Analogue Docking

Analogue docking generates at most 20 conformers per analogue by default. Override num_conformers_per_analogue when a broader search is needed.

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`	SMILES is not found
`IndexError`	index is out of range
`ValueError`	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`	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`	SMILES is not found
`IndexError`	index is out of range
`ValueError`	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]`	proteins for each complex (ordered by score)

Raises:

Type	Description
`KeyError`	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 = 20, 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[AnalogueDockingResult]

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	`20`
`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`	destination folder	`None`
`max_credits`	`int \| None`	maximum credits for the workflow	`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[AnalogueDockingResult]`	workflow object representing the submitted analogue-docking workflow

Raises:

Type	Description
`HTTPStatusError`	request to the API fails

Analogue Docking