Referenced by add_symm_sf4(), add_symm_zns(), add_vrts(), align_helix(), align_pdbs(), align_pdbs_function(), align_sf4(), align_zns(), analyze_base_pair_test(), dsRNA_grow::append_Aform_residue(), append_sequence_to_pose(), InteractionDistMinimizer::apply(), A3BPeptideBuilder::apply(), CovalentPeptidomimeticDockDesign::apply(), CovalentPeptidomimeticCreator::apply(), TriazoleCreator::apply(), RNA_ScoreMover::apply(), CrystDesign::apply(), aro_pack_pdbstats_from_pose(), base_type_num(), benzene_pair_score_test(), block_stack_test(), blosum_score_alignment(), build_helix_test(), build_next_nucleotide_test(), build_on_helix(), build_toy_pose(), calc_rms_test(), calc_rmsd_test(), calc_scores(), calculate_pairwise_RMSD(), calculate_theoretical_RNA_length(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), check_centroid(), check_fullatom(), check_structures(), ChiMover::ChiMover(), cluster_outfile_test_OLD(), cluster_rotamers(), coarse_close_loop_test(), coarse_frag_test(), coarse_rb_test(), coarse_rna_denovo_test(), coarse_to_full_test(), collect_residue_types(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), color_by_lj_test(), StepWiseJobQueen::complete_larval_job_maturation(), connectivity_test(), convert_silent_file_to_pose_data_list(), convert_to_coarse_test(), convert_to_native_test(), convert_to_olc(), copy_DOFS_local(), copy_virtual_variant_type(), correct_dunbrack(), correct_rama(), count_contacts(), MPDomainAssembly::create_residue_from_olc(), create_rna_benchmark_test(), create_rna_vall_torsions_test(), define_states_test(), derive(), CrystDesign::design_cycle(), dinucleotide_test(), dist_matrix_test(), dna_test(), drrafter_error_estimation(), each_aa_test(), entropy_calculate_test(), env_sugar_test(), erraser_monte_carlo(), figure_out_icoord_test(), files_for_openMM_test(), CrystDesign::filter_and_report(), filter_combine_long_loop(), fit_helix_in_map(), fixbb_design(), frag_extract_test(), gather_ss_pct(), general_initialize(), generate_partial_threads(), get_base_pair_coordinate_system(), get_basepair_atoms(), get_contacts(), get_H_atom(), get_icoor(), get_info_test(), get_min_frag_rmsd(), get_pose_and_numbering(), get_pose_by_id(), get_pose_energy_breakdown(), get_poseToRelax(), get_ring_atoms(), get_ring_centroids_and_stubs(), get_rmsd(), get_RNA_binding_residues(), get_subPose(), get_WC_atom(), graft_pdb(), hermann_phase_two(), hermann_phase_two_minimize(), homolog_finder(), icoor_test(), import_and_dump_pdb(), HECTAllMover::init_on_new_input(), HECTUBQMover::init_on_new_input(), initialize_elements(), input_subset_poses(), is_regular_helix(), is_semi_rot(), journal_club_syn_chi(), juke_sam_test(), load_as_fullatom(), loop_closure_test(), LoopBuild_main(), main(), make_helix(), make_motif_task(), match_main(), methane_pair_score_test(), mg_hires_pdbstats_from_pose(), mg_modeler_test(), mg_pdbstats_from_pose(), mg_pdbstats_test(), minimize_pdb(), minimizer_test(), mismatch_test(), modeler_closure_test(), modeler_map_test(), morph_pdbs_test(), multiple_variant_type_test(), mutate_residue(), mutate_residues_wrapper(), my_main(), nucleobase_probe_score_test(), o2prime_packer(), MainWindow::on_button_run_packer_clicked(), output_minipose_coords_test(), output_residue_types(), pack_phosphates(), pack_polar_hydrogens(), parse_pathway_test(), pdb_little_motif_test(), pdb_scoring(), pdb_to_silent_file(), pdb_to_silent_file_simple(), pdbslice(), pdbstats_test(), peptide_plane_test(), peptide_plane_test_OLD(), polar_pdbstats_from_pose(), polar_pdbstats_test(), poses_from_cmd_line(), poses_from_cmd_line_noPDBtag(), post_rebuild_bulge_assembly(), predict_chem_map_test(), prepare_full_length_start_model(), prepare_threaded_model(), dsRNA_grow::prepend_Aform_residue(), print_all_torsions_test(), print_hbonds_test(), print_internal_coord_test(), print_secstruct_test(), proline_rama_pdbstats_from_pose(), protein_helix_test(), pymol_struct_type_test(), quick_score_test(), rb_entropy_test(), rebuild_centroid_test(), rebuild_test(), reference_sasa(), refine(), repack(), repack_minimize_test(), repack_test(), resample_full_model_test(), rhiju_pdbstats(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_close_chainbreaks_test(), rna_design_gap_test(), rna_design_test(), rna_features_from_pose(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_helix_pdbstats_from_pose(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_motif_test(), rna_o2prime_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), rna_resample_test(), rna_sample_virtual_sugar(), rna_stack_pdbstats_from_pose(), rna_stats_test(), rna_suitename(), rna_torsion_check_test(), rotamerize_rna_test(), sample_rama_test(), sample_trp_test(), sample_trp_tyr_test(), sasa_test(), score12_plot_test(), score_rnp(), screen_phosphates(), set_pep_cst(), setup_pose_setup_class(), setup_pose_with_loop(), sidechain_sample(), slice_ellipsoid_envelope(), slice_pdb(), slice_sample_res_and_surrounding(), spinner_test(), ss_ds_ts_assign_test(), stepwise_lores_test(), stepwise_monte_carlo_legacy(), stepwise_template_test(), sugar_frag_RNA_test(), sugar_geometry_RNA_test(), swa_rna_sample(), sweep_params_from_match_constraint_file(), tar_motif_test(), test(), test_function(), thermal_sampler(), CovalentPeptidomimeticDockDesign::update_hydrogens(), and CovalentPeptidomimeticCreator::update_hydrogens().
