qp.cluster.spheres_bad.extract_clusters

qp.cluster.spheres_bad.extract_clusters(path, out, center_residues, sphere_count=2, first_sphere_radius=4.0, max_atom_count=None, merge_cutoff=0.0, smooth_method='box_plot', ligands=[], capping=1, charge=True, ligand_charge={}, count=True, xyz=True, hetero_pdb=False, include_ligands=2, **smooth_params)[source]

Extract active site coordination spheres. Neighboring residues determined by Voronoi tessellation.

Parameters:

  • path (str) – Path to PDB file

  • out (str) – Path to output directory

  • center_residues (list) – List of resnames of the residues to use as the cluster center

  • sphere_count (int) – Number of coordinations spheres to extract

  • first_sphere_radius (float) – the radius cutoff of the first sphere

  • max_atom_count (int) – the maximum number of atoms in the whole cluster

  • merge_cutoff (int) – the distance cutoff when merging two centers of spheres

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

  • ligands (list) – Other ligand IDs to include, in addition to AAs and waters

  • capping (int) – Whether to cap chains with nothing (0), H (1), or ACE/NME (2)

  • charge (bool) – If true, total charge of coordinating AAs will be written to out/charge.csv

  • ligand_charge (dict) – The dict containing each ligand’s name and charge

  • count (bool) – If true, residue counts will be written to out/count.csv

  • xyz (bool) – If true, XYZ files will be written according to the output PDBs

  • hetero_pdb (bool) – If true, keep all the heteroatoms in the cluster PDB output

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

  • smooth_params – params of the specific smooth method