Detect

Automatic pocket detection from a static protein structure.

This module provides the PocketDetector class, which implements the pocket-identification pipeline:

1. Load a PDB structure and strip hydrogen atoms.
2. Compute the convex hull of alpha carbon positions.
3. Fill the hull with a coarse grid of equidistant points, progressively refining the resolution.
4. Remove grid points that clash with protein atoms.
5. Filter isolated points that lack sufficient neighbors.
6. Partition the remaining points into distinct pockets.
7. Cluster each pocket with k-means and output encompassing spheres.

PocketDetector(config=None)

The main class to run pocket detection.

Initialize Pocket detector.

PARAMETER	DESCRIPTION
config	Pocket detection configuration. TYPE: PocketDetectConfig | None DEFAULT: None

config = config

run(path_pdb, output_prefix='')