Referenced by MinTestMover::add_coordinate_constraints_to_pose(), add_side_chains_partialthread(), add_triazole_constraints(), align_pdbs(), align_pdbs_function(), analyze_base_pair_test(), CalcIrms::apply(), RMSByResStatistics::apply(), BuriedUnsatPolarsFinder::apply(), zinc_helix_cap::apply(), MirrorSymmTest::apply(), InteractionDistMinimizer::apply(), abbinding::apply(), mtransferase::apply(), PhDocking::apply(), LocalRmsd::apply(), ElecDensMinPackMinMover::apply(), CustomMover::apply(), HolesTrainingDataMover::apply(), A3BHbsCreatorMover::apply(), A3BPeptideBuilder::apply(), CovalentPeptidomimeticDockDesign::apply(), CovalentPeptidomimeticCreator::apply(), MikeLinkerMover::apply(), TriazoleCreator::apply(), MinTestMover::apply(), LDConverterMover::apply(), SampleTiltProtocol::apply(), RosettaHolesMover::apply(), DockGlycansProtocol::apply(), PhProtocol::apply(), RNA_ScoreMover::apply(), CalcCdrRms::apply(), FastThreadingMover::apply(), MembraneMinMover::apply(), MembraneViewMover::apply(), MembraneSfxnMover::apply(), MembraneDockingxMover::apply(), MembraneRelaxMover::apply(), MembraneSampleMover::apply(), MembraneTransformMover::apply(), CrystDesign::apply(), CrystRelax::apply(), TestQuickRelaxMover::apply(), MPDomainAssembly::apply(), generate_hbond_geometry::apply(), ScoreFunctionFingerprintMover::apply(), assign_rigid_body_settings_to_clusters_test(), atom_vdw_test(), backrub_min_test(), backrub_protocol(), base_doublet_rmsd_test(), base_pair_to_base_pair_test(), benzene_pair_score_test(), block_stack_test(), bp_score_calibrate(), build_bb_independent_rotamers(), build_helix_test(), build_next_nucleotide_test(), build_template(), buns_for_pose(), bzip_test(), ca_to_allatom_main(), PhDocking::calc_energies(), abbinding::calc_energies_and_sasa(), calc_rmsd_test(), calculate_binding_energy(), calculate_helical_tail_variance(), calculate_pairwise_RMSD(), calculate_rmsd_variance(), calculate_sasa(), calculate_theoretical_RNA_length(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), calculate_tm_variance(), ccd_test(), cen_fold(), change_docking_pose(), check_clash(), check_structures(), chi_stats_test(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), cluster_rotamers(), cluster_silent_file_data(), coarse_close_loop_test(), coarse_frag_test(), coarse_rb_test(), coarse_to_full_test(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), color_by_lj_test(), compare_dna_energies(), compare_energies(), StepWiseJobQueen::complete_larval_job_maturation(), compute_motif_score(), compute_sixAneighbors(), compute_tenAneighbors(), compute_twelveAneighbors(), dsRNA_grow::constrain_and_minimize(), constrain_loop_ends(), HbondZinc::constrain_zinc(), constraint_set_slice(), converged(), convert_silent_file_to_pose_data_list(), convert_to_native_test(), copy_rotamerized_torsions(), copyresidueposition(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_dihedral_constraint(), create_rna_benchmark_test(), create_score_function_from_weights_and_refEs(), create_scorefxn(), cst_relax_test(), define_states_test(), delta_chi_correction_test(), densityTools(), derive(), design(), CrystDesign::design_cycle(), design_test(), design_using_resfile(), dinucleotide_test(), dna_chain_check(), dna_coupled_rotamer_design_test(), dna_deriv_test(), dna_deriv_test_old(), dna_design_test_old(), dna_dr_loop_test(), dna_dr_test(), dna_io_test(), dna_nbr_radii_test(), dna_specificity_test(), dna_stats(), do_color_by_score(), CrystDesign::do_reversion(), do_the_match(), do_work(), dostuff(), double_helix_test(), drrafter_error_estimation(), dump_clash_pdb(), dump_energy_kinemage(), dump_pose_diff(), each_aa_test(), easy_loop_model_test(), easy_target