Referenced by utility::options::OptionCollection::add_built_in_options(), protocols::abinitio::JumpSpecificAbrelax::add_constraints(), apps::public1::scenarios::chemically_conjugated_docking::add_extra_bodies(), add_rosetta_options_0(), add_user_constraints(), adjust_ref_weights(), align_pdbs(), UBQ_E2Mover::analyze_and_filter(), UBQ_GTPase_disulfide_Mover::analyze_and_filter(), analyze_base_pair_test(), ThisApplication::analyze_tree(), protocols::abinitio::ApplicationContext::ApplicationContext(), ConstraintToolMover::apply(), RDCToolMover::apply(), PeptoidRotamerRecoverer::apply(), CenRelaxMover::apply(), dsRNA_grow::apply(), MirrorSymmTest::apply(), TestMMOP::apply(), ConstraintMinimizer::apply(), PickBAB::apply(), DeleteSegments::apply(), ElecDensMinPackMinMover::apply(), InterfaceStrandFinderMover::apply(), HolesTrainingDataMover::apply(), apps::pilot::CustomStarTreeMover::apply(), PBPotentialMover::apply(), CovalentPeptidomimeticCreator::apply(), MikeLinkerMover::apply(), Packing_energies::apply(), SSM_energies::apply(), MinTestMover::apply(), LigandDockingHbondsReporter::apply(), LDConverterMover::apply(), LoopHashRelax_Sampler::apply(), Foldptn::apply(), MinPackMinMover::apply(), RosettaHolesMover::apply(), IdentifyCDRClusters::apply(), RNA_ScoreMover::apply(), ExposedStrandMover::apply(), HDdesignMover::apply(), SimulateCryoMover::apply(), RescoreCenrot::apply(), ZincSiteEvaluator::apply(), MPFindInterfaceTestMover::apply(), HBondReporter::apply(), MyProtocol::apply(), CrystDesign::apply(), CrystFFTDock::apply(), MPFoldingMover::apply(), ViewMembraneProteinMover::apply(), MPDomainAssembly::apply(), Minimize::apply(), compute_Irmsd::apply(), apply_south_syn_to_dinucleotide_pose(), attach_abego_pools(), backrub_protocol(), base_pair_to_base_pair_test(), build_full_model_test(), build_next_nucleotide_test(), build_template(), BuildFullModel::BuildFullModel(), byres_analysis(), calc_B_values(), calc_ddg(), calc_rms_test(), calc_rmsf_and_avrg(), CalcIrms::CalcIrms(), calculate_binding_energy(), calculate_distances(), calculate_pairwise_RMSD(), CaToAllAtom::CaToAllAtom(), cen_fold(), check_inputs_for_errors(), check_option_conflicts(), check_required(), check_structures(), HDdesignMover::cloak_and_setup(), cluster_outfile_test(), cluster_outfile_test_OLD(), cluster_rotamers(), cluster_rotamers_wrapper(), cluster_silent(), cluster_silent_file_data(), cluster_test(), coarse_rna_denovo_test(), coarse_to_full_test(), collect_residue_types(), color_by_lj_test(), combine_refinement(), compare_frags_pose(), RelaxJobQueen::complete_larval_job_maturation(), compute_chem_shift_RMSD(), compute_intrinsic_deviation(), connectivity_test(), convert(), correct_rama(), count_contacts(), create_and_score_fragments(), create_ensemble(), create_MPpose(), create_rna_vall_torsions_test(), create_scorefxn(), create_theozyme_pdb(), cs_rosetta_rna_pdb(), cst_relax_test(), basic::database::db_partition_from_options(), define_movemap_extending_chain(), define_states_test(), define_variables(), DeleteSegments::DeleteSegments(), delta_chi_correction_test(), derive(), design(), design_cluster(), CrystDesign::design_cycle(), design_hits(), design_homodimer(), design_test(), designloop(), determine_output_name(), dinucleotide_test(), distribute_jobs(), dna_motif_matcher(), dna_stats(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), do_erraser2(), do_event_prediction(), do_initial_checks(), do_options_checks(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), dock(), doit(), DomainAssemblerNDocker::DomainAssemblerNDocker(), dostuff(), drrafter_error_estimation(), easy_target_test(), entropy_calculate_test(), erraser2_test(), erraser_monte_carlo(), extract_pdbs_test(), fa_refine_and_design(), basic::resource_manager::locator::FileSystemResourceLocator::FileSystemResourceLocator(), fill_designable_set(), InterfaceDDGBindJobInputter::fill_jobs(), fillPoseAndDataList(), filter_combine_long_loop(), find_close_parents(), ZincSiteEvaluator::find_zinc_site(), BBG_Cyclic_Mover::fix_disulf(), FloppyTailMover::FloppyTailMover(), protocols::abinitio::JumpSpecificAbrelax::fold(), Foldptn::Foldptn(), FragmentAssemblyMover::FragmentAssemblyMover(), basic::database::full_cache_name(), ga_main(), TCDock::gather_hits(), gen_pep_bb_frag(), gen_pep_bb_rama(), gen_pep_bb_sequential(), general_initialize(), SetupHotspotMover::generate_csts(), protocols::abinitio::JumpSpecificAbrelax::generate_scorefxn(), generateRankedAlignments(), get_aln(), get_bin_size(), utility::sql_database::DatabaseSessionManager::get_db_session(), basic::database::get_db_session(), get_env_bin_number(), get_exclid(), get_filename(), get_fragments(), get_info_test(), get_min_frag_rmsd(), get_options(), get_options_from_options_collection(), get_pose_energy_breakdown(), get_pts(), get_quota_per_silent(), get_res_data_ss(), get_rmsd(), get_rotamer_type_index(), get_scanres(), utility::sql_database::DatabaseSessionManager::get_session_mysql(), utility::sql_database::DatabaseSessionManager::get_session_postgres(), get_silent_file_tags(), get_stepwise_score_function(), get_symm_residue_name(), get_tasks_from_command_line(), get_vallfrags(), go(), protocols::jd2::RECONMPIJobDistributor::go(), graft_pdb(), graphics_main(), harvest_motifs(), harvest_scores(), HemeReplace::HemeReplace(), hermann_phase_two(), hermann_phase_two_minimize(), HubDenovo::HubDenovo(), import_and_dump_pdb(), TCDock::init(), MPInterfaceStatistics::init_from_cmd(), TestQuickRelaxMover::init_from_cmd(), MPDomainAssembly::init_from_cmd(), UBQ_E2Mover::init_on_new_input(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), FloppyTailMover::init_on_new_input(), abbinding::init_options(), PhDocking::init_options(), SampleTiltProtocol::init_options(), PhProtocol::init_options(), protocols::abinitio::JumpSpecificAbrelax::initialize_constraint_forest(), initialize_initalizeZNcst(), initialize_native_pose(), initialize_peptide(), ChallengeMover::initialize_pose(), initialize_rigid_body_sampler(), initialize_sequence_mask(), insert_stage_tag(), protocols::abinitio::JumpSpecificAbrelax::insert_template_frags(), basic::options::int2afteroption(), basic::options::intafteroption(), interface_repack_test(), JDtestmover::JDtestmover(), apps::pilot::KicSandbox::KicSandbox(), lariat_modeling(), ligand_dock_main_jd1(), utility::options::OptionCollection::load(), load_checkpoint(), HBondReporter::load_job_data(), LocalRmsd::LocalRmsd(), loop_closure_test(), LoopBuild_main(), ClosabilityScore::loophash_query(), luxr_test(), main(), make_1mer_frags(), make_disulfides(), makesplitwork(), makesplitwork_3bpy(), match_main(), MC_run(), merge_motifs(), mg_modeler_test(), minimize_pdb(), minimize_with_constraints(), minimizer_test(), modeler_closure_test(), molten_get_vallfrags(), morph_pdbs_test(), motif_dna_packer_design(), motif_scan(), MSA_design(), MSA_design_main(), apps::pilot::MultiTemplateAlignChunkMover::MultiTemplateAlignChunkMover(), mutate_and_score_RNP(), my_main(), MyScoreMover::MyScoreMover(), not1_loop_test(), not1_test(), nucleobase_probe_score_test(), one_chain_MC_sampling(), utility::sql_database::session::open_mysql_session(), utility::sql_database::session::open_postgres_session(), OPT_KEY(), optimize_embedding(), optimize_pose(), basic::options::optional_positive_intafteroption(), output_results(), output_single_motif(), pack_phosphates(), Packing_energies::Packing_energies(), PairDistance::PairDistance(), basic::database::parse_database_connection(), parse_extra_atom_list(), parse_pathway_test(), pdb_scoring(), pdb_to_silent_file(), pdb_to_silent_file_simple(), pep_phipsi_analysis(), pep_rmsd_analysis(), pep_scan_analysis(), PickBAB::PickBAB(), place_waters_and_minimize(), SimulateCryoMover::pose_to_xyz(), PoseWrap::PoseWrap(), posewrap_from_command_line(), post_rebuild_bulge_assembly(), basic::options