- i -

• i : create_a3b_hbs , hist2d , lactamize
• I : test.T110_numeric
• i : test.T150_PyMOL_Integration , test.T650_LoopsKIC , test_terpenes , vancomycin
• i_omg_atom : create_a3b_hbs
• I_sc : basic::options::OptionKeys::evaluation
• ia_ener : dddm
• icoor_05_2009 : basic::options::OptionKeys::corrections::chemical
• ideal_dat_map : build_restypes
• ideal_helix : basic::options::OptionKeys::mp::benchmark::ideal_helix
• ideal_sugars : basic::options::OptionKeys::score
• 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_rings : basic::options::OptionKeys::rings
• identical_match_dis : basic::options::OptionKeys::willmatch
• idx : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common
• ifs : assign_charges
• ignore_default_docking_task : basic::options::OptionKeys::docking
• ignore_fa_sol_at_positions : basic::options::OptionKeys::hydrate
• 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_list : basic::options::OptionKeys::tcrmodel
• ignore_native_residues_in_rmsd : basic::options::OptionKeys::helical_bundle_predict
• ignore_prediction_residues_in_rmsd : basic::options::OptionKeys::helical_bundle_predict
• ignore_secstruct : basic::options::OptionKeys::rna::denovo
• 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 : create_a3b_hbs , lactamize , oop_scan , test.T200_Scoring , test_nu_angles , torsion_scoring , vancomycin
• ile : evaluate_beta_mutants
• ile_rt : evaluate_beta_mutants
• implicit_hydrogen_radii_set : basic::options::OptionKeys::sasa
• improve_orientation : basic::options::OptionKeys::docking::ligand
• in : basic::options::OptionKeys::in
• inc_weight : rpb
• include_ab_templates : basic::options::OptionKeys::tcrmodel
• include_all_aa : basic::options::OptionKeys::mean_field
• 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::optE , basic::options::OptionKeys::score
• include_lipids : basic::options::OptionKeys::in
• include_loop_ss_chunks : basic::options::OptionKeys::cm::hybridize
• include_lys : local
• include_neighbor_base_stacks : basic::options::OptionKeys::score::rna
• include_only_C_S_in_hsasa : basic::options::OptionKeys::sasa
• include_patches : basic::options::OptionKeys::chemical
• include_path : pilot_app_settings
• 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_vrt : basic::options::OptionKeys::corrections::water
• include_water : basic::options::OptionKeys::packstat
• inclusion_recursion_limit : basic::options::OptionKeys::parser
• increase_chainbreak : basic::options::OptionKeys::jumps
• increase_cycles : basic::options::OptionKeys::abinitio
• increase_vdw_radii : basic::options::OptionKeys::relax::centroid
• increment : create_a3b_hbs
• independent_cycles : basic::options::OptionKeys::remodel::RemodelLoopMover
• indexed_structure_store : basic::options::OptionKeys::indexed_structure_store
• indexoffset : basic::options::OptionKeys::lh::fragpdb
• indices : internal_coordinates , make_comparison
• indole_coo : basic::options::OptionKeys::constel
• info : basic::options::OptionKeys::parser
• info1 : erraser_analysis
• info2 : erraser_analysis
• 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_repack : basic::options::OptionKeys::coupled_moves , basic::options::OptionKeys::ddg
• initial_structures : basic::options::OptionKeys::rna::denovo
• initialize_rigid_body_dofs : basic::options::OptionKeys::symmetry
• inner : test_terpenes
• 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 : build_restypes , cal_NBR_radius , hist2d , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• inp_lig : basic::options::OptionKeys::fingerprint
• inpfile : build_restypes , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• input : gaussian-sampling , make_static_database
• input_ab_scheme : basic::options::OptionKeys::antibody
• input_empty_pose : basic::options::OptionKeys::jd2
• input_etables : basic::options::OptionKeys::score
• input_file : basic::options::OptionKeys::nmr::pcs , basic::options::OptionKeys::nmr::pre , basic::options::OptionKeys::nmr::rdc
• input_files : basic::options::OptionKeys::epr_deer
• input_fv : basic::options::OptionKeys::antibody
• input_pdb : basic::options::OptionKeys::LoopModel , basic::options::OptionKeys::loops , basic::options::OptionKeys::RBSegmentRelax , rna_decompose , rna_rosetta_ready_set , rna_rosetta_to_pdb
• 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::denovo
• inputdata : make_static_database
• inputfile : hist2d
• inputfiles : cal_NBR_radius , hist2d
• ins_begin : basic::options::OptionKeys::loodo
• insert : basic::options::OptionKeys::ufv::insert
• insert_pdb : basic::options::OptionKeys::ufv::insert , chrisk
• insert_segment2_from_pdb : basic::options::OptionKeys::remodel::domainFusion
• insert_segment_from_pdb : basic::options::OptionKeys::remodel::domainFusion
• insres : clean_pdb_keep_ligand
• int : 3d_histogram , app_runner , auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , closure_error , correlation_time , DRRAFTER , drrafter_rna , dummy-distribution , enumerate_junctions , execute , explosion_error , gaussian-sampling , general_RNP_setup_script , get_lowest_scoring_relaxed_models , histogram , make_comparison , percent_subangstrom , pivot_selection , pyrosetta.distributed.cluster.hkdf , relax_starting_structure , run_backbone , run_sidechain , score_vs_rmsd , setup_for_complex_scoring_general
• int64_p : utility::json_spirit
• integration_test : basic::options::OptionKeys::magnesium , basic::options::OptionKeys::stepwise::rna
• INTEGRATION_TEST : basic::options::OptionKeys::testing
• inter_group_neighbors_cutoff : basic::options::OptionKeys::pose_metrics
• inter_subsub_cst : basic::options::OptionKeys::smhybrid
• interaction_graph_threads : basic::options::OptionKeys::multithreading
• 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_distance : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• interface_num : make_symmdef_file_denovo
• interface_only : basic::options::OptionKeys::mh::match
• interface_packing_distance : basic::options::OptionKeys::carbohydrates::glycan_dock
• 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
• interpolation : 3d_histogram , hist2d , plot
• 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
• intlist : kmeans_adaptive_kernel_density_bb_dependent_rotlib , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• 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
• Iox : PREcst , predPRE
• iphold_cen_cycles : basic::options::OptionKeys::docking::ligand
• iphold_fa_cycles : basic::options::OptionKeys::docking::ligand
• ir_rmsd : find_position_matches_using_inverse_rotamers
• Ired : PREcst , predPRE
• Irms : basic::options::OptionKeys::evaluation
• is_1ycr : evaluate_beta_mutants
• is_beta_length : InterfaceStrandFinder
• is_complexes : InterfaceStrandFinder
• is_exposure_radius : InterfaceStrandFinder
• is_known_strands : InterfaceStrandFinder
• is_max_RMSD : InterfaceStrandFinder
• is_maxE : InterfaceStrandFinder
• is_mdm4 : evaluate_beta_mutants
• is_vector_length : InterfaceStrandFinder
• isomaltose : test.C001_Carbohydrates_Demo01
• iss : test.T008_Serialization
• iterate_reset : basic::options::OptionKeys::rdc
• iterate_tol : basic::options::OptionKeys::rdc
• iterate_weights : basic::options::OptionKeys::rdc
• iterations : autocorrelation , basic::options::OptionKeys::ddg , score_vs_time , torsion_vs_time
• iterator : subloop_histogram