- i -

• I_sc : basic::options::OptionKeys::evaluation
• ia_ener : dddm
• icoor_05_2009 : basic::options::OptionKeys::corrections::chemical
• ideal_helix : basic::options::OptionKeys::mp::benchmark::ideal_helix
• idealize : basic::options::OptionKeys::mh::harvest , basic::options::OptionKeys::relax::range
• idealize_after_loop_close : basic::options::OptionKeys::loops
• idealize_before_loop_close : basic::options::OptionKeys::loops
• idealize_before_protocol : basic::options::OptionKeys::run
• idealize_final_structures : basic::options::OptionKeys::cluster
• idealize_graft_cdrs : basic::options::OptionKeys::antibody::design
• idealize_h3_stems_before_modeling : basic::options::OptionKeys::antibody
• idealize_rings : basic::options::OptionKeys::rings
• identical_match_dis : basic::options::OptionKeys::willmatch
• ifs : assign_charges
• ignore_chain : pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• ignore_default_docking_task : basic::options::OptionKeys::docking
• ignore_full_res_output : basic::options::OptionKeys::carbohydrates::clash_check
• ignore_hydrogens : basic::options::OptionKeys::carbohydrates::clash_check
• ignore_improper_res : basic::options::OptionKeys::bbg
• ignore_io_errors : basic::options::OptionKeys::mh
• ignore_ligand_chi : basic::options::OptionKeys::packing
• ignore_secstruct : basic::options::OptionKeys::rna::farna
• ignore_sequence_seperation : basic::options::OptionKeys::fold_cst
• ignore_terminal_ss_elements : basic::options::OptionKeys::score
• ignore_unrecognized_res : basic::options::OptionKeys::in
• ignore_waters : basic::options::OptionKeys::in
• ignore_zero_occupancy : basic::options::OptionKeys::run
• ignorechain : clean_pdb_keep_ligand
• ii : test::T200_Scoring
• implicit_hydrogen_radii_set : basic::options::OptionKeys::sasa
• improve_orientation : basic::options::OptionKeys::docking::ligand
• in : basic::options::OptionKeys::in
• include_arg : local
• include_asp : local
• include_catres_in_interface_detection : basic::options::OptionKeys::enzdes
• include_current : basic::options::OptionKeys::remodel::design
• include_dna_potentials : basic::options::OptionKeys::dna::design::specificity
• include_extrashell_to_set_origin : basic::options::OptionKeys::fingerprint
• include_glu : local
• include_hydrogens : basic::options::OptionKeys::fingerprint
• include_hydrogens_explicitly : basic::options::OptionKeys::sasa
• include_intra_res_protein : basic::options::OptionKeys::score
• include_lipids : basic::options::OptionKeys::in
• include_lys : local
• include_neighbor_base_stacks : basic::options::OptionKeys::score
• include_only_C_S_in_hsasa : basic::options::OptionKeys::sasa
• include_patches : basic::options::OptionKeys::chemical
• include_probe_radius_in_atom_radii : basic::options::OptionKeys::sasa
• include_stage5 : basic::options::OptionKeys::abinitio
• include_sugars : basic::options::OptionKeys::in
• include_surfaces : basic::options::OptionKeys::in
• include_water : basic::options::OptionKeys::packstat
• IncludeDict : BuildBindings
• IncludeDictNew : BuildBindings
• increase_chainbreak : basic::options::OptionKeys::jumps
• increase_cycles : basic::options::OptionKeys::abinitio
• increase_vdw_radii : basic::options::OptionKeys::relax::centroid
• independent_cycles : basic::options::OptionKeys::remodel::RemodelLoopMover
• indexed_structure_store : basic::options::OptionKeys::indexed_structure_store
• indexoffset : basic::options::OptionKeys::lh::fragpdb
• 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_dist_cutoff : basic::options::OptionKeys::abinitio::star
• initial_pack : basic::options::OptionKeys::backrub
• initial_pose : app::delta_score_per_mutation
