Detect

PocketDetectConfig

Bases: BaseModel, YamlIO

clashing_cutoff: float = 3.0

In measuring the pockets, any points closer than this cutoff to receptor atoms will be removed.

n_cores: int = 1

The number of processors to use.

n_neighbors: int = 4

In measuring the pockets, any points with fewer than this number of neighbors will be deleted. These are usually just stray points that don't belong to any real pocket.

n_spheres: int = 5

The number of inclusion spheres to generate for each pocket.

pocket_detection_resolution: float = 4.0

The distance between probe points used to initially find the pockets

pocket_measuring_resolution: float = 1.0

The distance between probe points used to measure identified pockets in greater detail. Should divide --pocket_detection_resolution evenly.

sphere_padding: float = 5.0

How much larger the radius of the inclusion spheres should be, beyond what is required to encompass the identified pockets.

use_ray: bool = False

Parallelize computations with ray.

log()

Log all configuration parameters.