Referenced by aa2sim_all(), aa2sim_ca(), aa2sim_sc(), add_side_chains_partialthread(), adjust_ref_weights(), all_pair_energies(), BuriedUnsatPolarsFinder.apply(), xtal_water_bunsat.apply(), zinc_helix_cap.apply(), CartRefineWrapperMover.apply(), MirrorSymmTest.apply(), RelaxCDRsMover.apply(), ComputeProfileMover.apply(), InteractionDistMinimizer.apply(), khSandbox.apply(), KHSandbox.apply(), ElecDensMinPackMinMover.apply(), FoldTreeOutputter.apply(), ChallengeMover.apply(), apps::pilot::SampleSecondaryStructureAlignmentMover.apply(), SilentProlineFixMover.apply(), A3BPeptideBuilder.apply(), CovalentPeptidomimeticDockDesign.apply(), CovalentPeptidomimeticCreator.apply(), TriazoleCreator.apply(), MinTestMover.apply(), LigandRepackMinimizeProtocol.apply(), MinCenrotMover.apply(), FastThreadingMover.apply(), RepackMinCenrotMover.apply(), SwapElementsMover2.apply(), generate_hbond_geometry.apply(), compute_Irmsd.apply(), run_score_patchdock_hotspot.apply(), run_score_hotspot.apply(), MinPackMin.backbone_minimization(), backrub_min_test(), base_pair_to_base_pair_test(), InterfaceStrandFinderMover.bb_score(), ExposedStrandMover.bb_score(), HDmakerMover.bb_score(), benchmark_contacts(), benzene_pair_score_test(), bk_test(), bk_test2(), block_stack_test(), bp_score_calibrate(), brute_force_matcher(), build_full_model_test(), build_helix_test(), build_next_nucleotide_test(), HbondZinc.build_rotamers(), build_template(), bunsats(), byres_analysis(), bzip_test(), HDdesignMover.calc_bb_E(), demo.D090_Ala_scan.calc_binding_energy(), PhDocking.calc_energies(), abbinding.calc_energies_and_sasa(), ConstraintStatsMover.calc_native_stats(), calc_rama(), calc_rama2b(), calc_rama_scores(), calc_scores(), ConstraintStatsMover.calc_stats(), calculate_hASA_by_type_and_attractiveE(), calculate_hASA_by_type_and_exposure(), calculate_hASA_by_type_and_nbcount(), calculate_hydrophobic_accessible_surface_area(), calculate_percent_hydrophobic_distribution(), calculate_percent_hydrophobic_stats(), calculate_total_hASA_within_distance_avg_values(), calculate_total_hASA_within_distance_avgresiduevalues_allnbs_conditionalonnumnbs(), calculate_total_hASA_within_distance_exact_hASA_values(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs_exposedornot_conditionalonnumnbs(), calculate_total_hASA_within_distance_miniSASAvalues_allnbs_exposedornot_conditionalonnumnbs(), capri15_relax(), capri_t033_loop_test(), capri_t033_trim_dock_test(), ccd_test(), centroid_rescore_test(), chi_stats_test(), protocols::abinitio::JumpSpecificAbrelax.close_loops(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), cluster_rotamers(), coarse_close_loop_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(), configure_master_mover(), HbondZinc.constrain_zinc(), count_contacts(), create_and_score_fragments(), create_bp_jump_database_test(), create_cs_rosetta_rna_scorefxn(), create_rna_benchmark_test(), create_scorefxn(), cs_rosetta_rna_pdb(), cst_relax_test(), define_interface(), delete_test(), delta_chi_correction_test(), densityTools(), derive(), design_test(), dinucleotide_test(), diversify_sam_loop_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_motif_matcher(), dna_specificity_test(), dna_stats(), do_backrub(), do_color_by_score(), do_erraser2(), do_KIC(), do_minimization(), protocols::abinitio::JumpSpecificAbrelax.do_rerun(), dostuff(), double_helix_test(), dump_clash_pdb(), dump_efactor_pdb(), dump_insert_pdb_and_remodel_blueprint(), easy_target_test(), endo_test(), erraser2_test(), erraser_monte_carlo(), evaluate_beta_mutants.evaluate_interface(), fa_scorefxn_test(), figure_out_secstruct(), BuildFullModel.fill_and_sample_full_model(), fill_designable_set(), fillPoseAndDataList(), find_hppatches_distance(), find_hppatches_nb_graph(), full_protein_repack(), ClosabilityScore.gap_bound_cst_score(), generate_combined_model(), generate_disulfide_conformations(), protocols::abinitio::JumpSpecificAbrelax.generate_scorefxn(), BuriedUnsatPolarsFinder.generous_hbond(), get_atom_lk_burial(), get_atom_lk_energy(), get_atom_lk_energy_by_residue_no_count_pair(), get_hbond_score(), get_loop_scorefxn(), get_loop_scorefxn_old(), get_opte_data(), get_packing_score(), get_pose_energy_breakdown(), get_relax_scorefxn(), get_res_avg_lk_burial(), get_res_data_ss(), get_res_water_energy(), get_rmsd(), get_stepwise_score_function(), get_total_rebuild_fullatom_scorefxn(), get_water_hbond_score(), go(), grid_matcher(), hard_minimize(), hard_pack(), HbondZincBackbone.has