- i -

• I_sc : basic::options::OptionKeys::evaluation
• icoor_05_2009 : basic::options::OptionKeys::corrections::chemical
• 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_h3_stems_before_modeling : basic::options::OptionKeys::antibody
• identical_match_dis : basic::options::OptionKeys::crossmatch , basic::options::OptionKeys::willmatch
• ignore_default_docking_task : basic::options::OptionKeys::docking
• ignore_improper_res : basic::options::OptionKeys::bbg
• ignore_io_errors : basic::options::OptionKeys::mh
• ignore_ligand_chi : basic::options::OptionKeys::packing
• ignore_missing_bondangle_params : basic::options::OptionKeys::MM
• ignore_sequence_seperation : basic::options::OptionKeys::fold_cst
• ignore_unrecognized_res : basic::options::OptionKeys::in
• ignore_waters : basic::options::OptionKeys::in
• ignore_zero_occupancy : basic::options::OptionKeys::run
• implicit_hydrogen_radii_set : basic::options::OptionKeys::sasa
• improve_orientation : basic::options::OptionKeys::docking::ligand
• in : basic::options::OptionKeys::in
• include_catres_in_interface_detection : basic::options::OptionKeys::enzdes
• include_dna_potentials : basic::options::OptionKeys::dna::design::specificity
• include_hydrogens : basic::options::OptionKeys::fingerprint
• include_hydrogens_explicitly : basic::options::OptionKeys::sasa
• include_lipids : basic::options::OptionKeys::in
• include_lips : basic::options::OptionKeys::membrane
• 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
• increase_chainbreak : basic::options::OptionKeys::jumps
• increase_constraints : basic::options::OptionKeys::constraints
• increase_cycles : basic::options::OptionKeys::abinitio
• increase_vdw_radii : basic::options::OptionKeys::relax::centroid
• independent_cycles : basic::options::OptionKeys::remodel::RemodelLoopMover
• indexoffset : basic::options::OptionKeys::lh::fragpdb
• inform : basic::options
• init_was_called : basic
• initial_dist_cutoff : basic::options::OptionKeys::abinitio::star
• initial_perturb : basic::options::OptionKeys::antibody::design
• initial_repack : basic::options::OptionKeys::ddg
• initialize_rigid_body_dofs : basic::options::OptionKeys::symmetry
• inner_iteration_scale : basic::options::OptionKeys::flexpack::annealer
• inneriterations_scaling : basic::options::OptionKeys::packing
• inout : basic::options::OptionKeys::inout
• input_etables : basic::options::OptionKeys::score
• input_fv : basic::options::OptionKeys::antibody
• input_motifs : basic::options::OptionKeys::mh
• input_pdb : basic::options::OptionKeys::LoopModel , basic::options::OptionKeys::loops , basic::options::OptionKeys::RBSegmentRelax , basic::options::OptionKeys::SSrbrelax
• 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
• insert : basic::options::OptionKeys::ufv::insert
• insert_pdb : basic::options::OptionKeys::ufv::insert
• insert_segment_from_pdb : basic::options::OptionKeys::remodel::domainFusion
• instructions : basic::options::OptionKeys::antibody::design
• int64_p : utility::json_spirit
• integration_test : basic::options::OptionKeys::stepwise::rna
• inter_group_neighbors_cutoff : basic::options::OptionKeys::pose_metrics
• inter_subsub_cst : basic::options::OptionKeys::smhybrid
• interactive : basic::options::OptionKeys::run
• interface_cutoff : basic::options::OptionKeys::pepspec , basic::options::OptionKeys::pose_metrics
• interface_ddg : basic::options::OptionKeys::ddg
• interface_dis : basic::options::OptionKeys::antibody::design
• interface_size : basic::options::OptionKeys::crossmatch , basic::options::OptionKeys::willmatch
• 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
• intrares_elec_correction_scale : basic::options::OptionKeys::score
• 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
• inversion_subs : basic::options::OptionKeys::smhybrid
• invrate_jump_move : basic::options::OptionKeys::jumps
• Irms : basic::options::OptionKeys::evaluation
• iterate_reset : basic::options::OptionKeys::rdc
• iterate_tol : basic::options::OptionKeys::rdc
• iterate_weights : basic::options::OptionKeys::rdc
• iterations : basic::options::OptionKeys::ddg , basic::options::OptionKeys::dna::design
• IUPAC : basic::options::OptionKeys::run