qp.cluster.spheres_bad.get_next_neighbors

qp.cluster.spheres_bad.get_next_neighbors(start, neighbors, sphere_count, ligands, first_sphere_radius=3, smooth_method='boxplot', include_ligands=2, **smooth_params)[source]

Iteratively determines spheres around a given starting atom

Parameters:

  • start (Bio.PDB.Residue) – Starting metal atom

  • neighbors (dict) – Adjacency list of neighboring atoms

  • sphere_count (int) – Number of spheres to extract

  • ligands (list) – A list of ligands to include

  • smooth_method ((“boxplot” | “dbscan” | “dummy_atom”)) – The method used to smoothen the spheres

  • include_ligands (int) – the mode of including ligands in the sphere

  • smooth_params – params of the specific smooth method

Returns:

  • metal_id (str) – Active site identifier

  • seen (set) – Set of residues from all spheres

  • spheres (list of sets) – Sets of residues separated by spheres