_test(), endo_test(), enforce_atoms_coplanar(), enforce_triazole_distance(), env_sugar_test(), erraser_monte_carlo(), extract_pdbs_test(), extract_scores(), fa_refine_and_design(), fa_scorefxn_test(), figure_out_domain_neighbors(), figure_out_secstruct(), files_for_openMM_test(), fill_hbond_neighbors(), CrystDesign::filter_and_report(), filter_combine_long_loop(), PhProtocol::finalize_res_list(), find_buried_unsatisfied_polars(), find_clashes(), find_close_parents(), find_dna_rotamers(), find_neighbors_directional(), finely_sample_base_pair_test(), FloppyTailMover::FloppyTailMover(), flxbb_nobu(), gen_pep_bb_sequential(), general_initialize(), generate_combined_model(), get_central_pose(), get_clash_pairs(), get_complex_score(), get_disordered_regions(), get_hb_srbb_score(), get_icoor(), get_interface_energies(), get_interface_residues(), CrystDesign::get_interface_residues(), get_min_frag_rmsd(), get_neighbor_residues(), CrystDesign::get_neighbor_residues(), MPInterfaceStatistics::get_number_hbonds(), get_perresE(), get_pose_energy_breakdown(), get_res_data_ss(), get_res_hbond_bb_score_raw(), get_rmsd(), get_sasa(), get_sc(), MPInterfaceStatistics::get_size(), get_stepwise_score_function(), get_subpose(), get_unbound_protein_score(), CrystDesign::greedy_revert_unsats(), grid_matcher(), hard_minimize(), hard_pack(), harvest_motifs(), has_clash(), HbondZinc::hbond_constraint(), HECTMover::HECTMover(), helix_ST(), hermann_phase_two(), hermann_phase_two_minimize(), hessian_estimate(), homolog_finder(), HubDenovo::HubDenovo(), idealize_tf_pose(), GlycomutagenesisProtocol::init(), initialize_base_pair(), initialize_fa_rep(), initialize_o2prime_pack(), initialize_rigid_body_sampler(), interface_energy_ratio(), interface_repack_test(), intra_dna_stats(), is_clash(), iterative_optE(), journal_club_syn_chi(), juke_sam_test(), kono_sarai_stats(), kono_sarai_zscore(), lariat_modeling(), loop_closure_test(), loop_modeling_test(), loop_rebuilding_test(), LoopBuild_main(), luxr_test(), main(), make_etable(), make_sf(), map_morph(), MC_run(), methane_pair_score_test(), mg_modeler_test(), dsRNA_grow::minimize(), minimize_and_score(), minimize_helix(), minimize_pdb(), minimize_poses(), minimize_protocol(), minimize_test(), minimizer_test(), mismatch_test(), mm_pack_test(), modeler_closure_test(), modeler_map_test(), morph_pdbs_test(), MPframeworkTest1Mover::move_together(), multiple_variant_type_test(), mutate_and_score_RNP(), mutate_residues_wrapper(), my_main(), MembraneViewMover::new_fastrelax_cycle(), not1_test(), nucleobase_probe_score_test(), one_chain_MC_sampling(), one_chain_ST_MC(), OPT_KEY(), output_centroid_silent_struct(), output_to_silent(), pack_it(), pack_phosphates(), pack_polar_hydrogens(), pack_rotamers_test(), pack_sidechains(), parse_pathway_test(), pdb_little_motif_test(), pdb_scoring(), pdb_to_silent_file(), pdb_to_silent_file_simple(), peptide_plane_test(), peptide_plane_test_OLD(), perturb_bb_and_relax(), phosphate_stats(), PickSSE::PickSSE(), post_rebuild_bulge_assembly(), PhProtocol::prepack_pose(), DockGlycansProtocol::prepare_scoring_function(), prepare_start_model(), PhDocking::print_hbonds(), PhProtocol::print_hbonds(), print_hbonds_test(), print_internal_coord_test(), protein_helix_test(), pymol_struct_type_test(), quick_score_test(), rb_entropy_test(), rb_test(), rebuild_centroid_test(), rebuild_test(), DockGlycansProtocol::record_pose_metrics(), refine_pose(), region_density_score(), region_score(), PhProtocol::relax_pose(), relax_test(), remove_duplicate_motifs(), HbondZinc::repack(), HbondZincBackbone::repack(), repack(), repack_minimize_test(), repack_test(), resample_full_model_test(), rescore_test(), reset_sfxn(), retrieve_residue_pair_energies(), abbinding::return_raw_scores(), rhiju_pack(), rna_assemble_all_combinations_test(), rna_assemble_test(), rna_backbone_rebuild_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_chain_closure_test(), 