- i -

• ideal_COMs() : protocols::forge::remodel
• idealize_combined_pose() : protocols::grafting
• idealize_hydrogens() : core::conformation
• idealize_last_n_glycans_in_pose() : core::pose::carbohydrates
• idealize_loop() : protocols::loops
• idealize_position() : core::conformation
• identify_chunks() : protocols::rna::movers
• identify_hbonds_1way() : core::scoring::hbonds
• identify_hbonds_1way_AHdist() : core::scoring::hbonds
• identify_hbonds_1way_membrane() : core::scoring::hbonds
• identify_intra_res_hbonds() : core::scoring::hbonds
• identify_sheet_id_by_residue_end() : protocols::features::strand_assembly
• ignore_template() : protocols::tcr
• import_pose_from_silent_file() : protocols::stepwise::legacy::modeler::rna
• improper_build() : core::conformation
• in_archive_rank_() : protocols::jd2::archive
• in_file_buf_rank_() : protocols::jd2::archive
• in_master_rank_() : protocols::jd2::archive
• in_min_client_rank_() : protocols::jd2::archive
• in_ngbat_sphere() : protocols::neighbor
• in_nrg_graph() : protocols::neighbor
• increase_rotamer_precision() : core::pack::dunbrack
• increment_dihedrals() : protocols::ncbb
• increment_hbond_energy() : core::scoring::hbonds
• increment_npd_hbond_energy() : core::scoring::hbonds
• increment_stageid() : protocols::abinitio::abscript
• ind_remodel_tcr_cdr_loops() : protocols::tcr
• indel_motif() : protocols::evolution::AlignmentCleanerTools
• indel_motif_seq_id() : protocols::evolution::AlignmentCleanerTools
• index_if() : protocols::indexed_structure_store
• INFINITE_SEPARATION() : core::scoring::etable::count_pair
• info_to_rank() : protocols::ligand_docking
• inherit_cuts() : protocols::environment
• init() : core::init , protocols::init
• init_backrub_mover_with_options() : protocols::backrub
• init_beta_correction() : core::init
• init_beta_july15_correction() : core::init
• init_beta_nov16_correction() : core::init
• init_common_options() : protocols::ncbb
• init_complex_options() : core::init
• init_correct_correction() : core::init
• init_crash_reporter() : core::init
• init_crystal_refinement_correction() : core::init
• init_dna_correction() : core::init
• init_facts_correction() : core::init
• init_gen_potential_settings() : core::init
• init_hbond_sp2_correction() : core::init
• init_mpi() : core::init
• init_node_info() : core::pack::hbonds
• init_nonideal_correction() : core::init
• init_options() : core::init
• init_packing_score_discrim() : core::scoring::packstat
• init_packing_score_respred() : core::scoring::packstat
• init_paths() : core::init
• init_pre_beta_nov15_etable() : core::init
• init_profiling() : core::init
• init_resources() : core::init
• init_restore_score12prime() : core::init
• init_revert_to_pre_talaris_2013_mistake() : core::init
• init_revert_to_talaris() : core::init
• init_score_function_corrections() : core::init
• init_shapovalov_lib_fixes_enable_correction() : core::init
• init_source_revision() : core::init
• init_spades_score_function_correction() : core::init
• init_str_selector() : protocols::environment
• init_tracers() : core::init
• initial_pose_for_residues() : protocols::indexed_structure_store
• InitialAntiCausalCoefficient() : core::scoring::electron_density::SplineInterp
• InitialCausalCoefficient() : core::scoring::electron_density::SplineInterp
• initialize_and_read_srsrdl() : core::pack::dunbrack
• initialize_atomid_map() : core::pose
• initialize_AtomID_Map() : core::scoring::packing
• initialize_atomid_map_AtomID() : core::pose
• initialize_atomid_map_heavy_only() : core::pose
• initialize_atoms_for_which_we_need_new_dofs() : core::pose::rna
• initialize_atomtype_2_probe_radius_map() : protocols::match
• initialize_attachment_type_name() : protocols::stepwise::monte_carlo::mover
• initialize_core_id_globals() : core::id
• initialize_cpdata_for_atom() : core::scoring::trie
• initialize_disulfide_bonds() : core::pose
• initialize_dof_id_map() : core::pose
• initialize_full_model_parameter_type_name() : core::pose::full_model_info
• initialize_ga_randomizer_from_entity_task() : protocols::pack_daemon
• initialize_group_list() : protocols::noesy_assign
• initialize_HBEval_lookup() : core::scoring::hbonds
• initialize_hbs() : core::pose::ncbb
• initialize_input_streams() : protocols::stepwise::modeler::protein
• initialize_input_streams_with_residue_info() : protocols::stepwise::modeler::protein
• initialize_jump_sampler() : protocols::recces::sampler
• initialize_move_type_name() : protocols::stepwise::monte_carlo::mover
• initialize_native_and_align_pose() : core::import_pose
• initialize_ncbbs() : core::pose::ncbb
