) args = parser.parse_args() first_it_id = args.first_iteration last_it_id = args.last_iteration if args.plot: import matplotlib.pyplot as plt # failproofing for segment plotting if first_it_id == last_it_id and \ args.plot_segments: raise Exception("Need more than 1 iteration for --segments\n") #get the actual Iteration from logger module logger = Logger(args.logdir) keep_coords_frequency = int( logger.loadConfigParameter('keep-coords-frequency', iteration_id=first_it_id)) first_iteration = logger.loadIteration(first_it_id) if last_it_id == -1: last_it_id = logger.getLastIterationId() # load md module if not args.input_md_conf: args.input_md_conf = logger.loadConfigFile(first_iteration.getId()) md_module = MD_module(args.input_md_conf, debug=False) # Load cpptraj input file as one string with linebreaks and delete the last line break try: cpptraj_lines_file = open(args.cpptraj_lines_file_path, 'r') except: print('Error: could not open ' + args.cpptraj_lines_file_path) cpptraj_lines = ''