new_contents: import os
  import glob
  import argparse
  from AdaptivePELE.utilities import utilities
  
  
  def parseArguments():
      """
          Parse the command-line options
  
          :returns: object -- Object containing the options passed
      """
      desc = "Program that writes a pkl for the topology object."
      parser = argparse.ArgumentParser(description=desc)
      parser.add_argument("path", type=str, help="Path where the topology files are stored")
      args = parser.parse_args()
  
      return args.path
  
  
  def main(top_path):
      sim_folder = os.path.abspath(os.path.join(top_path, os.path.pardir))
      epochs = utilities.get_epoch_folders(sim_folder)
      top = utilities.Topology(top_path)
      top.setTopologies(glob.glob(os.path.join(top_path, "topology*.pdb")))
      for epoch in epochs:
          top.readMappingFromDisk(os.path.join(sim_folder, epoch), int(epoch))
      top.writeTopologyObject()
  
  
  if __name__ == "__main__":
      path = parseArguments()
      main(path)
  
subject: Add generate_topology_object script