qp.manager.charge_embedding.parse_pdb

qp.manager.charge_embedding.parse_pdb(input_pdb, output_pdb, ff_dict)[source]

Write ff14SB partial charges into the B-factor column of a PDB file.

Only ATOM lines whose residue and atom names match entries in ff_dict are written to the output file.

Parameters:

  • input_pdb (str) – Path to the input PDB file.

  • output_pdb (str) – Path to the output PDB file with charges in the B-factor column.

  • ff_dict (dict) – Nested dict from get_ff14SB_dict().