str`	SMILES string of the analogue.	required
`index`	`int`	Index of the pose (0-based, ordered by score). Default 0 (best).	`0`

Returns:

Type	Description
`Calculation`	Calculation containing the docked ligand molecule with 3D coordinates.

Raises:

Type	Description
`KeyError`	If the SMILES is not found.
`IndexError`	If index is out of range.
`ValueError`	If the pose has no UUID.

get_poses

get_poses(smiles: str) -> list[Calculation]

Fetch all docked ligand poses as calculations with 3D coordinates.

Parameters:

Name	Type	Description	Default
`smiles`	`str`	SMILES string of the analogue.	required

Returns:

Type	Description
`list[Calculation]`	List of Calculations for each pose (ordered by score).

Raises:

Type	Description
`KeyError`	If the SMILES is not found.

get_complex

get_complex(smiles: str, index: int = 0) -> Protein

Fetch a protein-ligand complex structure for a specific analogue.

Parameters:

Name	Type	Description	Default
`smiles`	`str`	SMILES string of the analogue.	required
`index`	`int`	Index of the pose (0-based, ordered by score). Default 0 (best).	`0`

Returns:

Type	Description
`Protein`	Protein object with the full protein-ligand complex.

Raises:

Type	Description
`KeyError`	If the SMILES is not found.
`IndexError`	If index is out of range.
`ValueError`	If the complex has no structure UUID.

get_complexes

get_complexes(smiles: str) -> list[Protein]

Fetch all protein-ligand complex structures for a specific analogue.

Parameters:

Name	Type	Description	Default
`smiles`	`str`	SMILES string of the analogue.	required

Returns:

Type	Description
`list[Protein]`	List of Protein objects for each complex (ordered by score).

Raises:

Type	Description
`KeyError`	If the SMILES is not found.

submit_analogue_docking_workflow

submit_analogue_docking_workflow(
    analogues: list[str],
    initial_molecule: StructureInput,
    protein: Protein | ProteinUUID,
    analogue_names: list[str] | None = None,
    scoring_function: Literal["vina", "vinardo"] = "vinardo",
    exhaustiveness: int = 8,
    max_poses: int = 4,
    num_conformers_per_analogue: int = 100,
    require_posebusters: bool = False,
    run_local_optimization: bool = False,
    name: str = "Analogue 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

Submits an analogue-docking workflow to the API.

Parameters:

Name	Type	Description	Default
`analogues`	`list[str]`	SMILES strings to dock.	required
`initial_molecule`	`StructureInput`	Template to which to align molecules to.	required
`protein`	`Protein \| ProteinUUID`	Protein to dock. Can be input as a uuid or a Protein object.	required
`analogue_names`	`list[str] \| None`	Names parallel to `analogues`. When provided, each docked pose's `Molecule.name` is set to its analogue name (see `best_poses`), and must be the same length as `analogues`. If omitted, poses are identified by SMILES.	`None`
`scoring_function`	`Literal['vina', 'vinardo']`	Docking scoring function: "vina" or "vinardo".	`'vinardo'`
`exhaustiveness`	`int`	How many times Vina attempts to find a pose for each conformer.	`8`
`max_poses`	`int`	Maximum number of poses generated per input conformer.	`4`
`num_conformers_per_analogue`	`int`	Maximum number of conformers to generate per analogue.	`100`
`require_posebusters`	`bool`	Filter conformers based on PoseBusters validity before docking.	`False`
`run_local_optimization`	`bool`	Whether to run a local opt in docking pocket or just score.	`False`
`name`	`str`	Name of the workflow.	`'Analogue Docking Workflow'`
`folder_uuid`	`str \| None`	UUID of the folder to place the workflow in.	`None`
`folder`	`Folder \| None`	Folder object to store the workflow in.	`None`
`max_credits`	`int \| None`	Maximum number of credits to use for the workflow.	`None`
`webhook_url`	`str \| None`	URL that Rowan will POST to when the workflow completes.	`None`
`is_draft`	`bool`	If True, submit the workflow as a draft without starting execution.	`False`

Returns:

Type	Description
`Workflow`	Workflow object representing the submitted analogue-docking workflow.

Raises:

Type	Description
`requests.HTTPError`	if the request to the API fails.

Analogue Docking