precision.py 文件源码

def command_line(self):

        cpu = multiprocessing.cpu_count()
        cmd = csb.apps.ArgHandler(self.program, __doc__)

        cmd.add_scalar_option('pdb', 'p', str, 'the PDB database (a directory containing all PDB files)', required=True)
        cmd.add_scalar_option('native', 'n', str, 'native structure of the target (PDB file)', required=True)
        cmd.add_scalar_option('chain', 'c', str, 'chain identifier (if not specified, the first chain)', default=None)

        cmd.add_scalar_option('top', 't', int, 'read top N fragments per position', default=25)
        cmd.add_scalar_option('cpu', 'C', int, 'maximum degree of parallelism', default=cpu)
        cmd.add_scalar_option('rmsd', 'r', float, 'RMSD cutoff for precision and coverage', default=1.5)         
        cmd.add_scalar_option('output', 'o', str, 'output directory', default='.')

        cmd.add_boolean_option('save-structures', 's', 'create a PDB file for each fragment, superimposed over the native', default=False)

        cmd.add_positional_argument('library', str, 'Fragment library file in Rosetta NNmake format')

        return cmd