- i -

• i:() : draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_pair_decompose.m , gen_env_dep_orient_decompose.m
• icoor_test() : coarse_rna_test.cc
• id2torsion() : turner_test_one_chain.cc
• id_from_index() : fold_tree.cc , partial_pose.cc , read_cutpoint.cc
• ideal_A_form_torsions() : turner_two_chain.cc
• idealize_tf_pose() : dna_spec_test.cc , simple_dna_regression_test.cc
• identify_targeted_positions() : incorporate_motifs.cc
• identity_matrix() : extractNativeRepeats.cc
• if() : cal_env.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , draw_gen_env_dep_orient_decompose.m , draw_matrix.m , easy_loop_mover_refine.cc , kic.LoopRelaxMover.cc , draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m , minimalCstRelax.cc , draw_gen_env_dep_pair_decompose.m , draw_matrix.m
• iface_check_c3() : genmatch_m8.cc , gentetra_from_trimer.cc , gentetra_bpy_from_znhis.cc , gentetra.cc , genmatch_3bpy.cc , genmatch.cc , gensym_3bpy_from_dimer.cc
• iface_pdb_superimpose_diff_prot() : david_pocket_align_and_save.cc
• iface_pdb_superimpose_pose() : karen_pocket_save.cc , david_align_append_and_recompute_score_and_rmsd.cc , david_pocket_align_and_save.cc , david_rotation_experiment.cc
• ifc_clash() : isct_test.cc
• ik_arg_asp_frnt() : test_ikrs.cc , test_ikrs2.cc , test_ikrs_flymake.cc
• ik_arg_asp_side() : test_ikrs.cc , test_ikrs2.cc , test_ikrs_flymake.cc
• ik_arg_glu_frnt() : test_ikrs.cc , test_ikrs_flymake.cc , test_ikrs2.cc
• ik_arg_glu_side() : test_ikrs.cc , test_ikrs_flymake.cc , test_ikrs2.cc
• ik_his4() : gen_d2.cc , gen_d2_4his.cc
• ik_his_clamp() : gen_d2.cc , gen_d2_3his_ooc.cc , gen_d2_4his.cc , gen_d2_hhhc.cc , gen_homo_hc.cc
• ik_lys_ctp_asp() : test_ikrs.cc , test_ikrs2.cc
• ik_lys_ctp_glu() : test_ikrs.cc , test_ikrs2.cc
• import_and_dump_pdb() : swa_rna_util.cc
• imshow() : draw_matrix.m
• in_cnl() : cnl_env_lost_hbs.cc
• in_set() : nrg_res_set.cc
• increment_asymm_unit_recursively() : count_cycpep_sequences.cc
• increment_sequence() : count_cycpep_sequences.cc
• info() : Svm.cc
• init_myuniform() : test_leerichards.cc
• init_omega() : phil.hh
• init_phi() : phil.hh
• init_psi() : phil.hh
• init_torsions_still_present() : phil.hh
• init_usage_prompt() : remodel.cc , mp_seqrecov.cc , sequence_recovery.cc , rss_energy_calculator.cc , find_position_matches_using_inverse_rotamers.cc , analyze_ddG.cc , sequencerecovery.cc , surfacescore.cc
• initialize_atoms() : bootstrap_bcl_types.cc
• initialize_base_pair() : turner_rules_test.cc
• initialize_elements() : bootstrap_bcl_types.cc
• initialize_fa_rep() : turner_rules_test.cc
• initialize_for_grid_matcher() : turner_rules_test.cc
• initialize_free_and_fixed() : optE_test.cc
• initialize_from_pdb() : fit_helixparams.cc
• initialize_initalizeZNcst() : zn_match_symmdock.cc
• initialize_native_pose() : swa_protein_main.cc
• initialize_o2prime_pack() : turner_test_one_chain.cc , turner_test_double_helix.cc
• initialize_peptide() : pep_spec_flx.cc , pep_spec_flx.mov.cc , pepspec.cc
• initialize_pose() : plot_scoreterm.cc
• initialize_pymol_colors() : rna_test.cc
• initialize_rigid_body_sampler() : turner_rules_test.cc
• initialize_sequence_mask() : easy_target_test.cc
• initiate() : T10.virtual_inheritance.hpp
• initsyms() : tcdock.cc
• inlist() : make_truecyclicpeptide.cc
• input_alignments() : tj_util.hh
• input_alignmentsMapped() : filterImperfectAln.cc , tj_util.hh
• input_coordCstsMapped() : minimalCstHomology.cc
• INPUT_PATH() : test_explicit_membrane_input.cc , test_coenzymes.cc
• input_subset_poses() : tj_util.hh
• input_torsion_M_v_lists() : turner_rules_test.cc
• insert_chunk() : rna_assemble_test.cc
• insert_stage_tag() : multistage_rosetta_scripts.cc
• inside_polygon() : mpframework_test2.cc
• instantiate() : T20.template.hpp
• instantiate_templates() : T15.inner_class.hpp
• int2str() : util.hh
• int2string() : CycDsulf.cc
• interface_between_chains() : mpframework_test.cc
