frag_pele/Analysis/analyser.py
def parse_arguments():
    """
            Parse user arguments

            Output: list with all the user arguments
        """
    # All the docstrings are very provisional and some of them are old, they would be changed in further steps!!
    parser = argparse.ArgumentParser(description="""Computes the mean of the 25% lowest values of the sampling simulation
    for each fragment grown. """)
    required_named = parser.add_argument_group('required named arguments')
    # Growing related arguments
    required_named.add_argument("path_to_analyze",
                                help="""Path of the folder to be analyzed, where all simulations are stored.""")

    parser.add_argument("-r", "--rep_pref", default='report_',
                                help="""Prefix of the report file: usually 'report_'. """)
    parser.add_argument("-s", "--steps", default=False,
                        help="Used to filter by N PELE steps")
    parser.add_argument("-f", "--file", default=False,
                        help="Used to set the flag 'export file? to True'")
    parser.add_argument("-o", "--out", default="",
                        help="Name of the output file")
    parser.add_argument("-e", "--equil_folder", default="sampling_results*",
                        help="Prefix of the equilibration folder (where the results are)")
    parser.add_argument("-c", "--col", default="Binding Energy",
                        help="Name of the column that we will use to find the minimum value of the PELE report")
    parser.add_argument("-q", "--quart", default=0.25,
                        help="Quartile that will be used to compute the mean")
    parser.add_argument("-csv", "--export_csv", default=True,
                        help="By default a csv file with a summary of all reports will be stored. If you do not"
                        "want to save it, set the flag to False.")
    parser.add_argument("-l", "--limit_column", default=None, type=str,
                        help="Column used to subset the results.")
    parser.add_argument("-lu", "--limit_up", default=None, type=float,
                        help="Top value to create the new subset of samples.")
    parser.add_argument("-ld", "--limit_down", default=None, type=float,
                        help="Lowest value to create the new subset of samples.")

    args = parser.parse_args()

    return args.path_to_analyze, args.rep_pref, args.steps, args.file, args.out, args.equil_folder, args.col, \
           args.quart, args.export_csv, args.limit_column, args.limit_up, args.limit_down

            Parse user arguments

            Output: list with all the user arguments
        
Parse user arguments
Output: list with all the user arguments
Parse user arguments Output : list with all the user arguments
def parse_arguments():
    parser = argparse.ArgumentParser(description="""Computes the mean of the 25% lowest values of the sampling simulation
    for each fragment grown. """)
    required_named = parser.add_argument_group('required named arguments')
    required_named.add_argument("path_to_analyze",
                                help="""Path of the folder to be analyzed, where all simulations are stored.""")
    parser.add_argument("-r", "--rep_pref", default='report_',
                                help="""Prefix of the report file: usually 'report_'. """)
    parser.add_argument("-s", "--steps", default=False,
                        help="Used to filter by N PELE steps")
    parser.add_argument("-f", "--file", default=False,
                        help="Used to set the flag 'export file? to True'")
    parser.add_argument("-o", "--out", default="",
                        help="Name of the output file")
    parser.add_argument("-e", "--equil_folder", default="sampling_results*",
                        help="Prefix of the equilibration folder (where the results are)")
    parser.add_argument("-c", "--col", default="Binding Energy",
                        help="Name of the column that we will use to find the minimum value of the PELE report")
    parser.add_argument("-q", "--quart", default=0.25,
                        help="Quartile that will be used to compute the mean")
    parser.add_argument("-csv", "--export_csv", default=True,
                        help="By default a csv file with a summary of all reports will be stored. If you do not"
                        "want to save it, set the flag to False.")
    parser.add_argument("-l", "--limit_column", default=None, type=str,
                        help="Column used to subset the results.")
    parser.add_argument("-lu", "--limit_up", default=None, type=float,
                        help="Top value to create the new subset of samples.")
    parser.add_argument("-ld", "--limit_down", default=None, type=float,
                        help="Lowest value to create the new subset of samples.")
    args = parser.parse_args()
    return args.path_to_analyze, args.rep_pref, args.steps, args.file, args.out, args.equil_folder, args.col, \
           args.quart, args.export_csv, args.limit_column, args.limit_up, args.limit_down
def parse_arguments ( ) : parser = argparse . ArgumentParser ( description = """Computes the mean of the 25% lowest values of the sampling simulation
    for each fragment grown. """ ) required_named = parser . add_argument_group ( 'required named arguments' ) required_named . add_argument ( "path_to_analyze" , help = """Path of the folder to be analyzed, where all simulations are stored.""" ) parser . add_argument ( "-r" , "--rep_pref" , default = 'report_' , help = """Prefix of the report file: usually 'report_'. """ ) parser . add_argument ( "-s" , "--steps" , default = False , help = "Used to filter by N PELE steps" ) parser . add_argument ( "-f" , "--file" , default = False , help = "Used to set the flag 'export file? to True'" ) parser . add_argument ( "-o" , "--out" , default = "" , help = "Name of the output file" ) parser . add_argument ( "-e" , "--equil_folder" , default = "sampling_results*" , help = "Prefix of the equilibration folder (where the results are)" ) parser . add_argument ( "-c" , "--col" , default = "Binding Energy" , help = "Name of the column that we will use to find the minimum value of the PELE report" ) parser . add_argument ( "-q" , "--quart" , default = 0.25 , help = "Quartile that will be used to compute the mean" ) parser . add_argument ( "-csv" , "--export_csv" , default = True , help = "By default a csv file with a summary of all reports will be stored. If you do not" "want to save it, set the flag to False." ) parser . add_argument ( "-l" , "--limit_column" , default = None , type = str , help = "Column used to subset the results." ) parser . add_argument ( "-lu" , "--limit_up" , default = None , type = float , help = "Top value to create the new subset of samples." ) parser . add_argument ( "-ld" , "--limit_down" , default = None , type = float , help = "Lowest value to create the new subset of samples." ) args = parser . parse_args ( ) return args . path_to_analyze , args . rep_pref , args . steps , args . file , args . out , args . equil_folder , args . col , args . quart , args . export_csv , args . limit_column , args . limit_up , args . limit_down
Parse user arguments
Output: list with all the user arguments
Parse user arguments Output : list with all the user arguments
"""
            Parse user arguments

            Output: list with all the user arguments
        """ # All the docstrings are very provisional and some of them are old, they would be changed in further steps!! # Growing related arguments