- i -

• ia_ener : dddm
• ifs : assign_charges
• ignore_chain : toolbox::make_rna_rosetta_ready
• ignorechain : clean_pdb_keep_ligand
• ii : test::T200_Scoring
• include_arg : local
• include_asp : local
• include_glu : local
• include_lys : local
• IncludeDict : BuildBindings
• IncludeDictNew : BuildBindings
• inform : basic::options
• init_temp : loops , loops_kic , test::T650_LoopsKIC
• init_temp_high : demo::D080_Loop_modeling
• init_temp_low : demo::D080_Loop_modeling
• init_was_called : basic
• initial_pose : app::delta_score_per_mutation
• inner_cycles : loops , loops_kic , test::T650_LoopsKIC
• inner_cycles_high : demo::D080_Loop_modeling
• inner_cycles_low : demo::D080_Loop_modeling
• inner_num : dddm
• input : app::surface_docking::surface_docking
• input_class : app::pyrosetta_toolkit::window_modules::ligand_ncaa_ptm_manager::ligand_ncaa_ptm_manager
• insres : clean_pdb_keep_ligand
• int64_p : utility::json_spirit
• interface_cutoff : demo::D090_Ala_scan
• interface_num : make_symmdef_file_denovo
• interfaces : make_symmdef_file_denovo
• ISRELEASED : setup