• interface_energy_ratio() : smhybrid.cc
• interface_energymap() : cterdesign.cc
• interface_repack_test() : dna_spec_test.cc , simple_dna_regression_test.cc
• interface_residue_ddg() : pocket_suggest_target_residues_by_ddg.cc
• interface_residues() : ward_design.cc
• interface_rmsd() : david_align_and_recompute_score_and_rmsd.cc , david_align_append_and_recompute_score_and_rmsd.cc , ragul_darc_minimize.cc , simon_darc_minimize.cc , minimize_ppi.cc
• interp_linear() : cryst_design.cc
• intersect() : mpframework_test2.cc
• intersecting_bpy_axes() : gensym_3bpy_from_dimer.cc , gentetra_bpy_from_znhis.cc
• intersecting_disulfide_axes() : gentetra_from_trimer.cc , genmatch_3bpy.cc , gentetra.cc
• intra_dna_stats() : dna_spec_test.cc , simple_dna_regression_test.cc
• invariants_for_cyclic_permutation() : count_cycpep_sequences.cc
• invert_exclude_residues() : pcs_score_individual_residues.cc , pcs_score_residues.cc , pcs_score_select.cc , pcs_score_select_helices.cc
• invert_value() : count_cycpep_sequences.cc
• iprod() : RDCTest.cc
• is_acceptor() : sel_hbonds.cc
• is_atom_clash() : turner_test_double_helix.cc
• is_beta_aminoacid() : bettercluster.cc
• is_bonded_neighbor_atoms_at_phosphate_interface() : parin_test.cc
• is_buried_ring() : get_pharmacophore_without_bound_rna.cc , sarah_get_pharmacophores.cc , ragul_get_ligand_hbonds.cc , get_rna_ring_sasa.cc , get_rna_pharmacophore_with_water.cc , get_rna_pharmacophore.cc
• is_clash() : pep_spec_flx.cc
• is_cluster_member() : parin_test.cc
• is_cut() : fold_from_loops.cc
• is_desired_resnum() : chet_report_rmsd.cc
• is_donor_h() : sel_hbonds.cc
• is_hbond() : cnl_env_lost_hbs.cc , lig_polar_sat.cc , sel_hbonds.cc
• is_in_list() : design_truecycpeptide_fromstub.cc , design_cycpeptide_MPI.cc , bettercluster.cc , design_truecycpeptide_fromstub.cc
• is_in_list_of_lists() : design_cycpeptide_MPI.cc
• is_interface_bbatom() : david_align_and_recompute_score_and_rmsd.cc , david_align_append_and_recompute_score_and_rmsd.cc , david_recompute_score_and_rmsd.cc
• is_interface_CA() : johnk_interface_recompute_score_and_rmsd.cc
• is_interface_heavyatom() : simon_darc_minimize.cc , minimize_ppi.cc , ragul_darc_minimize.cc , johnk_interface_recompute_score_and_rmsd.cc , david_rotation_experiment.cc , david_pocket_align_and_save.cc , david_align_append_and_recompute_score_and_rmsd.cc , david_align_and_recompute_score_and_rmsd.cc , karen_pocket_save.cc , karen_compare_pocket_rmsd.cc , david_recompute_score_and_rmsd.cc
• is_interface_heavyatom_pair() : david_pocket_align_and_save.cc
• is_interface_residue() : david_find_best_contact_pocket.cc , pocket_suggest_target_residues_by_ddg.cc
• is_interface_sc() : johnk_interface_geosol_minimization.cc
• is_locked() : filter_sequences.cc
• is_loop() : fold_from_loops.cc
• is_loop_neighbor() : fold_from_loops.cc , fold_from_loops_devel.cc
• is_nat_rot() : analyze_rtmin_failures.cc
• is_near_C2Z_iface() : gensym_3bpy_from_dimer.cc
• is_new_cluster_center_rotamer() : parin_test.cc
• is_new_cluster_center_second_stage() : parin_test.cc
• is_new_cluster_center_xyz() : parin_test.cc
• is_nonempty_input_silent_file() : swa_rna_analytical_closure.cc
• is_regular_helix() : rna_test.cc
• is_semi_rot() : torsional_potential_corrections.cc
• is_small() : phil.hh
• is_subset() : rna_graft.cc
• isBoundary() : design_contrast_and_statistic.cc
• isBuried() : design_contrast_and_statistic.cc
• isctfast() : gen_d2_hhhc.cc , gen_d2_4his.cc , gen_d2_3his_ooc.cc , gen_d2.cc , gen_d2_3his_ooc.cc
• isHydroNonPolar() : design_contrast_and_statistic.cc
• isNegative() : design_contrast_and_statistic.cc
• isOverlapping() : overlap_score.hh
• isPolarUncharge() : design_contrast_and_statistic.cc
• isPositive() : design_contrast_and_statistic.cc
• isThisAnimalADog() : T10.virtual_inheritance.hpp
• isThisAnimalADog< 1 >() : T10.virtual_inheritance.hpp
• isUnique() : batchrelax_mpi.cc
• iterative_optE() : optE_test.cc