qp.cluster.spheres.voronoi

qp.cluster.spheres.voronoi(model, center_residue: CenterResidue, ligands, smooth_method, output_path, **smooth_params)[source]

Compute the Voronoi tessellation of a protein structure.

Builds a Voronoi diagram from all atoms in the model and returns an adjacency list of neighboring atoms. Optionally applies smoothing via dummy atoms to improve boundary handling for surface-exposed residues.

Parameters:

  • model (Bio.PDB.Model.Model) – Protein structure model containing all residues.

  • center_residue (CenterResidue) – Center residue definition (currently unused but kept for API).

  • ligands (list) – Ligand residue names to include (currently unused but kept for API).

  • smooth_method (str) – Smoothing method: 'dummy_atom' fills voids with dummy atoms, otherwise no smoothing is applied.

  • output_path (str) – Directory for debug output (e.g., dummy.xyz).

  • **smooth_params – Additional parameters passed to fill_dummy() (e.g., mean_distance, noise_amp).

Returns:

Adjacency list mapping each Bio.PDB.Atom to a list of (neighbor_atom, distance) tuples for all Voronoi neighbors.

Return type:

dict