Profile Containers

Structured containers for extracted interaction profiles, used internally by Molecule and available for serialization and visualization.

class shepherd_score.container.profiles.Surface(positions=None, esp=None, probe_radius=1.2)

Bases: object

Container for a molecule’s molecular-surface interaction profile.

Backs the surf_pos/surf_esp/probe_radius properties that previously lived directly on Molecule as loose attributes.

Parameters:

• positions (ndarray | None)

• esp (ndarray | None)

• probe_radius (float)

positions

Surface point cloud, shape (M, 3). None if no surface was generated.

Type:

np.ndarray or None

esp

Electrostatic potential at each surface point, shape (M,). None if not generated.

Type:

np.ndarray or None

probe_radius

Probe radius used to define the solvent-accessible surface.

Type:

float

Pharmacophore is defined in shepherd_score.pharm_utils.pharmacophore and re-exported from shepherd_score.container for convenience. See Pharmacophore Utilities for priority-label semantics.