• initialize_o2prime_pack_scorefxn() : protocols::stepwise::modeler
• initialize_offsets() : protocols::multistage_rosetta_scripts::cluster
• initialize_oops() : core::pose::ncbb
• initialize_pack_scorefxn() : protocols::stepwise::modeler
• initialize_parameters() : core::pose::full_model_info
• initialize_pose_and_other_poses_from_command_line() : core::import_pose
• initialize_pose_and_other_poses_from_options() : core::import_pose
• initialize_pose_and_other_poses_from_options_and_input_poses() : core::import_pose
• initialize_sample_scorefxn() : protocols::stepwise::modeler
• initialize_sampler() : protocols::recces::sampler
• initialize_srsrdl() : core::pack::dunbrack
• initialize_ss() : protocols::comparative_modeling
• initialize_stub() : protocols::toolbox::rigid_body
• initialize_tag_is_done() : core::io::silent
• initialize_task_from_entity_resfile_and_secondary_resfile() : protocols::pack_daemon
• initialize_temperatures() : core::pack
• initialize_temperatures_off_rotamer_pack() : core::pack
• initialize_template_db_files() : protocols::tcr
• initialize_template_ignore_list() : protocols::tcr
• initialize_thermal_sampler() : protocols::recces::sampler
• initialize_xyz_parameters() : protocols::stepwise::modeler::rna::rigid_body
• inline_intraresidue_atom_pair_energy() : core::scoring
• inline_residue_atom_pair_energy() : core::scoring
• inline_residue_atom_pair_energy_backbone_backbone() : core::scoring
• inline_residue_atom_pair_energy_sidechain_backbone() : core::scoring
• inline_residue_atom_pair_energy_sidechain_sidechain() : core::scoring
• inline_residue_atom_pair_energy_sidechain_whole() : core::scoring
• input_legrand_sasa_dats() : core::scoring::sasa
• input_pdb_files_from_command_line() : protocols::jd2
• input_sasa_dats() : core::scoring , core::scoring::packstat::old
• 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_ideal_bonds_at_polymer_junction() : core::conformation
• insert_ideal_mainchain_bonds() : core::conformation
• insert_mg() : protocols::denovo_design::components
• insert_peptide_edges() : protocols::denovo_design
• 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
• insert_residue_into_atom_tree() : core::conformation
• inside_boundaries() : core::membrane
• inside_polygon() : core::membrane
• instantiate_any_virtual_sugars() : protocols::stepwise::modeler::rna::sugar
• instantiate_water_at_octahedral_vertex() : protocols::magnesium
• interface_builder_tracer() : protocols::ligand_docking
• INTERFACE_CALC() : protocols::anchored_design
• interface_distance_tracer() : protocols::ligand_docking::ligand_options
• interp3() : core::scoring::electron_density::SplineInterp
• interp4() : core::scoring::electron_density::SplineInterp
• interp_dspline() : core::scoring::electron_density
• interp_linear() : core::scoring::electron_density
• interp_spline() : core::scoring::electron_density
• interpolate_polylinear_by_value() : core::pack::dunbrack
• interpolate_polylinear_by_value_angles_degrees() : core::pack::dunbrack
• interpolate_polylinear_by_value_angles_degrees< 1 >() : core::pack::dunbrack
• interpolate_polylinear_by_value_noangles() : core::pack::dunbrack
• interpolate_rotamers() : core::pack::dunbrack
• interpolate_sampled_to_grid() : core::scoring::fiber_diffraction
• interpolate_value_and_deriv() : core::scoring
• interpolation_type_enum_to_string() : protocols::canonical_sampling
• interpolation_type_string_to_enum() : protocols::canonical_sampling
• intersect() : core::membrane
• interval_to_loop() : protocols::forge::methods
• intervals_to_confirmation_loops() : protocols::forge::methods
• intervals_to_loops() : protocols::forge::methods
• intracomponent_contact() : core::pose::symmetry
• introduce_datamap_cuts() : protocols::environment
• inv_virtual_type_for_conf() : core::conformation
• invalid_hhpair() : protocols::denovo_design::architects
• invalidate_residues_spanning_cuts() : protocols::medal
• inverse_rt6() : core::scoring::motif
• invert_exclude_residues() : core::scoring
• invert_include_residues() : protocols::evaluation
• involved_in_phosphate_torsion() : core::import_pose , protocols::rna::denovo
• invstub() : protocols::sic_dock
• iota_torsion_pre_methylene_post_methylene_para_aramid() : core::id
• ipow() : protocols::ligand_docking::ga_ligand_dock
• iprod() : core::scoring
• irt() : protocols::motifs
• is_aa_name_unknown() : core::chemical
• is_aromatic() : core::scoring::constraints
• is_atom_axial_or_equatorial() : core::conformation
• is_atom_axial_or_equatorial_to_ring() : core::chemical::rings , core::conformation , core::pose
• is_atom_bin_in_range() : core::pose::rna
• is_base_2() : core::scoring::elec
