- i -

• I_sc() : basic::options::OptionKeys::evaluation , evaluation
• icoor_05_2009() : basic::options::OptionKeys::corrections::chemical , corrections::chemical
• idealize_after_loop_close() : basic::options::OptionKeys::loops , loops
• idealize_before_loop_close() : basic::options::OptionKeys::loops , loops
• idealize_before_protocol() : run
• idealize_final_structures() : basic::options::OptionKeys::cluster , cluster
• idealize_h3_stems_before_modeling() : antibody , basic::options::OptionKeys::antibody
• identical_match_dis() : basic::options::OptionKeys::crossmatch , crossmatch , willmatch
• ifft() : numeric::fourier
• ifft2() : numeric::fourier
• ifft3() : numeric::fourier
• ifft3_dynamic() : numeric::fourier
• ignore_default_docking_task() : basic::options::OptionKeys::docking , docking
• ignore_improper_res() : basic::options::OptionKeys::bbg , bbg
• ignore_io_errors() : basic::options::OptionKeys::mh , mh
• ignore_ligand_chi() : packing
• ignore_missing_bondangle_params() : basic::options::OptionKeys::MM , MM
• ignore_sequence_seperation() : basic::options::OptionKeys::fold_cst , fold_cst
• ignore_unrecognized_res() : basic::options::OptionKeys::in , in
• ignore_waters() : basic::options::OptionKeys::in , in
• ignore_zero_occupancy() : run
• implicit_hydrogen_radii_set() : sasa
• improve_orientation() : basic::options::OptionKeys::docking::ligand , docking::ligand
• in() : basic::options::OptionKeys::in , in
• in_sin_cos_range() : numeric
• include_catres_in_interface_detection() : basic::options::OptionKeys::enzdes , enzdes
• include_dna_potentials() : basic::options::OptionKeys::dna::design::specificity , dna::design::specificity
• include_hydrogens() : basic::options::OptionKeys::fingerprint , fingerprint
• include_hydrogens_explicitly() : sasa
• include_lipids() : basic::options::OptionKeys::in , in
• include_lips() : basic::options::OptionKeys::membrane , membrane
• include_neighbor_base_stacks() : score
• include_only_C_S_in_hsasa() : sasa
• include_patches() : basic::options::OptionKeys::chemical , chemical
• include_probe_radius_in_atom_radii() : sasa
• include_stage5() : abinitio , basic::options::OptionKeys::abinitio
• include_sugars() : basic::options::OptionKeys::in , in
• include_surfaces() : basic::options::OptionKeys::in , in
• include_water() : packstat
• increase_chainbreak() : basic::options::OptionKeys::jumps , jumps
• increase_constraints() : basic::options::OptionKeys::constraints , constraints
• increase_cycles() : abinitio , basic::options::OptionKeys::abinitio
• increase_vdw_radii() : relax::centroid
• independent_cycles() : remodel::RemodelLoopMover
• indexoffset() : basic::options::OptionKeys::lh::fragpdb , lh::fragpdb
• inform() : basic::options
• ini_func1() : numeric::random
• ini_func2() : numeric::random
• init() : basic , devel
• initial_dist_cutoff() : abinitio::star , basic::options::OptionKeys::abinitio::star
• initial_perturb() : antibody::design , basic::options::OptionKeys::antibody::design
• initial_repack() : basic::options::OptionKeys::ddg , ddg
• initialize() : basic::options
• initialize_rigid_body_dofs() : symmetry
• initialize_sturm() : numeric::kinematic_closure
• inner_iteration_scale() : basic::options::OptionKeys::flexpack::annealer , flexpack::annealer
• inner_product() : numeric
• inneriterations_scaling() : packing
• inout() : basic::options::OptionKeys::inout , inout
• inplace_product() : numeric
• inplace_transpose_product() : numeric
• input_etables() : score
• input_fv() : antibody , basic::options::OptionKeys::antibody
• input_motifs() : basic::options::OptionKeys::mh , mh
• input_pdb() : basic::options::OptionKeys::LoopModel , basic::options::OptionKeys::loops , LoopModel , loops , RBSegmentRelax , SSrbrelax
• input_res() : basic::options::OptionKeys::in::file , in::file
• input_res1() : stepwise
• input_res2() : stepwise
• input_score_filter() : basic::options::OptionKeys::cluster , cluster
• input_seq() : pepspec
• insert() : ufv::insert
• insert_middle() : utility
• insert_or_ignore() : basic::database
• insert_pdb() : ufv::insert
• insert_segment_from_pdb() : remodel::domainFusion
• instructions() : antibody::design , basic::options::OptionKeys::antibody::design
• int2afteroption() : basic::options
• intafteroption() : basic::options
• integration_test() : stepwise::rna
• inter_group_neighbors_cutoff() : pose_metrics
• inter_subsub_cst() : smhybrid
• interactive() : run
• interface_cutoff() : pepspec , pose_metrics
• interface_ddg() : basic::options::OptionKeys::ddg , ddg
• interface_dis() : antibody::design , basic::options::OptionKeys::antibody::design
• interface_size() : basic::options::OptionKeys::crossmatch , crossmatch , willmatch
• intermediate_scorefiles() : run
• intermediate_structures() : run
• intermedrelax() : basic::options::OptionKeys::loops , loops
• intermolecular_frequency() : stepwise::monte_carlo
• interpolate_2d_func_of_angles() : basic
• interpolate_bilinear() : basic
• interpolate_bilinear_by_value() : basic
• interpolate_get_angle_bins() : basic
• interpolated() : numeric::interpolation::full::bin_density , numeric::interpolation::full::bin_width , numeric::interpolation , numeric::interpolation::periodic_range::full , numeric::interpolation::periodic_range::half , numeric::interpolation::periodic_range::periodic_value::full , numeric::interpolation::periodic_range::periodic_value::half
• interpolated_delta() : numeric::interpolation
• interval() : basic::options::OptionKeys::ms::checkpoint , ms::checkpoint
• interval_data_dump() : basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• interval_pose_dump() : basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• intrares_elec_correction_scale() : score
• inv_kin_lig_loop_design_filename() : basic::options::OptionKeys::murphp , murphp
• inv_kT_nataa() : basic::options::OptionKeys::optE , optE
• inv_kT_natrot() : basic::options::OptionKeys::optE , optE
• inv_kT_natstruct() : basic::options::OptionKeys::optE , optE
• inverse() : numeric
• inversion_subs() : smhybrid
• invrate_jump_move() : basic::options::OptionKeys::jumps , jumps
• Irms() : basic::options::OptionKeys::evaluation , evaluation
• is_a_finitenumber() : numeric
• is_eq() : utility::json_spirit
• is_false_string() : utility
• is_identity_matrix() : numeric::model_quality
• is_legal_greater_than() : numeric::kdtree
• is_legal_kdtree_below_node() : numeric::kdtree
• is_legal_less_than() : numeric::kdtree
• is_letter() : numeric::expression_parser
• is_numeral() : numeric::expression_parser
• is_string_numeric() : utility
• is_true_string() : utility
• is_undefined() : numeric
• isinf() : numeric
• isnan() : numeric
• iterate_reset() : rdc
• iterate_tol() : rdc
• iterate_weights() : rdc
• iterations() : basic::options::OptionKeys::ddg , basic::options::OptionKeys::dna::design , ddg , dna::design
• IUPAC() : run