Referenced by TCDock.__dock_base__(), ObjexxFCL::FArray1< T >.a(), ObjexxFCL::FArray1A< T >.a(), ObjexxFCL::FArray1D< T >.a(), ObjexxFCL::FArray1P< T >.a(), ObjexxFCL::KeyFArray1D< T >.a(), absorb_surrounded_canonicals(), PoseWrap.absrms_to_orig_subsubs(), numeric.access_Real_MathNTensor(), ObjexxFCL::Fortran.ACHAR(), ui::task::TaskView.action_output_open(), ui::task::TaskView.action_output_save_as(), PoseWrap.add_apcs_local(), protocols::abinitio::JumpSpecificAbrelax.add_constraints(), add_coordinate_constraints(), MinTestMover.add_coordinate_constraints_to_pose(), add_deviations(), protocols::moves::SimpleCstMover.add_distmax(), protocols::moves::SimpleCstMover.add_distmin(), utility::json_spirit.add_esc_chars(), apps::public1::scenarios::chemically_conjugated_docking.add_extra_bodies(), PoseWrap.add_floating_sc_csts(), basic::database::schema_generator::Schema.add_foreign_key(), apps::pilot::SampleSecondaryStructureAlignmentMover.add_gap_constraints_to_pose(), A3BHbsCreatorMover.add_hbond_and_omega_constraints_starting_at_seqpos(), add_histograms_together(), binder::IncludeSet.add_include(), binder.add_includes_to_set(), HemeBindingMover.add_initial_constraints(), utility::keys::ClassKeyMap< K, T, C >.add_key(), utility::keys::ClassKeyVector< K, T, C >.add_key(), utility::keys::SmallKeyMap< K, T >.add_key(), utility::keys::SmallKeyVector< K, T >.add_key(), numeric::interpolation::spline::CompoundInterpolator.add_range(), binder.add_relevant_include_for_decl(), binder.add_relevant_includes(), binder::ClassBinder.add_relevant_includes(), numeric::model_quality::RmsData.add_rms(), add_scores(), add_shell(), add_symm_sf4(), add_symm_zns(), pseudoTrace.add_to_C(), pseudoTrace.add_to_N(), ZincMinimize.add_zinc_constraints(), pseudoTraceRecords.addTrace(), adesign(), aidr_as_float(), alapose(), detail::bigint.align(), Link.align_c(), align_carboxyl_diiron_OLD(), ClusterCycDisulf.align_clusters(), align_helix(), Link.align_n(), PoseWrap.align_orig_pose(), align_pose(), align_sf4(), align_zns(), allifnone(), already_minimized(), analyze_interface_test(), ThisApplication.analyze_tree(), anglestats_local(), detail::ansi_color_escape< Char >.ansi_color_escape(), ObjexxFCL::ChunkVector< T >.append(), append_alanines(), append_jumpless_pose(), append_sequence_to_pose(), pointGroupHit.append_symmops(), CountContact.apply(), EnvToolMover.apply(), ConstraintToolMover.apply(), ZincMatchFilter.apply(), zinc1_homodimer_setup.apply(), CalcIrms.apply(), RMSByResStatistics.apply(), BuriedUnsatPolarsFinder.apply(), xtal_water_bunsat.apply(), zinc_helix_cap.apply(), GunnTest.apply(), PrintFeatures.apply(), RotateSAXS.apply(), DougsDockDesignMinimizeMagicMover.apply(), PeptoidDihedralGrabber.apply(), PeptiodMovieMover.apply(), PeptoidRotamerRecoverer.apply(), CartRefineWrapperMover.apply(), CenRelaxMover.apply(), dsRNA_grow.apply(), MirrorSymmTest.apply(), HemeBindingMover.apply(), GraftDesignCDRs.apply(), ComputeProfileMover.apply(), ConstraintMinimizer.apply(), InjectorMover.apply(), khSandbox.apply(), KHSandbox.apply(), mtransferase.apply(), GlycomutagenesisProtocol.apply(), LocalRmsd.apply(), PairDistance.apply(), PickBAB.apply(), Sasa.apply(), FloppyTailMover.apply(), HECTMover.apply(), sasa_qdMover.apply(), UBQ_E2Mover.apply(), PepMinMover.apply(), FoldTreeOutputter.apply(), HelicalPdbGeneratorMover.apply(), InterfaceStrandFinderMover.apply(), CustomMover.apply(), RDF_Mover.apply(), ChiMover.apply(), CycBBMover.apply(), BBMover.apply(), HolesTrainingDataMover.apply(), SimpleBBMover.apply(), MySlideMover.apply(), MyRotMover.apply(), ScMinMover.apply(), apps::pilot::CustomStarTreeMover.apply(), apps::pilot::SampleSecondaryStructureAlignmentMover.apply(), A3BHbsCreatorMover.apply(), A3BHbsDockDesignMinimizeMover.apply(), A3BPeptideBuilder.apply(), CovalentPeptidomimeticCreator.apply(), B3AADihedralGrabber.apply(), TorsionVectorMover.apply(), TriazoleCreator.apply(), TrizaolamerDockDesignMinimizeMover.apply(), JDmover.apply(), MyScoreMover.apply(), ComputeSAXSSpectrum.apply(), PrintPDDF.apply(), MinTestMover.apply(), LDConverterMover.apply(), HotspotPlacementMover.apply(), LoopHashRelax_Sampler.apply(), MakeCanonicalHelix.apply(), LigandRepackMinimizeProtocol.apply(), CenRotRelaxMover.apply(), RosettaHolesMover.apply(), IdentifyCDRClusters.apply(), GlycanClashCheckMover.apply(), APDBCMover.apply(), AnchorFinderMover.apply(), HbsDesignMover.apply(), OopDesignMover.apply(), PeptoidDesignMover.apply(), CaToAllAtom.apply(), UBQ_GTPase_disulfide_Mover.apply(), BacksideHbondFinderMover.apply(), MetalSiteFinderMover.apply(), TNM.apply(), OutputCenrotIntCoord.apply(), SmoothFragRepackMover.apply(), RepackMinCenrotMover.apply(), DetectSymmetry.apply(), SwapElementsMover1.apply(), SwapElementsMover