• is_base_phosphate_atom_pair() : core::chemical::rna
• is_blank_seq() : core::import_pose
• is_canonical() : protocols::cyclic_peptide_predict
• is_canonical_beta3_aa() : core::chemical
• is_canonical_D_aa() : core::chemical
• is_canonical_L_aa_excluding_gly() : core::chemical
• is_canonical_L_aa_or_gly() : core::chemical
• is_catalytic_seqpos() : protocols::enzdes::enzutil
• is_close_chain_break() : protocols::stepwise::legacy::modeler::protein
• is_cloud_integration_enabled() : protocols::network
• is_collinear() : core::kinematics::tree
• is_connected() : core::io::pose_from_sfr
• is_cutpoint_closed() : protocols::stepwise::modeler
• is_cutpoint_closed_atom() : core::pose::rna
• is_cutpoint_closed_by_atom_name() : core::pose::rna
• is_cutpoint_closed_torsion() : core::pose::rna
• is_cutpoint_open() : core::pose::rna
• is_disulfide_bond() : core::conformation
• is_glycosidic_omega2_torsion() : core::pose::carbohydrates
• is_glycosidic_omega3_torsion() : core::pose::carbohydrates
• is_glycosidic_omega_torsion() : core::conformation::carbohydrates , core::pose::carbohydrates
• is_glycosidic_phi_torsion() : core::conformation::carbohydrates , core::pose::carbohydrates
• is_glycosidic_psi_torsion() : core::conformation::carbohydrates , core::pose::carbohydrates
• is_glycosidic_torsion() : core::pose::carbohydrates
• is_H3_rama_kinked() : protocols::antibody
• is_heavyatom() : core::scoring
• is_ideal_pose() : core::pose
• is_ideal_position() : core::conformation , core::pose
• is_identical_rotamer() : protocols::splice
• is_in_bondAtomList() : core::io::mmtf
• is_in_list() : protocols::generalized_kinematic_closure
• is_inside() : protocols::hydrate
• is_interface_vector() : protocols::ligand_docking::ligand_options
• is_jump_intracomponent() : core::conformation::symmetry
• is_ligand() : protocols::magnesium
• is_ligand_heavyatom() : core::scoring
• is_ligand_heavyatom_residues() : core::scoring
• is_lower_cutpoint() : core::scoring::methods
• is_lower_terminus() : core::pose
• is_mainchain_torsion_also_ring_torsion() : core::chemical
• is_membrane_fixed() : protocols::membrane
• is_membrane_moveable_by_itself() : protocols::membrane
• is_mirror_symmetric() : core::conformation::symmetry , core::pose::symmetry
• is_multicomponent() : core::pose::symmetry
• is_nbr_atom() : core::scoring
• is_non_peptide_heavy_atom() : core::scoring
• is_nonempty_input_silent_file() : protocols::stepwise::legacy::modeler::rna
• is_not_neighbor_to_rigid() : protocols::topology_broker
• is_num_in_list() : protocols::rna::denovo
• is_orthonormal() : core::scoring::dna
• is_part() : protocols::seeded_abinitio
• is_phosphate_2() : core::scoring::elec
• is_polar_hydrogen() : core::scoring::rna::chemical_shift
• is_polymer_heavyatom() : core::scoring
• is_position_conserved_residue() : core::pose
• is_protein() : protocols::stepwise::modeler
• is_protein_backbone() : core::scoring
• is_protein_backbone_including_O() : core::scoring
• is_protein_CA() : core::scoring
• is_protein_CA_or_CB() : core::scoring
• is_protein_CA_or_equiv() : core::scoring
• is_protein_sidechain_heavyatom() : core::scoring
• is_pseudoresidue() : core::io::serialization
• is_referencepose_number() : core::pose
• is_res_exposed() : core::scoring::sasa
• is_residues_in_contact() : protocols::stepwise::modeler::rna
• is_rna_chainbreak() : core::pose::rna
• is_rot_sample_name() : core::pack::task
• is_same_sugar_pucker() : protocols::stepwise::legacy::modeler::rna
• is_sc_bb_clash() : core::pack::task::residue_selector
• is_sc_sc_clash() : core::pack::task::residue_selector
• is_scatom() : core::scoring
• is_scofx_cstfied() : protocols::enzdes::enzutil
• is_singlecomponent() : core::pose::symmetry
• is_sp2_proton_chi() : core::chemical
• is_sugar_2() : core::scoring::elec
• is_sugar_virtual() : protocols::stepwise::modeler::rna::sugar
• is_symmetric() : core::conformation::symmetry , core::pose::symmetry
• is_this_strand_at_edge() : protocols::features::strand_assembly
• is_this_strand_at_edge_by_looking_db() : protocols::features::strand_assembly
• is_tna_chainbreak() : core::pose::rna
• is_torsion_valid() : core::pose::rna
• is_upper_cutpoint() : core::scoring::methods
• is_upper_terminus() : core::pose
• is_valid_backbone() : protocols::loophash
• is_virtual_base() : protocols::stepwise::modeler::rna
• isDigit() : protocols::sparta
• isDirExists() : protocols::sparta
• isPowerOfTwo() : core::scoring::fiber_diffraction
• isSpace() : protocols::sparta
• itoa() : protocols::sparta
• ixform_atr() : protocols::ligand_docking::ga_ligand_dock
• ixform_rep() : protocols::ligand_docking::ga_ligand_dock