_backbone_hbond(), has_clash(), HbondZinc.hbond_constraint(), helix_minimize(), helix_ST(), hermann_phase_two_minimize(), hessian_estimate(), idealize_tf_pose(), initialize_o2prime_pack(), initialize_rigid_body_sampler(), demo.D090_Ala_scan.interface_ddG(), interface_repack_test(), intra_dna_stats(), juke_sam_pos(), lariat_modeling(), lk_ball_wtd_deriv_test(), luxr_test(), main(), make_fragments(), MC_run(), measure_sequence_recovery(), methane_pair_score_test(), mg_modeler_test(), minimize_all_sidechains(), minimize_and_score(), minimize_helix(), minimize_pdb(), minimize_poses(), minimize_protocol(), minimize_sidechain(), minimize_test(), minimizer_test(), modeler_closure_test(), modeler_map_test(), modelSSLoop(), motif_dna_packer_design(), motif_scan(), demo.D040_Movemap.movemap(), MSA_design(), protocols::abinitio::JumpSpecificAbrelax.multi_fast_relax(), multivec2sf(), my_main(), not1_loop_test(), not1_test(), nucleobase_probe_score_test(), o2prime_packer(), one_chain_MC_sampling(), one_chain_ST_MC(), OPT_KEY(), optimize_pose(), optimize_weights(), pyrosetta.toolbox.py_jobdistributor.output_scorefile(), pack_interface(), pack_o2prime(), pack_phosphates(), pack_rotamers_test(), MinPackMin.pack_sidechains(), demo.D050_Packer_task.packer_task(), packRotamers(), pdb_scoring(), peptide_plane_test_OLD(), performMinimization(), place_waters_and_minimize(), demo.D020_Pose_scoring.pose_scoring(), post_rebuild_bulge_assembly(), prepare_start_model(), print_energies(), print_hbonds_test(), print_scorefxn(), protocols::abinitio::JumpSpecificAbrelax.process_decoy(), process_file_list(), process_for_motifs(), processChildren(), processChildrenIntensification(), proclose_test(), quick_score_test(), rb_test(), RBSegmentRelax_test(), real_test_GA(), rebuild_centroid_test(), rebuild_test(), region_constraint_score(), region_density_score(), region_score(), register_calcs(), protocols::abinitio::JumpSpecificAbrelax.relax(), relax_test(), HbondZinc.repack(), HbondZincBackbone.repack(), repack(), repack_pose(), repack_test(), res_lvl_analysis(), resample_full_model(), resample_full_model_test(), rescore_test(), rhiju_pack(), MinPackMin.rigid_body_minimization(), rna_backbone_rebuild_test(), rna_build_helix_test(), rna_design_gap_test(), rna_design_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_o2prime_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(), rotamer_trials_test(), RotamerAnalysis(), rotamerize_rna_test(), rottrial_residue(), rottrialmin_residue(), ConsensusFragmentMover.run(), ScoreBenchmark.run(), ScoreEachBenchmark.run(), run_pep_prep(), run_test(), RunPepSpec(), ChallengeMover.sample(), sample_rama_test(), demo.D070_Refinement.sample_refinement(), sample_state_to_state(), sample_trp_test(), sample_trp_tyr_test(), sasa_bunsats(), save_contact_info(), saxs_energy(), scan_hbond_jumps(), demo.D090_Ala_scan.scanning(), scmove_residue(), score12_plot_test(), score_clustered_frags(), score_folded_residues(), score_loop(), score_pdb(), ZincSiteEvaluator.score_pose(), score_test(), scoring_test(), screen_phosphates(), search_translations(), protocols::antibody::design::AntibodyDesignMoverGenerator.set_dock_high_res_scorefunction(), protocols::antibody::design::AntibodyDesignMoverGenerator.set_dock_low_res_scorefunction(), ZincMinimize.set_scorefunction(), protocols::antibody::design::AntibodyDesignMoverGenerator.set_scorefunction(), ScoreEachBenchmark.set_scorefxn(), ScoreAnalyticEtableBenchmark.setUp(), setup_rna_minimizer(), zinc1_homodimer_design.setup_scorefunctions(), sf2multivec(), show_clashes(), show_intrachain_energies(), show_protein_DNA_interactions(), show_residue_residue_clashes(), sidechain_fastrelax(), sidechain_sample(), simple_centroid_test(), simple_dna_test(), simple_hbond_test(), simple_loop_modeling_test(), simple_opte_test(), simple_relax(), single_position_motif_scan(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), small_min_test(), soft_pack(), spec_test(), stepwise_monte_carlo_legacy(), swa_rna_sample(), SymmAbRelaxTest(), test_gb(), test_rama(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_from_reproduce(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibility.test_reproducibility_minimizer_nstruct(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_packer_nstruct_multi_decoy_ids(), test_scorefxn_io(), tf_specificity_test(), two_base_pairs_test(), use_backrub(), vsasa_bunsats(), water_test(), water_test_fixed_O(), zf_relax_test(), zf_test(), and zif268_test().
