old_contents: from ANN_simulation_trp_cage import *
  
  sutils.generate_coordinates_from_pdb_files(folder_for_pdb = '../target')
  
new_contents: from ANN_simulation_trp_cage import *
  import argparse, subprocess
  
  parser = argparse.ArgumentParser()
  parser.add_argument("--file", type=str, default="", help="specify which pdb file to generate coordinates from")
  args = parser.parse_args()
  
  
  sutils.generate_coordinates_from_pdb_files(folder_for_pdb = '../target/' + args.file)
  
  
subject: update generate_coordinates.py: support generating coordinates for a single file