frag_pele/Covalent/pdb_corrector.py
def parseArguments():
    """
        Parse the command-line options
    """
    desc = "It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with."
    parser = argparse.ArgumentParser(description=desc)
    required_named = parser.add_argument_group('required named arguments')
    required_named.add_argument("-i", "--input_pdb", type=str,  
                                help="Path to the input PDB complex.")
    required_named.add_argument("-rc", "--residue_chain", type=str,   
                                help="Chain of the residue that has the ligand covalently attached")
    required_named.add_argument("-rn", "--residue_number", type=str,
                                help="Residue number of the residue that has the ligand covalently attached")
    required_named.add_argument("-o", "--output_pdb", type=str,
                                help="Output PDB path.")
    parser.add_argument("-lr", "--ligand_resname", default="UNK",
                        help="Residue name of the ligand that is covalently attached to the previous residue")
    parser.add_argument("-lc", "--ligand_chain", default=" ",
                        help="Chain of the ligand that is covalently attached to the previous residue")
    parser.add_argument("-v", "--verbose", default=False, action='store_true',
                        help="Set true to activate all unneded prints.")
    parser.add_argument("-e", "--extract_ligand", default=True, action='store_false',
                        help="Set true to inactivate the extraction of a ligand in a PDB file.")
    args = parser.parse_args()

    return args.input_pdb, args.residue_chain, args.residue_number, args.output_pdb, \
           args.ligand_resname, args.ligand_chain, args.verbose, args.extract_ligand

        Parse the command-line options
    
Parse the command-line options
Parse the command - line options
def parseArguments():
    desc = "It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with."
    parser = argparse.ArgumentParser(description=desc)
    required_named = parser.add_argument_group('required named arguments')
    required_named.add_argument("-i", "--input_pdb", type=str,  
                                help="Path to the input PDB complex.")
    required_named.add_argument("-rc", "--residue_chain", type=str,   
                                help="Chain of the residue that has the ligand covalently attached")
    required_named.add_argument("-rn", "--residue_number", type=str,
                                help="Residue number of the residue that has the ligand covalently attached")
    required_named.add_argument("-o", "--output_pdb", type=str,
                                help="Output PDB path.")
    parser.add_argument("-lr", "--ligand_resname", default="UNK",
                        help="Residue name of the ligand that is covalently attached to the previous residue")
    parser.add_argument("-lc", "--ligand_chain", default=" ",
                        help="Chain of the ligand that is covalently attached to the previous residue")
    parser.add_argument("-v", "--verbose", default=False, action='store_true',
                        help="Set true to activate all unneded prints.")
    parser.add_argument("-e", "--extract_ligand", default=True, action='store_false',
                        help="Set true to inactivate the extraction of a ligand in a PDB file.")
    args = parser.parse_args()
    return args.input_pdb, args.residue_chain, args.residue_number, args.output_pdb, \
           args.ligand_resname, args.ligand_chain, args.verbose, args.extract_ligand
def parseArguments ( ) : desc = "It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with." parser = argparse . ArgumentParser ( description = desc ) required_named = parser . add_argument_group ( 'required named arguments' ) required_named . add_argument ( "-i" , "--input_pdb" , type = str , help = "Path to the input PDB complex." ) required_named . add_argument ( "-rc" , "--residue_chain" , type = str , help = "Chain of the residue that has the ligand covalently attached" ) required_named . add_argument ( "-rn" , "--residue_number" , type = str , help = "Residue number of the residue that has the ligand covalently attached" ) required_named . add_argument ( "-o" , "--output_pdb" , type = str , help = "Output PDB path." ) parser . add_argument ( "-lr" , "--ligand_resname" , default = "UNK" , help = "Residue name of the ligand that is covalently attached to the previous residue" ) parser . add_argument ( "-lc" , "--ligand_chain" , default = " " , help = "Chain of the ligand that is covalently attached to the previous residue" ) parser . add_argument ( "-v" , "--verbose" , default = False , action = 'store_true' , help = "Set true to activate all unneded prints." ) parser . add_argument ( "-e" , "--extract_ligand" , default = True , action = 'store_false' , help = "Set true to inactivate the extraction of a ligand in a PDB file." ) args = parser . parse_args ( ) return args . input_pdb , args . residue_chain , args . residue_number , args . output_pdb , args . ligand_resname , args . ligand_chain , args . verbose , args . extract_ligand
Parse the command-line options
Parse the command - line options
"""
        Parse the command-line options
    """