Referenced by adjust_pose_chi(), align_pdbs(), align_pdbs_function(), analyze_base_pair_test(), apply_backbone(), apply_filter_base_stack_direction(), apply_ideal_A_form_torsions(), apply_nucleoside(), apply_nucleoside_torsion(), apply_south_syn_to_dinucleotide_pose(), apply_suite_torsion(), apply_suite_torsions(), assign_rigid_body_settings_to_clusters_test(), assign_stack_faces(), base_doublet_rmsd_test(), base_pair_to_base_pair_test(), block_stack_test(), build_next_nucleotide_test(), calculate_pairwise_RMSD(), check_filter_base_stack(), cluster_rigid_body_settings_test(), cluster_silent_file_data(), copy_rotamerized_torsions(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_rna_benchmark_test(), define_states_test(), delta_chi_correction_test(), dinucleotide_test(), do_the_match(), double_helix_test(), erraser_monte_carlo(), filter_combine_long_loop(), finely_sample_base_pair_test(), get_backbone(), get_fixed_res(), get_input_res(), get_min_frag_rmsd(), get_nucleoside(), get_pose_energy_breakdown(), get_ring_centroids_and_stubs(), get_silent_file_tags(), get_suite_ideal_A_form_torsions(), grid_matcher(), helix_ST(), hermann_phase_two_minimize(), homolog_finder(), ideal_A_form_torsions(), import_and_dump_pdb(), initialize_base_pair(), initialize_o2prime_pack(), initialize_rigid_body_sampler(), is_regular_helix(), lariat_modeling(), MC_run(), mg_hires_pdbstats_from_pose(), mg_pdbstats_from_pose(), minimize_and_score(), minimize_pdb(), minimize_poses(), mismatch_test(), multiple_variant_type_test(), my_main(), o2prime_packer(), one_chain_MC_sampling(), one_chain_ST_MC(), output_sugar_geometry_parameters(), pack_phosphates(), pdb_stats(), pdb_to_silent_file(), pdbstats_test(), polar_pdbstats_from_pose(), post_rebuild_bulge_assembly(), print_all_torsions_test(), rna_backbone_rebuild_test(), rna_chain_closure_test(), rna_close_loop_test(), rna_features_from_pose(), rna_helix_pdbstats_from_pose(), rna_motif_test(), rna_resample_test(), rna_sample_virtual_sugar(), rna_stack_pdbstats_from_pose(), rna_suitename(), rotamerize_rna_test(), rotamerize_structure(), rotate_into_nucleobase_frame(), sample_new_base_in_two_base_pair_pose(), sample_state_to_state(), save_torsions(), dsRNA_grow::set_Aform_torsions(), setup_crazy_fold_tree(), setup_dinucleotide_pose(), setup_double_helix_pose(), setup_one_chain_pose(), setup_pose(), setup_pose_setup_class(), setup_rna_working_parameters(), setup_two_base_pair_pose(), setup_two_base_pair_pose_with_chainbreak(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), swa_rna_cluster(), swa_rna_sample(), test(), test_function(), thermal_sampler(), two_base_pairs_test(), two_base_pairs_via_loop_closure_test(), vary_geometry_RNA(), and vdw_stats().
