frag_pele/Analysis/backtrackConnectivity.py
def parse_arguments():
    """
        Parse the command-line options

        :returns: str, str, str --  path to file to backtrack,
            output path where to write the files, name of the files
    """
    desc = "Adds the connectivity information to a trajectory file that does not have it.\n"
    parser = argparse.ArgumentParser(description=desc)
    parser.add_argument("pathway", type=str, help="Trajectory file with the backtracked pathway.")
    parser.add_argument("pdb_with_connects", type=str, help="PDB of the final structure prepared. Must contain"
                                                            " CONNECTS section. Remember to not delete water molecules!")
    parser.add_argument("--ligand_chain", type=str, default="L", help="Chain of the ligand.")
    parser.add_argument("-o", type=str, default=None, help="Output file with the new trajectory.")

    args = parser.parse_args()
    return args.pathway, args.pdb_with_connects, args.ligand_chain, args.o

        Parse the command-line options

        :returns: str, str, str --  path to file to backtrack,
            output path where to write the files, name of the files
    
Parse the command-line options
Parse the command - line options
def parse_arguments():
    desc = "Adds the connectivity information to a trajectory file that does not have it.\n"
    parser = argparse.ArgumentParser(description=desc)
    parser.add_argument("pathway", type=str, help="Trajectory file with the backtracked pathway.")
    parser.add_argument("pdb_with_connects", type=str, help="PDB of the final structure prepared. Must contain"
                                                            " CONNECTS section. Remember to not delete water molecules!")
    parser.add_argument("--ligand_chain", type=str, default="L", help="Chain of the ligand.")
    parser.add_argument("-o", type=str, default=None, help="Output file with the new trajectory.")
    args = parser.parse_args()
    return args.pathway, args.pdb_with_connects, args.ligand_chain, args.o
def parse_arguments ( ) : desc = "Adds the connectivity information to a trajectory file that does not have it.\n" parser = argparse . ArgumentParser ( description = desc ) parser . add_argument ( "pathway" , type = str , help = "Trajectory file with the backtracked pathway." ) parser . add_argument ( "pdb_with_connects" , type = str , help = "PDB of the final structure prepared. Must contain" " CONNECTS section. Remember to not delete water molecules!" ) parser . add_argument ( "--ligand_chain" , type = str , default = "L" , help = "Chain of the ligand." ) parser . add_argument ( "-o" , type = str , default = None , help = "Output file with the new trajectory." ) args = parser . parse_args ( ) return args . pathway , args . pdb_with_connects , args . ligand_chain , args . o
Parse the command-line options
Parse the command - line options
"""
        Parse the command-line options

        :returns: str, str, str --  path to file to backtrack,
            output path where to write the files, name of the files
    """
str, str, str --  path to file to backtrack,
output path where to write the files, name of the files
str str str -- path to file to backtrack output path where to write the files name of the files