::pre_tracer_process(), predict_AE(), Prepare(), print_pep_analysis(), print_pep_csts(), basic::options::process(), process_file_list(), process_the_pose(), processChildrenIntensification(), quick_score_test(), rb_entropy_test(), read_ERMS(), read_fasta(), read_FileVector(), read_input_weights(), read_membrane(), read_native_pose(), read_native_sequence_for_entity_elements(), read_PCAfile(), read_pose(), read_silent_input_as_library(), read_soft_segment_file(), read_structures(), read_template_structures(), read_thickness(), basic::options::real2afteroption(), basic::options::real3afteroption(), basic::options::realafteroption(), rebuild_centroid_test(), rebuild_test(), relaxloop(), remove_duplicate_motifs(), A3BHbsCreatorMover::repack(), repack_cluster(), repack_step(), report(), report_and_dump(), res_lvl_analysis(), resample_full_model_test(), reverse_convert(), rhiju_pdbstats(), rna_assemble_all_combinations_test(), rna_assemble_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_denovo(), rna_denovo_legacy(), rna_design_test(), rna_fullatom_minimize_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_idealize_test(), rna_motif_test(), rna_resample_test(), rna_sample_virtual_sugar(), RNA_ScoreMover::RNA_ScoreMover(), rna_thread_test(), RosettaHolesMover::RosettaHolesMover(), RotamerAnalysis(), rotamerize_rna_test(), run(), protocols::abinitio::JumpSpecificAbrelax::run(), DomainAssemblerNDocker::run(), MPI_Refinement_Launcher::run(), MPI_LoopHash_Launcher::run(), DockFragmentsMover::run(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), SolutionRescoreMover::run(), HubDenovo::run(), run_3bpy(), run_aio(), run_diiron_glu(), apps::pilot::momeara::HBondConformation::run_example_hbond_sweep(), run_m8(), run_mc(), run_parallel_docking(), run_pep_prep(), run_tyr_his(), run_zn2his(), RunPepSpec(), sample_rama_test(), sample_state_to_state(), save_cluster_tree_lite(), saxs_energy(), scheme_score(), score_rnp(), scoreall(), screen_phosphates(), sequence_tolerance_main(), sequence_tolerance_mf_main(), set_basic_dock_options(), SimulateCryoMover::set_bfactors(), set_file_output(), set_up_engine(), HECTMover::set_up_taskfactory(), protocols::abinitio::JumpSpecificAbrelax::setup(), protocols::abinitio::Application::setup(), setup_ca_constraints(), setup_copy_DOF_input(), setup_dinucleotide_pose(), setup_double_helix_pose(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), setup_for_folding(), protocols::abinitio::JumpSpecificAbrelax::setup_fragments(), protocols::abinitio::JumpSpecificAbrelax::setup_jumps(), setup_mask(), TryScoreFilter::setup_pose(), setup_pose_setup_class(), setup_pose_with_loop(), setup_rna_working_parameters(), setup_score_function(), setup_segment_insert(), apps::pilot::SampleSecondaryStructureAlignmentMover::setup_startree(), zinc1_homodimer_design::setup_taskfactory(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), protocols::abinitio::JumpSpecificAbrelax::setup_templates(), XMLprinterMover::setup_tf(), setup_tf(), setup_two_base_pair_pose_with_chainbreak(), sicdock_thread_num(), simple_opte_test(), simple_rotamer_recovery(), skipping_relax(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), spinner_test(), split_fa_dun(), basic::options::start_files(), stepwise_monte_carlo_legacy(), stepwise_template_test(), basic::options::stringafteroption(), superimpose_pdb(), swa_rna_cluster(), swa_rna_sample(), SymFixbbMover::SymFixbbMover(), SymmAbRelaxTest(), SymmSilentFileTest(), HDdesignMover::task_constraint_setup(), TCDock::TCDock(), test(), test_NMrelaxer(), thermal_sampler(), SimulateCryoMover::three_fine_projections_from_xyz(), transform_pose(), basic::options::truefalseoption(), TryScoreFilter::TryScoreFilter(), two_base_pairs_test(), two_base_pairs_via_loop_closure_test(), UBQ_E2Mover::UBQ_E2Mover(), user_overwrites_options(), water_test(), write_checkpoint(), zf_relax_test(), and ZincMinimize::zn_min_pack().
