qp.manager.charge_embedding.get_charges¶

qp.manager.charge_embedding.get_charges(charge_embedding_cutoff, charge_embedding_charges=None)[source]¶

Generate the MM point charge embedding file (ptchrges.xyz).

Orchestrates the full charge embedding pipeline: renames residues for ff14SB compatibility, assigns partial charges into the B-factor column, removes QM cluster atoms, and writes the remaining MM atoms within the cutoff distance as a point charge XYZ file.

Parameters:

charge_embedding_cutoff (float) – Distance cutoff in angstroms from the QM cluster centroid for including MM point charges.
charge_embedding_charges (str, optional) – Path to a JSON file containing custom partial charges. When None (default), the built-in AMBER ff14SB charges are used. See load_custom_charges() for the expected file format.