frag_pele/Analysis/interaction_detector.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("-tpdb", "--tar_pdb", required=True,
                                help="""Target PDB file.""")
    required_named.add_argument("-rpdb", "--ref_pdb", required=True,
                                help="""Reference PDB file.""")

    parser.add_argument("-ch", "--chain", default="L",
                        help="Ligand chain.")
    parser.add_argument("-d", "--dist", default=4,
                        help="Interaction distance threshold.")
    parser.add_argument("-w2r", "--write2report", default=False, action='store_true',
                        help="Write a report file with the interactions.")
    parser.add_argument("-ah", "--addh", default=False, action='store_true',
                        help="If set it takes into account ligand H's in the interaction.")
    parser.add_argument("-o", "--outfile", default=False,
                        help="If set it takes into account ligand H's in the interaction.")

    args = parser.parse_args()

    return args.tar_pdb, args.ref_pdb, args.chain, args.dist, args.write2report, args.addh, args.outfile

            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("-tpdb", "--tar_pdb", required=True,
                                help="""Target PDB file.""")
    required_named.add_argument("-rpdb", "--ref_pdb", required=True,
                                help="""Reference PDB file.""")
    parser.add_argument("-ch", "--chain", default="L",
                        help="Ligand chain.")
    parser.add_argument("-d", "--dist", default=4,
                        help="Interaction distance threshold.")
    parser.add_argument("-w2r", "--write2report", default=False, action='store_true',
                        help="Write a report file with the interactions.")
    parser.add_argument("-ah", "--addh", default=False, action='store_true',
                        help="If set it takes into account ligand H's in the interaction.")
    parser.add_argument("-o", "--outfile", default=False,
                        help="If set it takes into account ligand H's in the interaction.")
    args = parser.parse_args()
    return args.tar_pdb, args.ref_pdb, args.chain, args.dist, args.write2report, args.addh, args.outfile
def parse_arguments ( ) : parser = argparse . ArgumentParser ( description = """""" ) required_named = parser . add_argument_group ( 'required named arguments' ) required_named . add_argument ( "-tpdb" , "--tar_pdb" , required = True , help = """Target PDB file.""" ) required_named . add_argument ( "-rpdb" , "--ref_pdb" , required = True , help = """Reference PDB file.""" ) parser . add_argument ( "-ch" , "--chain" , default = "L" , help = "Ligand chain." ) parser . add_argument ( "-d" , "--dist" , default = 4 , help = "Interaction distance threshold." ) parser . add_argument ( "-w2r" , "--write2report" , default = False , action = 'store_true' , help = "Write a report file with the interactions." ) parser . add_argument ( "-ah" , "--addh" , default = False , action = 'store_true' , help = "If set it takes into account ligand H's in the interaction." ) parser . add_argument ( "-o" , "--outfile" , default = False , help = "If set it takes into account ligand H's in the interaction." ) args = parser . parse_args ( ) return args . tar_pdb , args . ref_pdb , args . chain , args . dist , args . write2report , args . addh , args . outfile
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