ribolands/pathfinder.py
def parse_model_details(parser):
    """ ViennaRNA Model Details Argument Parser.  """
    model = parser.add_argument_group('ViennaRNA model details')

    model.add_argument("-T", "--temp", type = float, default = 37.0, 
        metavar = '<flt>',
        help = 'Rescale energy parameters to a temperature of temp C.')

    model.add_argument("-4", "--noTetra", action = "store_true",
        help = """Do not include special tabulated stabilizing 
        energies for tri-, tetra- and hexaloop hairpins.""")

    model.add_argument("-d", "--dangles", type = int, default = 2, 
        metavar = '<int>',
        help = """How to treat dangling end energies for bases adjacent to
        helices in free ends and multi-loops.""")

    model.add_argument("--noGU", action = "store_true",
        help = 'Do not allow GU/GT pairs.')

    model.add_argument("--noClosingGU", action = "store_true",
        help = 'Do not allow GU/GT pairs at the end of helices.')

    model.add_argument("-P", "--paramFile", action = "store", default = None,
        metavar = '<str>',
        help = """Read energy parameters from paramfile, instead of 
        using the default parameter set.""")
 ViennaRNA Model Details Argument Parser.  
ViennaRNA Model Details Argument Parser.
ViennaRNA Model Details Argument Parser .
def parse_model_details(parser):
    model = parser.add_argument_group('ViennaRNA model details')
    model.add_argument("-T", "--temp", type = float, default = 37.0, 
        metavar = '<flt>',
        help = 'Rescale energy parameters to a temperature of temp C.')
    model.add_argument("-4", "--noTetra", action = "store_true",
        help = """Do not include special tabulated stabilizing 
        energies for tri-, tetra- and hexaloop hairpins.""")
    model.add_argument("-d", "--dangles", type = int, default = 2, 
        metavar = '<int>',
        help = """How to treat dangling end energies for bases adjacent to
        helices in free ends and multi-loops.""")
    model.add_argument("--noGU", action = "store_true",
        help = 'Do not allow GU/GT pairs.')
    model.add_argument("--noClosingGU", action = "store_true",
        help = 'Do not allow GU/GT pairs at the end of helices.')
    model.add_argument("-P", "--paramFile", action = "store", default = None,
        metavar = '<str>',
        help = """Read energy parameters from paramfile, instead of 
        using the default parameter set.""")
def parse_model_details ( parser ) : model = parser . add_argument_group ( 'ViennaRNA model details' ) model . add_argument ( "-T" , "--temp" , type = float , default = 37.0 , metavar = '<flt>' , help = 'Rescale energy parameters to a temperature of temp C.' ) model . add_argument ( "-4" , "--noTetra" , action = "store_true" , help = """Do not include special tabulated stabilizing 
        energies for tri-, tetra- and hexaloop hairpins.""" ) model . add_argument ( "-d" , "--dangles" , type = int , default = 2 , metavar = '<int>' , help = """How to treat dangling end energies for bases adjacent to
        helices in free ends and multi-loops.""" ) model . add_argument ( "--noGU" , action = "store_true" , help = 'Do not allow GU/GT pairs.' ) model . add_argument ( "--noClosingGU" , action = "store_true" , help = 'Do not allow GU/GT pairs at the end of helices.' ) model . add_argument ( "-P" , "--paramFile" , action = "store" , default = None , metavar = '<str>' , help = """Read energy parameters from paramfile, instead of 
        using the default parameter set.""" )
ViennaRNA Model Details Argument Parser.
ViennaRNA Model Details Argument Parser .
""" ViennaRNA Model Details Argument Parser.  """
parser