• initial_repack : basic::options::OptionKeys::ddg
• initialize_rigid_body_dofs : basic::options::OptionKeys::symmetry
• inner_cycle_rounds : basic::options::OptionKeys::antibody::design
• inner_cycles : loops , loops_kic , test::T650_LoopsKIC
• inner_cycles_high : demo::D080_Loop_modeling
• inner_cycles_low : demo::D080_Loop_modeling
• inner_iteration_scale : basic::options::OptionKeys::flexpack::annealer
• inner_kt : basic::options::OptionKeys::antibody::design
• inner_num : dddm
• inneriterations_scaling : basic::options::OptionKeys::packing
• inout : basic::options::OptionKeys::inout
• inp_lig : basic::options::OptionKeys::fingerprint
• input : app::surface_docking::surface_docking
• input_class : app::pyrosetta_toolkit::window_modules::ligand_ncaa_ptm_manager::ligand_ncaa_ptm_manager
• input_etables : basic::options::OptionKeys::score
• input_fv : basic::options::OptionKeys::antibody
• input_pdb : basic::options::OptionKeys::LoopModel , basic::options::OptionKeys::loops , basic::options::OptionKeys::RBSegmentRelax
• input_res : basic::options::OptionKeys::in::file
• input_res1 : basic::options::OptionKeys::stepwise
• input_res2 : basic::options::OptionKeys::stepwise
• input_score_filter : basic::options::OptionKeys::cluster
• input_seq : basic::options::OptionKeys::pepspec
• input_silent_res : basic::options::OptionKeys::rna::farna
• ins_begin : basic::options::OptionKeys::loodo
• insert : basic::options::OptionKeys::ufv::insert
• insert_disulfide_constraint_weight : basic::options::OptionKeys::run
• insert_pdb : basic::options::OptionKeys::ufv::insert
• insert_segment2_from_pdb : basic::options::OptionKeys::remodel::domainFusion
• insert_segment_from_pdb : basic::options::OptionKeys::remodel::domainFusion
• insres : clean_pdb_keep_ligand
• int64_p : utility::json_spirit
• integration_test : basic::options::OptionKeys::magnesium , basic::options::OptionKeys::stepwise::rna
• inter_group_neighbors_cutoff : basic::options::OptionKeys::pose_metrics
• inter_subsub_cst : basic::options::OptionKeys::smhybrid
• interaction_shell : basic::options::OptionKeys::cryst
• interactive : basic::options::OptionKeys::run
• interface_cutoff : basic::options::OptionKeys::pepspec , basic::options::OptionKeys::pose_metrics , demo::D090_Ala_scan
• interface_ddg : basic::options::OptionKeys::ddg
• interface_dis : basic::options::OptionKeys::antibody::design
• interface_num : make_symmdef_file_denovo
• interface_only : basic::options::OptionKeys::mh::match
• interface_size : basic::options::OptionKeys::willmatch
• interfaces : make_symmdef_file_denovo
• intermediate_scorefiles : basic::options::OptionKeys::run
• intermediate_structures : basic::options::OptionKeys::run
• intermedrelax : basic::options::OptionKeys::loops
• intermolecular_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• interval : basic::options::OptionKeys::ms::checkpoint
• interval_data_dump : basic::options::OptionKeys::canonical_sampling::sampling
• interval_pose_dump : basic::options::OptionKeys::canonical_sampling::sampling
• intf : basic::options::OptionKeys::intf
• inv_kin_lig_loop_design_filename : basic::options::OptionKeys::murphp
• inv_kT_nataa : basic::options::OptionKeys::optE
• inv_kT_natrot : basic::options::OptionKeys::optE
• inv_kT_natstruct : basic::options::OptionKeys::optE
• invrate_jump_move : basic::options::OptionKeys::jumps
• Irms : basic::options::OptionKeys::evaluation
• ISRELEASED : setup
• iter : basic::options::OptionKeys::mp::mutate_relax
• iterate_reset : basic::options::OptionKeys::rdc
• iterate_tol : basic::options::OptionKeys::rdc
• iterate_weights : basic::options::OptionKeys::rdc
• iterations : basic::options::OptionKeys::ddg