qp.cluster.spheres.check_atom_valence

qp.cluster.spheres.check_atom_valence(res: Bio.PDB.Residue.Residue, tree: Bio.PDB.NeighborSearch.NeighborSearch, atom: Literal['N', 'C', 'CG'], cn: int) → bool[source]

Check whether a backbone atom already has sufficient bonded neighbors.

Uses a 1.8 A distance search to find neighbors. Also checks for peptide bond partners (C/CG bonded to N, or N bonded to C/CG).

Parameters:

  • res (Bio.PDB.Residue.Residue) – Residue containing the atom.

  • tree (Bio.PDB.NeighborSearch) – Spatial search object for the structure.

  • atom (str) – Atom name to check ('N', 'C', or 'CG').

  • cn (int) – Minimum coordination number indicating the atom is already saturated.

Returns:

True if the atom already has enough neighbors (no capping needed).

Return type:

bool