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_thread_test(), rna_torsion_check_test(), rotamer_trials_test(), rotamerize_rna_test(), rotamerize_structure(), protocols::abinitio::Application::run(), SolutionRescoreMover::run(), HubDenovo::run(), run(), run_hd(), run_hh(), ScoreEachBenchmark::run_long_ranged_two_body_energy(), ScoreEachBenchmark::run_one_body_energy(), run_pep_prep(), ScoreEachBenchmark::run_short_ranged_two_body_energy(), run_test(), sample_new_base_in_two_base_pair_pose(), sample_rama_test(), sample_state_to_state(), sample_trp_test(), sample_trp_tyr_test(), sasa_test(), save_contact_info(), scan_hbond_jumps(), score12_plot_test(), score_and_minimize(), score_loop(), score_pdb(), ZincSiteEvaluator::score_pose(), score_rnp(), scoring_test(), screen_phosphates(), search_translations(), set_fullatom_flag_test(), ZincMinimize::set_scorefunction(), ScoreAnalyticEtableBenchmark::setUp(), setup_coord_csts(), setup_crazy_fold_tree(), setup_double_helix_pose(), zinc2_homodimer_setup::setup_filter_clashes(), InteractionGraphPerformanceBenchmark::setup_for_current_default_sfxn(), FastRelaxPerformanceBenchmark::setup_for_mmstd(), InteractionGraphPerformanceBenchmark::setup_for_mmstd(), FastRelaxPerformanceBenchmark::setup_for_sc12he(), InteractionGraphPerformanceBenchmark::setup_for_sc12he(), FastRelaxPerformanceBenchmark::setup_for_sc12sp2(), InteractionGraphPerformanceBenchmark::setup_for_sc12sp2(), FastRelaxPerformanceBenchmark::setup_for_score12(), InteractionGraphPerformanceBenchmark::setup_for_score12(), FastRelaxPerformanceBenchmark::setup_for_sp2hecart(), InteractionGraphPerformanceBenchmark::setup_for_sp2hecart(), CalcIrms::setup_native(), PhDocking::setup_pH_mode(), setup_pose(), setup_pose_setup_class(), zinc1_homodimer_design::setup_scorefunctions(), abbinding::setup_task_and_repack(), PhDocking::setup_task_and_repack(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), setup_two_base_pair_pose_with_chainbreak(), ScoreFunctionFingerprintMover::sfxn(), show_clashes(), show_intrachain_energies(), show_pairing_info(), show_protein_DNA_interactions(), show_residue_residue_clashes(), sicdock_thread_num(), sidechain_sample(), simple_dna_test(), simple_loop_modeling_test(), simple_minimization(), simple_packing(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), small_min_test(), soft_pack(), spec_test(), spinner_test(), split_fa_dun(), ss_ds_ts_assign_test(), ss_test(), stepwise_lores_test(), stepwise_monte_carlo_legacy(), stepwise_template_test(), sugar_frag_RNA_test(), sugar_geometry_RNA_test(), superimpose_A_to_all(), superimpose_pose_using_aln(), swa_rna_sample(), symm_self_rep(), tar_motif_test(), test(), test_dunbrack_io(), test_function(), test_gb(), test_known_value(), test_membrane_scoring_highres(), test_membrane_scoring_lowres(), test_rama(), test_scorefxn_io(), test_suck_res(), test_talaris(), test_vs_dots(), tf_specificity_test(), thermal_sampler(), transform_pose(), two_base_pairs_test(), two_region_rmsd(), UBQ_E2Mover::UBQ_E2Mover(), UBQ_GTPase_disulfide_Mover::UBQ_GTPase_disulfide_Mover(), unbound_protein_minimization(), unsatisfied_buried_polars(), varsoldist_rotamer_dots_for_pose(), vary_bond_length(), vary_geometry_backbone(), vary_geometry_RNA(), vary_geometry_sidechains(), water_test(), water_test_fixed_O(), write_respair_scores_to_database(), write_score_types_to_database(), zf_relax_test(), zf_test(), and zif268_test().
