Referenced by RNA_DeNovoJobQueen::add_chem_shift_info(), add_rosetta_options_9(), align_pdbs(), analyze_base_pair_test(), MPDomainAssembly::apply(), supercharge::apply(), DockGlycansProtocol::apply(), PhProtocol::apply(), ca_to_allatom_main(), calculate_binding_energy(), calculate_pairwise_RMSD(), calculate_sasa(), StepWiseJobQueen::complete_larval_job_maturation(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_scorefxn(), densityTools(), supercharge::design_supercharge(), supercharge::design_supercharge_AvNAPSA(), do_color_by_score(), drrafter_error_estimation(), extract_pdbs_test(), filter_combine_long_loop(), PhProtocol::finalize_res_list(), find_neighbors_directional(), gen_pep_bb_sequential(), get_clash_pairs(), get_complex_score(), get_stepwise_score_function(), get_unbound_protein_score(), harvest_motifs(), has_clash(), RNA_DeNovoJobQueen::initialize_constraints(), RNA_DeNovoJobQueen::initialize_scorefxn(), main(), make_scorefxn(), MC_run(), mg_modeler_test(), minimize_test(), mutate_and_score_RNP(), mutate_residues_wrapper(), my_main(), nucleobase_probe_score_test(), RNA_DeNovoJobQueen::output_silent_struct(), RNA_DeNovoJobQueen::output_to_silent_file(), pdb_to_silent_file(), post_rebuild_bulge_assembly(), supercharge::prepack_input_structure(), PhProtocol::prepack_pose(), DockGlycansProtocol::prepare_scoring_function(), PhProtocol::print_hbonds(), quick_score_test(), rebuild_test(), DockGlycansProtocol::record_pose_metrics(), PhProtocol::relax_pose(), repack_test(), resample_full_model_test(), rna_build_helix_test(), rna_design_test(), rna_features_from_pose(), rna_fullatom_minimize_test(), rna_motif_test(), rna_sample_virtual_sugar(), rna_score_test(), rna_thread_test(), SolutionRescoreMover::run(), ScoreEachBenchmark::run_long_ranged_two_body_energy(), ScoreEachBenchmark::run_one_body_energy(), run_pep_prep(), ScoreEachBenchmark::run_short_ranged_two_body_energy(), ScoreAnalyticEtableBenchmark::setUp(), zinc2_homodimer_setup::setup_filter_clashes(), 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(), zinc1_homodimer_design::setup_scorefunctions(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), simple_minimization(), simple_packing(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), ss_ds_ts_assign_test(), stepwise_monte_carlo_legacy(), swa_rna_sample(), thermal_sampler(), UBQ_E2Mover::UBQ_E2Mover(), UBQ_GTPase_disulfide_Mover::UBQ_GTPase_disulfide_Mover(), and unbound_protein_minimization().
1.8.7