qp.manager.charge_embedding.remove_qm_atoms

qp.manager.charge_embedding.remove_qm_atoms(pdb_file, xyz_file, output_pdb_file, threshold=0.5)[source]

Remove QM cluster atoms from a PDB file based on coordinate matching.

Atoms in the PDB whose coordinates are within threshold angstroms of any atom in the XYZ file are removed.

Parameters:

  • pdb_file (str) – Path to the full-protein PDB file.

  • xyz_file (str) – Path to the QM cluster XYZ file.

  • output_pdb_file (str) – Path to write the PDB with QM atoms removed.

  • threshold (float, optional) – Distance threshold in angstroms for matching atoms (default 0.5).