yapf

      out_pdbqt = os.path.join(out_dir, "%s_docked.pdbqt" % ligand_name)

      logger.info("About to call Vina")

      if platform.system() == 'Windows':

        args = [self.vina_cmd, "--config", conf_file, "--log", log_file, "--out", out_pdbqt]

        args = [

            self.vina_cmd, "--config", conf_file, "--log", log_file, "--out",

            out_pdbqt

        ]

      else:

        # I'm not sure why specifying the args as a list fails on other platforms,

        # but for some reason it only works if I pass it as a string.

        args = "%s --config %s --log %s --out %s" % (self.vina_cmd, conf_file, log_file, out_pdbqt)

        args = "%s --config %s --log %s --out %s" % (self.vina_cmd, conf_file,

                                                     log_file, out_pdbqt)

      call(args, shell=True)

      ligands, scores = vina_utils.load_docked_ligands(out_pdbqt)

      docked_complexes += [(protein_mol[1], ligand) for ligand in ligands]