- i -

• i : gen_env_dep_pair.m , draw_gen_env_dep_orient_decompose.m , pre_fill_dfire_2D.m , pre_fill_dfire.m , gen_env_dep_pair_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , cal_env.m , draw_matrix.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m
• ia_stats_filename : simple_interfaceanalyzer.cc
• igpb_denseig_current_default_sfxn : InteractionGraph.bench.hh
• igpb_denseig_sc12 : InteractionGraph.bench.hh
• igpb_lmig_current_default_sfxn : InteractionGraph.bench.hh
• igpb_lmig_mmstd : InteractionGraph.bench.hh
• igpb_lmig_sc12 : InteractionGraph.bench.hh
• igpb_lmig_sc12he : InteractionGraph.bench.hh
• igpb_lmig_sc12sp2 : InteractionGraph.bench.hh
• igpb_pdig_current_default_sfxn : InteractionGraph.bench.hh
• igpb_pdig_sc12 : InteractionGraph.bench.hh
• ii : cal_env.m , gen_env_dep_pair_decompose.m , gen_vdw_radius.m , gen_vdw_radius_soft.m
• ILE : gen_vdw_radius.m , load_pair_env_table.m , load_angle_r_table.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , load_pair_env_table_ref.m , gen_env_dep_orient.m , draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , draw_matrix.m , cal_env.m , load_pair_env_table.m
• immobile_domain : concatenate_poses.cc
• INPATH : test_C-terminal_conjugation.cc , test_non-canonical_connectivities.cc
• input_file : cl_complex_rescore.cc
• input_seq : pepspec.cc
• instantiate_format_float : format.cc
• instantiate_modules_filters : performance_benchmark.cc
• instantiate_modules_movers : performance_benchmark.cc
• instantiate_modules_packer_palettes : performance_benchmark.cc
• instantiate_modules_res_level_task_operations : performance_benchmark.cc
• instantiate_modules_residue_selectors : performance_benchmark.cc
• instantiate_modules_simple_metrics : performance_benchmark.cc
• instantiate_modules_task_operations : performance_benchmark.cc
• interface : pocket_suggest_target_residues_by_ddg.cc , karen_pocket_save.cc , minimize_ppi.cc , InterfaceAnalyzer.cc , cl_complex_rescore.cc , simon_darc_minimize.cc , ragul_darc_minimize.cc , SID_rescore.cc , johnk_interface_recompute_score_and_rmsd.cc , johnk_interface_geosol_minimization.cc , class_tests.cc , david_rotation_experiment.cc , david_recompute_score_and_rmsd.cc , david_find_surface_residues.cc , david_find_contacts.cc , david_find_complex_contacts.cc , david_find_best_contact_pocket.cc , david_fill_gaps.cc , david_extract_domain.cc , david_extract_dinucleotide_musashi_reference.cc , david_align_append_and_recompute_score_and_rmsd.cc , david_align_and_recompute_score_and_rmsd.cc , karen_compare_pocket_rmsd.cc
• INTERFACE_CONTACT_DIS : ward_design.cc
• interface_resi : pocket_suggest_target_residues_by_ddg.cc