- i -

• ideal_COMs() : protocols::forge::remodel
• idealize_combined_pose() : protocols::grafting
• idealize_loop() : protocols::loops
• identify_sheet_id_by_residue_end() : protocols::features::strand_assembly
• import_pose_from_silent_file() : protocols::stepwise::legacy::modeler::rna
• in_list() : protocols::farna
• in_ngbat_sphere() : protocols::neighbor
• in_nrg_graph() : protocols::neighbor
• in_vector() : protocols::stepwise::legacy::modeler
• increment_stageid() : protocols::abinitio::abscript
• inherit_cuts() : protocols::environment
• init() : protocols::init
• init_backrub_mover_with_options() : protocols::backrub
• init_rotamers_centroids() : protocols::make_rot_lib
• init_str_selector() : protocols::environment
• initialize_atomtype_2_probe_radius_map() : protocols::match
• initialize_attachment_type_name() : protocols::stepwise::monte_carlo
• initialize_ga_randomizer_from_entity_task() : protocols::pack_daemon
• initialize_group_list() : protocols::noesy_assign
• initialize_input_streams() : protocols::stepwise::modeler::protein
• initialize_input_streams_with_residue_info() : protocols::stepwise::modeler::protein
• initialize_move_type_name() : protocols::stepwise::monte_carlo
• initialize_native_and_align_pose() : protocols::stepwise::setup
• initialize_o2prime_pack_scorefxn() : protocols::stepwise::modeler
• initialize_pack_scorefxn() : protocols::stepwise::modeler
• initialize_pose_and_other_poses_from_command_line() : protocols::stepwise::setup
• initialize_sample_scorefxn() : protocols::stepwise::modeler
• initialize_ss() : protocols::comparative_modeling
• initialize_stub() : protocols::stepwise::sampler::rigid_body
• initialize_task_from_entity_resfile_and_secondary_resfile() : protocols::pack_daemon
• initialize_xyz_parameters() : protocols::stepwise::modeler::rna::rigid_body
• insert_cdr_into_antibody() : protocols::antibody::design
• insert_closed_range() : protocols::forge::methods
• insert_fragment() : protocols::frags
• insert_half_open_range() : protocols::forge::methods
• insert_point_mut_filter_vals() : protocols::design_opt , protocols::matdes
• insert_pose_into_pose() : protocols::grafting
• insert_random_fragments_in_flexible_protein_regions() : protocols::frags
• instantiate_any_virtual_sugars() : protocols::stepwise::modeler::rna::sugar
• interface_builder_tracer() : protocols::ligand_docking
• INTERFACE_CALC() : protocols::anchored_design
• interface_distance_tracer() : protocols::ligand_docking::ligand_options
• InterfaceScoreCalculator_tracer() : protocols::ligand_docking
• interpolation_type_enum_to_string() : protocols::canonical_sampling
• interpolation_type_string_to_enum() : protocols::canonical_sampling
• interval_to_loop() : protocols::forge::methods
• intervals_to_confirmation_loops() : protocols::forge::methods
• intervals_to_loops() : protocols::forge::methods
• introduce_datamap_cuts() : protocols::environment
• invalidate_residues_spanning_cuts() : protocols::medal
• invert_include_residues() : protocols::evaluation
• involved_in_phosphate_torsion() : protocols::farna
• invstub() : protocols::sic_dock
• irt() : protocols::motifs
• is_blank_seq() : protocols::stepwise::modeler::rna::helix
• is_catalytic_seqpos() : protocols::enzdes::enzutil
• is_close_chain_break() : protocols::stepwise::legacy::modeler::protein
• is_cutpoint_closed() : protocols::stepwise::modeler
• is_d_chiral() : protocols::simple_moves::chiral
• is_digit() : protocols::enzdes::enzutil
• is_in_list() : protocols::generalized_kinematic_closure
• is_interface_vector() : protocols::ligand_docking::ligand_options
• is_l_chiral() : protocols::simple_moves::chiral
• is_lowercase_letter() : protocols::enzdes::enzutil
• is_nonempty_input_silent_file() : protocols::stepwise::legacy::modeler::rna
• is_not_neighbor_to_rigid() : protocols::topology_broker
• is_num_in_list() : protocols::farna
• is_part() : protocols::seeded_abinitio , protocols::toolbox::task_operations
• is_protein() : protocols::stepwise::modeler
• is_residues_in_contact() : protocols::stepwise::modeler::rna
• is_same_sugar_pucker() : protocols::stepwise::legacy::modeler::rna
• is_scofx_cstfied() : protocols::enzdes::enzutil
• is_sugar_virtual() : protocols::stepwise::modeler::rna::sugar
• is_this_strand_at_edge() : protocols::features::strand_assembly
• is_this_strand_at_edge_by_looking_db() : protocols::features::strand_assembly
• is_uppercase_letter() : protocols::enzdes::enzutil
• is_valid_backbone() : protocols::loophash
• is_virtual_base() : protocols::stepwise::modeler::rna
• isDigit() : protocols::sparta
• isDirExists() : protocols::sparta
• isSpace() : protocols::sparta
• itoa() : protocols::sparta