Pocket Detection

Pocket detection workflow - detect potential binding sites on a protein.

MixMDPocketDiagnostics dataclass

MixMDPocketDiagnostics(density_center: tuple[float, float, float], peak_enrichment: float, integrated_excess_density: float)

Probe enrichment for a pocket found by mixed-solvent MD.

Attributes:

Name	Type	Description
density_center	tuple[float, float, float]	density-weighted center of the enriched region, in Å
peak_enrichment	float	maximum probe density relative to bulk solvent
integrated_excess_density	float	probe molecules above bulk, integrated over the region

Pocket dataclass

Pocket(sphere_centers: tuple[tuple[float, float, float], ...], sphere_radii: tuple[float, ...], volume: float, score: float, pocket_center: tuple[float, float, float], pocket_sides: tuple[float, float, float], residue_numbers: tuple[int, ...], mixmd: MixMDPocketDiagnostics | None = None)

A detected binding pocket.

Mixed-solvent MD pockets describe regions of enriched probe density, so their spheres and volume outline that region rather than the cavity.

Attributes:

Name	Type	Description
sphere_centers	tuple[tuple[float, float, float], ...]	centers of detected spheres, in Å
sphere_radii	tuple[float, ...]	radii of detected spheres, in Å
volume	float	pocket volume, in ų
score	float	method-specific ranking score; larger is better
pocket_center	tuple[float, float, float]	center of axis-aligned bounding box, in Å
pocket_sides	tuple[float, float, float]	side lengths of axis-aligned bounding box, in Å
residue_numbers	tuple[int, ...]	residue numbers lining the pocket
mixmd	MixMDPocketDiagnostics | None	probe-enrichment details for mixed-solvent MD pockets

MixMDReplicaDiagnostics dataclass

MixMDReplicaDiagnostics(index: int, seed: int, num_frames: int, num_probes: int, largest_probe_cluster_fraction: float | None, trajectory_uuid: str | None, topology_uuid: str | None, density_map_uuid: str | None)

One mixed-solvent MD replica.

Attributes:

Name	Type	Description
index	int	zero-based replica index
seed	int	replica random seed
num_frames	int	analyzed frames; zero for a failed replica
num_probes	int	probe molecules in the simulation
largest_probe_cluster_fraction	float | None	mean fraction of probes in the largest cluster
trajectory_uuid	str | None	UUID of the stored trajectory
topology_uuid	str | None	UUID of the trajectory topology protein
density_map_uuid	str | None	UUID of the stored probe-density map

MixMDResults dataclass

MixMDResults(reference_uuid: str | None, density_map_uuid: str | None, replicas: tuple[MixMDReplicaDiagnostics, ...])

Mixed-solvent MD replicas and consensus artifacts.

Attributes:

Name	Type	Description
reference_uuid	str | None	UUID of the protein defining pocket and map coordinates
density_map_uuid	str | None	UUID of the consensus probe-density map
replicas	tuple[MixMDReplicaDiagnostics, ...]	per-replica results, including failed replicas

PocketDetectionResult dataclass

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

Bases: WorkflowResult

Result from a pocket-detection workflow.

pockets property

pockets: list[Pocket]

Detected pockets, in the order returned by the backend.

mixmd property

mixmd: MixMDResults | None

Mixed-solvent MD replicas and artifacts, or None for Pocketeer runs.

messages property

messages: list[Message]

Any messages or warnings from the workflow, including MixMD reliability warnings.

get_reference_protein

get_reference_protein() -> Protein | None

Fetch and cache the protein defining mixed-solvent MD pocket and map coordinates.

Returns:

Type	Description
Protein | None	protein object, or None for Pocketeer runs

submit_pocket_detection_workflow

submit_pocket_detection_workflow(protein: Protein | ProteinUUID, merge_distance: float | None = None, settings: PocketeerSettings | MixMDSettings | None = None, validate_forcefield: bool = True, name: str = 'Pocket Detection 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[PocketDetectionResult]

Submits a pocket-detection workflow to the API.

Parameters:

Name	Type	Description	Default
protein	Protein | ProteinUUID	protein to analyze. Can be a UUID or a Protein object	required
merge_distance	float | None	Pocketeer distance for merging pocket spheres, in Å; defaults to 1.75. Set it on PocketeerSettings instead when passing settings	None
settings	PocketeerSettings | MixMDSettings | None	method settings; PocketeerSettings (default) for geometric detection or MixMDSettings for mixed-solvent molecular dynamics	None
validate_forcefield	bool	validate the protein forcefield compatibility before submitting a mixed-solvent MD run. Raises an error early if the protein cannot be parameterized or has clashing residues	True
name	str	name of the workflow	'Pocket Detection 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[PocketDetectionResult]	workflow object representing the submitted workflow

Raises:

Type	Description
ValueError	both merge_distance and settings, or both folder and folder_uuid, are given
HTTPStatusError	request to the API fails