frag_pele/Analysis/get_plots.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="""Script to perform plots. You can choose between different
    type of plots (depending on your input file): 'boxplot_single' if your input is the result of the analysis
    between two structures, for which you have computed the RMSD and the CA distance between them; 'boxplot_differences'
    if you want to show the comparison of RMSD and CA distance in two different files; and 'boxplot_atom_distances'
    if you have calculated atom-atom distances in three structures in order to show the differences.""")
    required_named = parser.add_argument_group('required named arguments')
    # Growing related arguments
    required_named.add_argument("-t", "--type", required=True, choices=['boxplot_single','boxplot_differences',
                                                                        'boxplot_atom_distances'],
                                help="""Plot type that you want to do. Choose between: boxplot_differences, 
                                boxplot_single. """)
    required_named.add_argument("-i", "--input", required=True,
                                help="""Path of the input file.""")

    parser.add_argument("-i2", "--input_2", default=False,
                        help=""""Path of the input file 2, only set if you want to do comparisons.""")

    parser.add_argument("-i3", "--input_3", default=False,
                        help=""""Path of the input file 2, only set if you want to do comparisons.""")

    args = parser.parse_args()

    return args.type, args.input, args.input_2, args.input_3

            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="""Script to perform plots. You can choose between different
    type of plots (depending on your input file): 'boxplot_single' if your input is the result of the analysis
    between two structures, for which you have computed the RMSD and the CA distance between them; 'boxplot_differences'
    if you want to show the comparison of RMSD and CA distance in two different files; and 'boxplot_atom_distances'
    if you have calculated atom-atom distances in three structures in order to show the differences.""")
    required_named = parser.add_argument_group('required named arguments')
    required_named.add_argument("-t", "--type", required=True, choices=['boxplot_single','boxplot_differences',
                                                                        'boxplot_atom_distances'],
                                help="""Plot type that you want to do. Choose between: boxplot_differences, 
                                boxplot_single. """)
    required_named.add_argument("-i", "--input", required=True,
                                help="""Path of the input file.""")
    parser.add_argument("-i2", "--input_2", default=False,
                        help=""""Path of the input file 2, only set if you want to do comparisons.""")
    parser.add_argument("-i3", "--input_3", default=False,
                        help=""""Path of the input file 2, only set if you want to do comparisons.""")
    args = parser.parse_args()
    return args.type, args.input, args.input_2, args.input_3
def parse_arguments ( ) : parser = argparse . ArgumentParser ( description = """Script to perform plots. You can choose between different
    type of plots (depending on your input file): 'boxplot_single' if your input is the result of the analysis
    between two structures, for which you have computed the RMSD and the CA distance between them; 'boxplot_differences'
    if you want to show the comparison of RMSD and CA distance in two different files; and 'boxplot_atom_distances'
    if you have calculated atom-atom distances in three structures in order to show the differences.""" ) required_named = parser . add_argument_group ( 'required named arguments' ) required_named . add_argument ( "-t" , "--type" , required = True , choices = [ 'boxplot_single' , 'boxplot_differences' , 'boxplot_atom_distances' ] , help = """Plot type that you want to do. Choose between: boxplot_differences, 
                                boxplot_single. """ ) required_named . add_argument ( "-i" , "--input" , required = True , help = """Path of the input file.""" ) parser . add_argument ( "-i2" , "--input_2" , default = False , help = """"Path of the input file 2, only set if you want to do comparisons.""" ) parser . add_argument ( "-i3" , "--input_3" , default = False , help = """"Path of the input file 2, only set if you want to do comparisons.""" ) args = parser . parse_args ( ) return args . type , args . input , args . input_2 , args . input_3
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