frag_pele/Analysis/sidecahins_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="""""")
    required_named = parser.add_argument_group('required named arguments')
    # Growing related arguments
    required_named.add_argument("-t", "--type", required=True, choices=['sidechains', 'atom_distances'],
                                help="""Computation type that you want to do. Choose between: sidechains, 
                                atom_distances. """)

    required_named.add_argument("-pdbt", "--pdb_target", required=True,
                                help="""Target pdb file. """)


    parser.add_argument("-pdbr", "--pdb_reference",
                        help="""Reference pdb file.""")

    parser.add_argument("-a", "--area", default=False,
                        help=""""The area (volume) that will be used to select which amino acids are close to the 
                        ligand. THE USAGE OF THIS FLAG HAS NOT BEEN DEBUG SO IS NOT RECOMMENDED TO ACTIVATE IT.""")

    parser.add_argument("-ch", "--chain", default="L",
                        help="Name of the ligand's chain")
    parser.add_argument("-o", "--out", default="report_rmsd.txt",
                        help="Output file name.")
    parser.add_argument("-rf", "--res_file", default=False,
                        help="""Filename that contains which amino acids do you want to select to do the rmsd
                        computations.""")


    args = parser.parse_args()

    return args.type, args.pdb_reference, args.pdb_target, args.area, args.out, args.chain, args.res_file

            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="""""")
    required_named = parser.add_argument_group('required named arguments')
    required_named.add_argument("-t", "--type", required=True, choices=['sidechains', 'atom_distances'],
                                help="""Computation type that you want to do. Choose between: sidechains, 
                                atom_distances. """)
    required_named.add_argument("-pdbt", "--pdb_target", required=True,
                                help="""Target pdb file. """)
    parser.add_argument("-pdbr", "--pdb_reference",
                        help="""Reference pdb file.""")
    parser.add_argument("-a", "--area", default=False,
                        help=""""The area (volume) that will be used to select which amino acids are close to the 
                        ligand. THE USAGE OF THIS FLAG HAS NOT BEEN DEBUG SO IS NOT RECOMMENDED TO ACTIVATE IT.""")
    parser.add_argument("-ch", "--chain", default="L",
                        help="Name of the ligand's chain")
    parser.add_argument("-o", "--out", default="report_rmsd.txt",
                        help="Output file name.")
    parser.add_argument("-rf", "--res_file", default=False,
                        help="""Filename that contains which amino acids do you want to select to do the rmsd
                        computations.""")
    args = parser.parse_args()
    return args.type, args.pdb_reference, args.pdb_target, args.area, args.out, args.chain, args.res_file
def parse_arguments ( ) : parser = argparse . ArgumentParser ( description = """""" ) required_named = parser . add_argument_group ( 'required named arguments' ) required_named . add_argument ( "-t" , "--type" , required = True , choices = [ 'sidechains' , 'atom_distances' ] , help = """Computation type that you want to do. Choose between: sidechains, 
                                atom_distances. """ ) required_named . add_argument ( "-pdbt" , "--pdb_target" , required = True , help = """Target pdb file. """ ) parser . add_argument ( "-pdbr" , "--pdb_reference" , help = """Reference pdb file.""" ) parser . add_argument ( "-a" , "--area" , default = False , help = """"The area (volume) that will be used to select which amino acids are close to the 
                        ligand. THE USAGE OF THIS FLAG HAS NOT BEEN DEBUG SO IS NOT RECOMMENDED TO ACTIVATE IT.""" ) parser . add_argument ( "-ch" , "--chain" , default = "L" , help = "Name of the ligand's chain" ) parser . add_argument ( "-o" , "--out" , default = "report_rmsd.txt" , help = "Output file name." ) parser . add_argument ( "-rf" , "--res_file" , default = False , help = """Filename that contains which amino acids do you want to select to do the rmsd
                        computations.""" ) args = parser . parse_args ( ) return args . type , args . pdb_reference , args . pdb_target , args . area , args . out , args . chain , args . res_file
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