2.apply(), MPFindInterfaceTestMover.apply(), NativeEnsemble.apply(), Benchmark.apply(), HBondReporter.apply(), MembraneMinMover.apply(), MyProtocol.apply(), FloatScRandomChi.apply(), BUNS_Output.apply(), CrystDesign.apply(), CrystCluster.apply(), CrystFFTDock.apply(), MPInterfaceStatistics.apply(), TestQuickRelaxMover.apply(), MPFoldingMover.apply(), CenRotCanonicalMover.apply(), CenRotRBRelaxMover.apply(), CenRotDockingMover.apply(), MPDomainAssembly.apply(), Minimize.apply(), ExemplarMover.apply(), NCMinimize.apply(), Hit.apply(), ConcertedTorsionMover.apply(), protocols::moves::SimpleCstMover.apply(), complex_interface_optimize.apply(), compute_Irmsd.apply(), run_score_patchdock_hotspot.apply(), run_score_hotspot.apply(), apply_all(), apply_angle_set(), apply_backbone_rotamer(), ConstraintConfig.apply_bb_csts(), ConstraintConfig.apply_cen_csts(), ConstraintConfig.apply_dcsts(), ConstraintConfig.apply_fa_csts(), apply_ideal_A_form_torsions(), apply_linked_constraints(), apply_mask(), apply_torsion_set(), apply_transform(), numeric::geometry.are_coplanar(), argmax(), aro_pack_output(), aro_pack_pdbstats_from_pose(), array2vecs(), utility::keys::ClassKeyMap< K, T, C >.assign(), utility::keys::SmallKeyMap< K, T >.assign(), ObjexxFCL::Chunk< T >.assign(), ObjexxFCL::format::Bite< T >.assign(), ObjexxFCL::ChunkVector< T >.assign(), ObjexxFCL::CArray< T >.assign(), ObjexxFCL::CArrayP< T >.assign(), IAMover.assign_IA_mover(), ObjexxFCL::Dimension.assign_if(), ObjexxFCL::Dimension.assign_if_bigger(), ObjexxFCL::Dimension.assign_if_bigger_nic(), ObjexxFCL::Dimension.assign_if_half(), ObjexxFCL::Dimension.assign_if_half_nic(), ObjexxFCL::Dimension.assign_if_nic(), assign_models(), assign_rigid_body_settings_to_clusters_test(), utility::vectorL< L, T, A >.at(), utility::vectorL< L, bool, A >.at(), numeric::xyzTriple< T >.at(), utility::small_vectorL< T, L, BUFFER_SIZE >.at(), atom_tree_torsion_test(), RDF_Mover.atom_type_name(), atom_types_test(), atom_vdw_test(), xtal_water_bunsat.atomid_is_contacting_crystallographic_water(), attach_abego_pools(), attach_simple_abego_pools(), average(), average_degree(), average_score_components(), avg_ca_position(), pointGroupHit.axis(), MinPackMin.backbone_minimization(), backbone_sampling(), backrub_min_test(), backrub_protocol(), balls_pdb(), balls_rms(), utility::io.base64_decode(), utility::io.base64_encode(), base_name(), Solver.be_shrunk(), Solver_NU.be_shrunk(), benchmark_contacts(), benzene_pair_score_test(), HBondReporter.bfactor(), numeric::interpolation::periodic_range::full.bin(), numeric::interpolation::periodic_range::half.bin(), bin2string(), numeric::MultiDimensionalHistogram.bin_index(), binder.bind_constructor(), binder.bind_function(), basic::database::insert_statement_generator::InsertGenerator.bind_row_data(), binder::ClassBinder.bind_with(), bitsasfloat(), utility::BitSet< B >.BitSet(), utility::BitVector< B >.BitVector(), bk_test(), bk_test2(), blosum_score_alignment(), Bola.Bola(), Tet4HMatchAligner.bondedN(), bp_score_calibrate(), utility::graph.breadth_first_search_prune(), numeric::kinematic_closure::radians.bridge_objects(), numeric::kinematic_closure.bridgeObjects(), numeric::kinematic_closure.bridgeObjects_nonredundant(), brute_force_matcher(), brute_mindis(), build_algned_linker(), build_bb_independent_rotamers(), numeric::kinematic_closure.build_dixon_matrices(), build_helix_test(), build_inverso_sequence(), build_polymer(), HbondZinc.build_rotamers(), numeric::kinematic_closure.build_sin_and_cos(), numeric::kinematic_closure.buildsturm(), buns_stats(), MatchSet.c2_clash_check(), MatchSet.c2_iface_check(), calc_B_values(), calc_base_centroid_rmsd(), calc_contacts(), calc_ddg(), calc_dist(), ConstraintStatsMover.calc_native_stats(), calc_rama_scores(), calc_RF(), numeric::model_quality.calc_rms(), calc_rmsd_and_clash_score(), numeric::alignment::QCPKernel< Real >.calc_rmsd_Theobald_method(), calc_RMSE(), calc_rmsf_and_avrg(), calc_sequence_score(), calc_shape_complementarity(), ConstraintStatsMover.calc_stats(), AllCrmsd.calculate(), calculate_average_residue_scores(), calculate_binding_energy(), calculate_burial(), calculate_helical_parameters(), MPInterfaceStatistics.calculate_interfaces(), calculate_moments(), calculate_order_scores(), calculate_percent_hydrophobic_distribution(), calculate_percent_hydrophobic_stats(), calculate_res_map(), Solver.calculate_rho(), Solver_NU.calculate_rho(), basic::TracerImpl.calculate_tracer_level(), calculate_variations(), capri15_relax(), capri_t033_loop_test(), capri_t033_trim_dock_test(), ObjexxFCL::CArray< T >.CArray(), ObjexxFCL::CArrayP< T >.CArrayP(), CAtrace.CAtrace(), numeric.ccd_angle(), ccd_close_zf_chainbreak(), ccd_loop_close(), ccd_test(), cen_design(), HubDenovo.cen_fold(), cen_fold(), center_ca(), center_heavy(), apps::pilot::SampleSecondaryStructureAlignmentMover.center_of_mass(), center_pose_at_origin(), centroid_rescore_test(), ch_o_pdbstats_from_pose(), chain_coords(), TwoChainInterface.chain_letter_to_number(), TwoChainTenANeighbors.chain_letter_to_number(), numeric::kinematic_closure.chainTORS(), numeric::kinematic_closure::radians.chainTORS(), numeric::kinematic_closure.chainXYZ(), numeric::kinematic_closure::radians.chainXYZ(), change_floating_sc_geometry(), ObjexxFCL::Fortran.CHAR(), PoseWrap.check(), check_all_poses_have_the_same_sequence(), check_angle_bounds(), check_chi_correct(), myspace.check_clash(), check_contact(), check_cubic_conv_test(), check_filter_rmsd(), check_for_contacts(), check_for_contacts_and_output_jump_o2prime(), check_for_contacts_and_output_jump_phosphate(), check_hydrophobic_contact(), check_intensities(), check_jump(), check_lengths(), check_protein_rna_clash(), check_redundant(), check_required_options(), check_rmsd(), PoseWrap.check_scattach_res(), utility::options::OptionCollection.check_specs(), check_spline(), basic::database.check_statement_sanity(), check_steric_overlap(), utility::options::OptionCollection.check_values(), checked_steal_fragment(), SphereNode.child(), choose_centroids(), ObjexxFCL::Chunk< T >.Chunk(), ObjexxFCL::ChunkVector< T >.ChunkVector(), CL.CL(), utility::options::VectorOption_T_< K, T >.cl_value(), numeric::geometry::hashing::xyzStripeHash.clash(), clash(), numeric::geometry::hashing::xyzStripeHash.clash_amount(), ClashCheck.clash_check(), MatchSet.clash_check(), numeric::geometry::hashing::xyzStripeHash.clash_check_ball(), ClashCheck.clash_check_naive(), MatchSet.clash_check_naive(), numeric::geometry::hashing::xyzStripeHash.clash_check_residue_pairs(), ClashCheck.clash_check_trimer(), SwapElementsMover1.clash_monomer(), numeric::geometry::hashing::xyzStripeHash.clash_not_resid(), numeric::geometry::hashing::xyzStripeHash.clash_raw(), ScoreFragmentSetMover.clash_score(), Bola.clashes(), Link.clashes(), utility::keys::ClassKeyMap< K, T, C >.ClassKeyMap(), utility::options::OptionCollection.cleaned(), cleanup_dna_chains(), numeric::VoxelGrid< T >.Clear(), xtal_water_bunsat.closest_crystallographic_water_dist(), numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >.closest_match(), numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >.closest_match_subset(), numeric::AgglomerativeHierarchicalClusterer.cluster(), cluster_rigid_body_settings_test(), cmp(), cmpcbc(), cmpHit(), cmprmsd(), cmpscore(), cmpxsc(), cnl_print(), cnl_store_hbs(), coarse_rb_test(), coarse_to_full_test(), detail.code_point_index(), numeric::xyzMatrix< T >.col(), numeric::MultiDimensionalHistogram.collapse(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), color_by_lj_test(), MatchSet.com(), numeric::model_quality.COMAS(), compare_cartesian_rmsd(), compare_chi1_2_angles(), compare_dna_energies(), compare_energies(), compare_frags_pose(), compare_gpu_result_against_cpu(), compare_residues_and_chi1_2_angles(), apps::pilot::frankdt.compare_segment_to_motif(), DomainDescription.compatible_sheet(), ObjexxFCL::Cstring.compress(), ObjexxFCL::Fstring.compress(), compute_folding_energies(), compute_interface_energy(), compute_intrinsic_deviation(), GunnTest.computeGunnTuples(), concave_hull(), concave_shell(), utility::signals::SignalHub< ReturnType, Signal >.connect(), numeric.const_access_Real_MathNTensor(), dsRNA_grow.constrain_and_minimize(), constraint_set_slice(), pointGroupHit.construct_from_basis(), contact_model_prediction(), contacts(), ObjexxFCL::IndexRange.contain(), ObjexxFCL::DynamicIndexRange.contain(), ObjexxFCL::StaticIndexRange.contain(), ObjexxFCL::DynamicIndexRange.contain_nic(), ObjexxFCL::FArray1< T >.contains(), ObjexxFCL::IndexRange.contains(), ObjexxFCL::DynamicIndexRange.contains(), ObjexxFCL::FArray1A< T >.contains(), ObjexxFCL::FArray1D< T >.contains(), ObjexxFCL::FArray1P< T >.contains(), ObjexxFCL::KeyFArray1D< T >.contains(), utility::json_spirit::Generator< Value_type, Ostream_type >.contains_composite_elements(), pointGroupHit.contains_symmop(), VecMaxElement.convert(), VecMinElement.convert(), VecMean.convert(), VecContains.convert(), convert_to_native_test(), convex_hull(), numeric::alignment.coordinate_array_broadcast_rmsd(), numeric::alignment.coordinate_array_rmsd(), numeric::alignment.coordinate_array_superimpose(), numeric::coordinate_fitting::CoordinateArray_RMSD_FlatLookup< Real >.CoordinateArray_RMSD_FlatLookup(), copy_asymm_unit_to_other_subunits(), CollectCoordinates.copy_coordinates(), copy_each_residue(), copy_residues(), copy_rotamerized_torsions(), copy_segment_bb(), protocols::abinitio::JumpSpecificAbrelax.copy_structure(), protocols::abinitio::ApplicationContext.copyStructure(), core_init_with_additional_options(), correct_dunbrack(), correct_rama(), correlation_coefficient(), count_analytically_cyclic(), count_analytically_improper_rotational(), count_bins(), SwapElementsMover2.count_clashes(), detail.count_code_points(), detail.count_digits< 4 >(), count_int_CBs_clashes(), count_numerically(), count_residue_hbonds(), count_semi_analytically_improper_rotational(), create_and_score_fragments(), create_bp_jump_database_test(), protocols::jumping::LibraryJumpSetup.create_jump_sample(), protocols::jumping::SpecificJumpSetup.create_jump_sample(), MainWindow.create_pose(), create_random_angle_from_range_list(), create_rna_benchmark_test(), create_starting_template(), utility::file.create_temp_filename(), createConstraintSet(), MatchSet.cross(), MatchSet.cross_homodimer(), numeric.cumulative(), DockFragmentsMover.cut_from_map(), cxdock_design(), cyclic_all_atom_rms(), cyclic_all_atom_rmsd(), cyclic_ca_rms(), cyclic_ca_rmsd(), cyclic_perm(), cyclic_superimpose(), cyclic_unique_bin(), cyclize_pose(), ui::network::BowmanModel.data(), ddg(), numeric::geometry::hashing::xyzStripeHash.debug_pdb(), utility.decode6bit(), dedup(), define_cut_points(), define_interface(), define_movemap_extending_chain(), define_states_test(), A3BHbsCreatorMover.delete_extra_residues(), delete_protein_from_pose(), delete_RNA_from_pose(), delete_test(), denom(), utility::DenseBoolMap< NUM_ELEMS, BASE_INDEX >.DenseBoolMap(), density_grid_search(), densityTools(), derive(), derive_MoveMap_from_cluster_lst(), describe_move(), HubDenovo.design(), design(), design_1comp(), design_AFILV(), design_AFILVEK(), design_AL(), design_all(), design_cluster(), CrystDesign.design_cycle(), design_dyad(), design_FILV(), design_FILVEK(), design_homodimer(), zinc1_homodimer_design.design_symmetric_homodimer_interface(), zinc2_homodimer_design.design_symmetric_homodimer_metal_interface(), design_target(), design_test(), protocols::jd2::RECONMPIJobDistributor.design_this_nodes_pose(), design_using_resfile(), designloop(), detect_neighbors(), devel_main(), numeric::interpolation::spline::CubicSpline.dF(), numeric::interpolation::spline::BicubicSpline.dFdx(), numeric::interpolation::spline::TricubicSpline.dFdx(), numeric::interpolation::spline::PolycubicSpline< N >.dFdxi(), numeric::interpolation::spline::BicubicSpline.dFdy(), numeric::interpolation::spline::TricubicSpline.dFdy(), numeric::interpolation::spline::TricubicSpline.dFdz(), RTminOptMultifunc.dfunc(), numeric::MultiDimensionalHistogram.dim_labels(), dimer_rms(), dinucleotide_test(), utility::signals::SignalHub< ReturnType, Signal >.disconnect(), dist(), DisulfEposDatabase.disulf(), GlycomutagenesisProtocol.disulfide_treatment(), diversify_sam_loop_test(), numeric::kinematic_closure.dixon_eig(), numeric::kinematic_closure.dixon_sturm(), numeric::kinematic_closure.dixonResultant(), dna_chain_check(), dna_coupled_rotamer_design_test(), dna_design_test_old(), dna_io_test(), dna_motif_matcher(), dna_nbr_radii_test(), dna_specificity_test(), do_clustering(), do_color_by_score(), CrystFFTDock.do_convolution(), do_cyclic_permutation(), do_event_prediction(), basic::YamlEmitter.do_indent(), basic::JsonEmitter.do_indent(), A3BHbsCreatorMover.do_mc(), basic::thread_manager::RosettaThreadManager.do_multistage_work_vector_in_threads(), PerturbStruct.do_mutate(), CrystDesign.do_reversion(), do_sc_min(), do_sc_relax(), Solver.do_shrinking(), Solver_NU.do_shrinking(), do_terminal_opt(), do_the_match(), basic::thread_manager::RosettaThreadManager.do_work_vector_in_threads(), dock(), InterfaceStrandFinderMover.dock_strands(), doit(), dostuff(), double_helix_test(), drrafter_error_estimation(), dump_bundle_pose(), dump_clash_pdb(), dump_coords(), dump_data(), dump_efactor_pdb(), dump_energy_kinemage(), dump_hbonds(), dump_movemap(), dump_multivec(), TCDock.dump_onecomp(), dump_pair_pose(), TCDock.dump_pdb(), Link.dump_pdb(), Bola.dump_pdb(), PoseWrap.dump_pdb(), dump_points_pdb(), dump_points_pdb_contacts(), dump_pose_diff(), dump_residue_kinemage(), dump_sequences(), OutputManager.dump_statistics(), dump_structure_kinemage(), dump_table(), TCDock.dump_top_hits(), dump_unique_atoms(), dumpsym(), dumpsym2(), dumpsym6(), each_aa_test(), myspace::DataClass.Emap_to_Evector(), utility.encode6bit(), numeric::MultiDimensionalHistogram.end(), basic::Emitter.end(), endo_test(), energy_cluster(), enforce_atoms_coplanar(), enforce_triazole_distance(), entropy_calculate_test(), env_sugar_test(), utility::vectorL< L, T, A >.erase_index(), utility::vectorL< L, bool, A >.erase_index(), basic::sampling::orientations::QuaternionGrid.euler(), numeric::Polynomial_1d.eval(), myspace.evaluate_and_write(), ZincSiteEvaluator.evaluate_coordinating_res_energies(), ZincSiteEvaluator.evaluate_coordinating_res_types(), ZincSiteEvaluator.evaluate_mutations_native(), evaluate_score(), ZincSiteEvaluator.evaluate_zinc_second_shell(), apps::pilot::momeara::HBondConformation.example_OH_pose(), pointGroupHit.expand(), expand_all_and_check_if_forms_lattice(), expand_chi_for_silent_structs(), numeric.expand_xforms(), extend_loop(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.extract_eigenvalues(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.extract_eigenvectors(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.extract_real_indices(), numeric::interpolation::spline::CubicSpline.F(), numeric::interpolation::spline::BicubicSpline.F(), numeric::interpolation::spline::TricubicSpline.F(), fa_cenpack_pdbstats_from_pose(), fa_refine_and_design(), detail.fallback_format(), detail::fallback_uintptr.fallback_uintptr(), ObjexxFCL::FArray< T >.FArray(), ObjexxFCL::FArray1D< T >.FArray1D(), fastpow2(), numeric::interpolation::spline::BicubicSpline.FdF(), fere_torsions(), numeric::fourier.fft(), numeric::fourier.fft2(), numeric::fourier.fft3(), figure_out_domain_map(), figure_out_domain_neighbors(), figure_out_fold_tree(), figure_out_nested_positions(), figure_out_secstruct(), figure_out_stems(), utility::file.file_delete(), files_for_openMM_test(), detail.fill(), fill_1D_vector(), fill_2D_vector(), fill_3D_vector(), fill_4D_vector(), fill_chainTORS_info(), fill_hbond_e(), fill_hbond_neighbors(), numeric::geometry::hashing::xyzStripeHash.fill_pairs(), fill_v_and_M(), MPInterfaceStatistics.fill_vectors_with_data(), fillPoseAndDataList(), ListFilter.filter(), CrystDesign.filter_and_report(), PhProtocol.finalize_res_list(), CapriTotalEnergy.finalize_total_energy(), ObjexxFCL::Cstring.find(), ObjexxFCL::Fstring.find(), find_backbone_rts_in_pose(), find_buried_unsatisfied_polars(), find_clashes(), find_closest_atom(), find_closest_points(), find_clusters(), utility::signals::SignalHub< ReturnType, Signal >.find_connection(), protocols::jd2::RECONMPIJobDistributor.find_consensus_sequence(), find_dna_chainbreaks(), find_dna_rotamers(), find_dsf(), ObjexxFCL::Fstring.find_first_not_of(), ObjexxFCL::Fstring.find_first_of(), pseudoTraceRecords.find_highest_score(), utility::options::OptionCollection.find_key_cl(), InterfaceStrandFinderMover.find_known_strand_start(), ObjexxFCL::Cstring.find_last(), ObjexxFCL::Fstring.find_last(), ObjexxFCL::Fstring.find_last_non_whitespace(), ObjexxFCL::Fstring.find_last_not_of(), ObjexxFCL::Fstring.find_last_of(), ObjexxFCL::Fstring.find_last_whitespace(), HemeReplace.find_ligand(), find_min_permutation(), find_nearest_res(), myspace.find_nearest_rot(), find_neighbors(), HbondZinc.find_neighbors(), HbondZincBackbone.find_neighbors(), find_neighbors_directional(), ObjexxFCL::Fstring.find_non_whitespace(), find_nonlocal_segment_alignments_in_pose(), find_residues_around_mutation(), utility::json_spirit.find_value(), ObjexxFCL::Fstring.find_whitespace(), HbondZinc.find_zinc(), HbondZincBackbone.find_zinc(), numeric::model_quality.findUU(), numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >.first_match(), fit_centroid_to_the_best_rot(), fit_helix_in_map(), binder.fix_boolean_types(), fix_sugar_bond_angles_CLOSE_BOND(), fix_sugar_bond_angles_EMPIRICAL(), fixbb_design(), rosetta_binders.fixedsizearray_add_on_binder(), fixH(), float_as_aidr(), numeric::VoxelArray< _Float, _Value >.floats_to_index(), ObjexxFCL.floops(), basic::TracerImpl.flush_all_channels(), fold_tree_generator(), utility::py.foo_all(), utility::py.foo_all_sp(), utility::py::Base.foo_int(), B.foo_member(), B.foo_member_const(), B.foo_static(), for(), formatter< detail::bigint >.format(), formatter< T, Char, enable_if_t< fmt::is_range< T, Char >::value &&(has_formatter< detail::value_type< T >, format_context >::value||detail::has_fallback_formatter< detail::value_type< T >, format_context >::value) > >.format(), formatter< TupleT, Char, enable_if_t< fmt::is_tuple_like< TupleT >::value > >.format(), detail.format_uint(), numeric::fourier::SHT.forwardS2(), utility.fractional_rank(), frag_extract_test(), numeric::kinematic_closure.frame(), numeric::kinematic_closure::radians.frame(), ObjexxFCL::Fstring.Fstring(), full_length_rmsd_over_reside_list_general(), basic::database.full_name(), binder.function_arguments(), binder.function_arguments_for_lambda(), binder.function_arguments_for_py_overload(), FunGroupTK.FunGroupTK(), utility::factory::Factory< P >.fxn_registry_transfer(), ObjexxFCL::format.G(), ga_main(), TCDock.gather_hits(), utility::vectorL_ZeroSelector< bool >.ge(), utility::keys::KeyLookup< K >.gen(), gen_fold_tree_for_nbr_segments(), gen_pep_bb_sequential(), numeric::random::mt19937_RG.gen_rand_all(), binder::Context.generate(), binder.generate_documentation_string_for_declaration(), generate_extended_pose(), generate_from_fiber(), generate_from_point(), utility::xsd_util.generate_human_readable_recursive(), protocols::jumping::SpecificJumpSetup.generate_jump_frags(), utility::xsd_util.generate_tag_given_options(), numeric::UniformRotationSampler.generateIcosahedralSamples(), numeric::fourier::SO3coeffs.genWigner_ds(), pseudoTrace.get(), pseudoTraceRecords.get(), BBG_Cyclic_Mover.get_A(), HBondReporter.get_aa_counts(), MPInterfaceStatistics.get_aa_statistics(), get_aligned_crd(), get_all(), numeric::interpolation::spline::PolycubicSpline< N >.get_all_derivs(), get_all_tor_id(), get_aln_resi(), get_ang_samp(), get_angle_sets(), get_angles(), get_area(), get_area_tot(), get_attachment_point_string(), get_avail_don_acc(), MPInterfaceStatistics.get_avg_charge(), MPInterfaceStatistics.get_avg_hydrophobicity(), MPInterfaceStatistics.get_avg_number_charges(), get_avrgcrd(), get_avrgpose(), get_base_pucker(), get_base_steps(), get_basepair_atoms(), get_boltzmann_probabilities(), get_bonded_rna_dof_ids(), get_bps_seq(), Solver.get_C(), get_ca_distances(), protocols::antibody::design::AntibodyDesignMoverGenerator.get_cdrs_movemap_with_overhang(), get_centroid(), MPInterfaceStatistics.get_charge(), get_chis_complicated(), CrystFFTDock.get_clash_score_exact(), get_close_and_lowE(), PoseWrap.get_closest_res_for_sc_attach(), numeric.get_cluster_data(), TCDock.get_cmp1(), TCDock.get_cmp2(), numeric::MathMatrix< T >.get_col(), get_contacts(), TCDock.get_contacts_by_component(), get_csts_from_pose(), get_cys_rts(), get_ddg(), get_deriv(), get_des_pos(), get_distances(), protocols::moves::SimpleCstMover.get_distmax(), protocols::moves::SimpleCstMover.get_distmin(), get_dots_area(), get_env_bin_number(), get_exclid(), get_filename(), get_frag_rmsd(), BBG_Cyclic_Mover.get_G(), get_hb_info(), get_hbond_rotation_samples(), apps::pilot::HelixMover.get_helix_center(), ConstraintConfig.get_highest_intrahub_seqsep(), MPInterfaceStatistics.get_hydrophobicity(), basic_format_args< Context >.get_id(), get_interface_energies(), get_interface_residues(), CrystDesign.get_interface_residues(), get_interface_score(), CrystFFTDock.get_interfaces_allatom(), numeric::interpolation::spline::SplineGenerator.get_interpolator(), BBG_Cyclic_Mover.get_L_move(), BBG_Cyclic_Mover.get_L_prime(), get_lig_rmsd(), get_lj_atom_score(), get_localreso(), get_logL_DMS(), numeric::MathNTensor< T, N >.get_mathmatrix(), get_median_structure(), get_min_frag_rmsd(), get_min_index(), get_moment_of_inertia(), TCDock.get_moments(), get_movable_jumps(), protocols::antibody::design::AntibodyDesignMoverGenerator.get_movemap_from_task(), get_mutations_from_file(), get_N(), get_n_bb_hbonds(), get_n_hbonds(), get_n_hbonds_from_pair(), get_n_mer_maltose(), get_n_mer_polyalanine(), get_n_pep_nbrs(), get_n_sc_hbonds(), get_neighbor_residues(), CrystDesign.get_neighbor_residues(), get_neighbor_subs(), Spacegroup.get_nsubdivisions(), MPInterfaceStatistics.get_number_charges(), MPInterfaceStatistics.get_number_hbonds(), MPInterfaceStatistics.get_number_of_residues(), get_obligated_rna_pairings(), get_perresE(), Link.get_phi(), get_phi_psi_mm(), get_point_groups(), numeric::interpolation::spline.get_PolycubicSpline_F(), numeric::interpolation::spline.get_PolycubicSpline_gradient(), get_pose_chains(), Link.get_psi(), get_pts(), basic.get_pymol_chain(), basic.get_pymol_chain_index_1(), SVC_Q.get_Q(), ONE_CLASS_Q.get_Q(), SVR_Q.get_Q(), get_radius(), CrystFFTDock.get_radius_of_pose(), TestQuickRelaxMover.get_repack_residues(), get_repl_xyz(), get_res_data_ss(), get_res_downstream_of_jump(), MPInterfaceStatistics.get_residue_size(), get_ring_centroids_and_stubs(), get_rmsd(), get_rmsd_debug(), get_rot_center(), get_rotamer_type_index(), get_rotset(), ClosabilityScore.get_rt_over_leap(), get_sasa(), get_sc(), get_scanres(), get_score_terms(), get_simple_RNA_protein_fold_tree(), MPInterfaceStatistics.get_size(), get_sphere_xyz(), get_subPose(), get_subpose(), get_suite_ideal_A_form_torsions(), apps::pilot::AlignChunkMover.get_superposition_transformation(), get_superposition_transformation(), get_t033_ss(), get_tag(), get_temp(), get_tenA_neighbor_residues(), binder.get_text(), get_torsion_list(), get_torsion_set(), myspace.get_touched_res(), binder.get_type_dependencies(), get_unbound_protein_score(), get_useful_fold_trees_for_gcc185(), utility::json_spirit.get_value(), BBG_Cyclic_Mover.get_VdRdPhi(), get_xyz(), utility::tag::Tag.getOption(), PerformanceBenchmark.getReport(), utility::tag::Tag.getTags(), binder::Context.global_insertion_operator(), protocols::jd2::RECONMPIJobDistributor.go(), protocols::jd2::RECONMPIJobDistributor.go_hardcoded(), go_main(), gpu_refold_test(), gpu_score_test(), graft_in_positions(), HbondZinc.graft_match(), HbondZincBackbone.graft_match(), graphics_main(), CrystDesign.greedy_revert_unsats(), grid_matcher(), zinc2_homodimer_setup.gridsearch_symmetric_alignments(), GunnTest.GunnTest(), hard_minimize(), harvest_scores(), ObjexxFCL::Cstring.has(), ObjexxFCL::Fstring.has(), utility::vectorL< L, T, A >.has(), utility::vectorL< L, bool, A >.has(), ObjexxFCL::Cstring.has_any_of(), ObjexxFCL::Fstring.has_any_of(), utility::options::ScalarOption_T_< K, T >.has_any_of_characters(), utility::options::VectorOption_T_< K, T >.has_any_of_characters(), has_cis_bonds(), utility::json_spirit.has_value(), InjectorMover.hash(), utility::tag::Tag.hasOption(), hbond_stats(), HBondedPairIterator.HBondedPairIterator(), header(), ui::ui_protocols::helical_bundle::HelicalBundleDialogueWidget.HelicalBundleDialogueWidget(), helix_axis(), helix_from_sequence(), helix_minimize(), helix_ST(), hermann_phase_two_minimize(), hessian_estimate(), homolog_finder(), numeric.hsv_to_rgb(), HubDenovo.HubDenovo(), id2torsion(), idealize_tf_pose(), MatchSet.iface_check(), iface_check_c3(), numeric::fourier.ifft(), numeric::fourier.ifft2(), numeric::fourier.ifft3(), numeric::fourier.ifft3_dynamic(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his_clamp(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), basic::TracerImpl.in(), in_cnl(), in_set(), binder::Config.includes_code(), utility::json_spirit::Generator< Value_type, Ostream_type >.indent(), ObjexxFCL::FArray1< T >.index(), ObjexxFCL::FArray1A< T >.index(), ObjexxFCL::FArray1D< T >.index(), ObjexxFCL::FArray1P< T >.index(), ui::network::BowmanModel.index(), ObjexxFCL::KeyFArray1D< T >.index(), numeric::alignment.indexed_coordinate_array_broadcast_rmsd(), numeric::VoxelArray< _Float, _Value >.indices_to_center(), TCDock.init(), myspace::GraftTester.init(), MatchBase.init(), numeric::geometry::hashing::SixDOffsetTree.init(), numeric::geometry::hashing::MinimalClashHash.init(), numeric::geometry::hashing::xyzStripeHash.init(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.init(), MatchSet.init(), numeric::random::mt19937_RG.init_by_array(), MatchSet.init_clash_check(), ClashCheck.init_clash_check(), UBQ_E2Mover.init_on_new_input(), UBQ_GTPase_disulfide_Mover.init_on_new_input(), HECTAllMover.init_on_new_input(), HECTUBQMover.init_on_new_input(), FloppyTailMover.init_on_new_input(), SequenceProfileDB.init_private_data_(), init_torsions_still_present(), numeric::random::mt19937_RG.initial_mask(), initialize_o2prime_pack(), inlist(), numeric::alignment::QCPKernel< Real >.inner_product(), input_torsion_M_v_lists(), utility::keys::ClassKeyMap< K, T, C >.insert(), utility::keys::SmallKeyMap< K, T >.insert(), basic::database.insert_or_ignore(), numeric::VoxelGrid< T >.InsertObjects(), inside_polygon(), InstantiateModulesBenchmark.instantiate_filters(), InstantiateModulesBenchmark.instantiate_movers(), InstantiateModulesBenchmark.instantiate_packer_palettes(), InstantiateModulesBenchmark.instantiate_res_selectors(), InstantiateModulesBenchmark.instantiate_reslvl_taskops(), InstantiateModulesBenchmark.instantiate_simple_metrics(), InstantiateModulesBenchmark.instantiate_taskops(), interface_energy_ratio(), interface_energymap(), interface_repack_test(), interface_residues(), interface_rmsd(), numeric::interpolation::spline::CompoundInterpolator.interpolate(), intersecting_bpy_axes(), intersecting_disulfide_axes(), pointGroupHit.intersects(), intra_dna_stats(), invariants_for_cyclic_permutation(), numeric::MathMatrix< T >.inverse_diagonal_matrix(), numeric::MathMatrix< T >.inverse_square_matrix(), numeric::MathMatrix< T >.inverse_tridiagonal_matrix(), numeric::fourier::SHT.inverseS2(), numeric::fourier::SHT.inverseSo3(), utility::vectorL< L, bool, A >.invert(), numeric::fourier::SO3coeffs.InvLegendre(), ObjexxFCL.is_any_of(), is_atom_clash(), Bola.is_connected(), Link.is_connected(), ObjexxFCL::FArray< T >.is_default(), numeric::MathMatrix< T >.is_diagonal(), utility::json_spirit.is_eq(), Solver.is_free(), ObjexxFCL::FArray2< T >.is_identity(), is_in_list(), is_in_list_of_lists(), binder::Config.is_include_skipping_requested(), numeric::IntervalSet< T >.is_inside(), is_loop(), is_loop_neighbor(), Solver.is_lower_bound(), is_regular_helix(), utility::options::OptionCollection.is_relevant(), PoseWrap.is_rsd_designable(), PoseWrap.is_rsd_repackable(), binder.is_std_function_bindable(), InterfaceStrandFinderMover.is_strand_exposed(), pseudoTrace.is_subset(), pointGroupHit.is_subset_of(), pointGroupHit.is_subset_of_ignore_shift(), numeric::MathMatrix< T >.is_tri_diagonal(), ObjexxFCL::FArray< T >.is_uniform(), Solver.is_upper_bound(), numeric::MathNTensor< T, N >.is_valid_position(), ObjexxFCL::FArray< T >.is_zero(), IsctFast.IsctFast(), isctfast(), zinc_stats::ZincStatisticGenerator.iterate_over_residues(), jacobi(), numeric.jacobi_rotation(), jitterloop(), ChallengeMover.jumps_from_pose(), jumps_to_root(), TCDock.justone(), Kernel.Kernel(), Kernel.kernel_linear(), Kernel.kernel_poly(), Kernel.kernel_precomputed(), Kernel.kernel_rbf(), Kernel.kernel_sigmoid(), utility::keys::KeyLookup< K >.key(), ObjexxFCL::KeyFArray1D< T >.KeyFArray1D(), KIC_loop_close(), numeric::fourier::kiss_fft_state.kiss_fft_state(), numeric::fourier.kiss_fft_stride(), numeric::fourier.kiss_fftnd(), kono_sarai_stats(), kono_sarai_zscore(), lariat_modeling(), ui::task::Node.leaf(), ui::task::PNode.leaf(), ui::util::TreeNodeModel< T >::Node.leaf(), ObjexxFCL::Cstring.left_justify(), ObjexxFCL::Fstring.left_justify(), utility::options::ScalarOption_T_< K, T >.legal_string(), utility::options::VectorOption_T_< K, T >.legal_string(), numeric::fourier::SO3coeffs.Legendre(), ObjexxFCL::Cstring.len_trim(), ObjexxFCL::Fstring.len_trim(), ObjexxFCL::Cstring.len_trim_whitespace(), ObjexxFCL::Fstring.len_trim_whitespace(), numeric::IntervalSet< T >.length(), ObjexxFCL::CArray< T >.length(), ObjexxFCL::CArrayP< T >.length(), ObjexxFCL::ChunkVector< T >.length(), ObjexxFCL::FArray1< T >.length(), ObjexxFCL::CArray< T >.length_squared(), ObjexxFCL::CArrayP< T >.length_squared(), ObjexxFCL::ChunkVector< T >.length_squared(), ObjexxFCL::FArray1< T >.length_squared(), utility::graph::RingDetection< Graph >.LengthOfSmallestCycleWithVertex(), levelof(), protocols::jumping::LibraryJumpSetup.LibraryJumpSetup(), ligand_centroid(), ligand_dock_main_jd1(), ligand_rmsd(), ligrot_test(), ListFilter.ListFilter(), lk_ball_wtd_deriv_test(), numeric::nls.lm_enorm(), numeric::nls.lm_lmdif(), numeric::nls.lm_lmpar(), numeric::nls.lm_printout_std(), numeric::nls.lm_qrfac(), numeric::nls.lm_qrsolv(), numeric::VoxelArray< _Float, _Value >.load(), load_coords(), TNM.load_normal_modes(), FragMonteCarlo.load_scorefiles(), local_rms(), local_rms_window(), numeric::geometry::hashing::SixDOffsetTree.lookup(), loop_closure_test(), loop_modeling_test(), loops_set_move_map(), ObjexxFCL::Cstring.lowercase(), ObjexxFCL::Fstring.lowercase(), lowercase(), ObjexxFCL.lowercase(), ObjexxFCL.lowercased(), apps::pilot::frankdt.lt(), luxr_setup(), m_inv_gen(), main(), apps::pilot::frankdt.main(), A3BHbsCreatorMover.make_a3b_pose(), make_bonded_rna_move(), make_coiled_coil(), basic::database.make_compound_statement(), TCDock.make_dimer(), make_disulfides(), make_dna_only_pose(), make_float_sc_min_mover(), make_frag_set(), make_frag_set_9mers(), VallReader.make_fragment_lines(), make_fragments(), make_helix(), make_move_map(), make_mutation_tag(), make_mutations(), make_native_olig(), VallReader.make_nmer_profile(), make_olig(), TCDock.make_pentamer(), make_pose(), make_rand_ss(), make_rand_ss_h(), make_rand_ss_hs(), make_random_perturbation(), HubDenovo.make_start_pose(), make_symm_data(), TCDock.make_tetramer(), TCDock.make_trimer(), make_two_trimers(), makemask(), makerots(), makesplitwork(), map_secstruct(), utility::json_spirit.map_to_obj(), mask_out_loop(), MatchLig.MatchLig(), numeric::MathNTensor< T, N >.MathNTensor(), numeric::model_quality.MatrixMult(), numeric::model_quality.maxsub(), MC_run(), mean(), numeric::MultiDimensionalHistogram.mean_squared_error(), measure_sequence_recovery(), basic::sampling::orientations::Permute.Member(), membrane_center_protein_core(), merge_motifs(), mg_hires_pdbstats_from_pose(), mg_pdbstats_from_pose(), HubDenovo.min_as_poly_ala(), min_index(), minimize(), minimize_all_sidechains(), minimize_ref_weights(), minimize_test(), minimize_with_constraints(), mirror_bin(), mismatch_test(), ObjexxFCL.mod(), protocols::antibody.model_cdrs(), modeler_closure_test(), modeler_map_test(), modelSSLoop(), molten_get_vallfrags(), motif_scan(), PoseWrap.move_chi(), Link.move_phi(), Link.move_psi(), MoveThenFixHMin.MoveThenFixHMin(), protocols::abinitio::JumpSpecificAbrelax.multi_fast_relax(), numeric::interpolation.multilinear_interpolation(), multimodel_gdt(), detail::bigint.multiply(), apps::pilot::MultiTemplateAlignChunkMover.MultiTemplateAlignChunkMover(), numeric::kinematic_closure.multMatrix(), numeric::kinematic_closure.multTransMatrix(), mutate_and_score_RNP(), mutate_random_residue(), mutate_to_ala(), mutate_to_sequence(), my_main(), MyRotMover.MyRotMover(), MyTransMover.MyTransMover(), utility::options::OptionCollection.n_part(), numeric::geometry::hashing::xyzStripeHash.nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.nbcount(), numeric::geometry::hashing::xyzStripeHash.nbcount_raw(), SphereSampler.nbr_begin(), SphereSampler.nbr_end(), SphereNode.neighbor(), utility::json_spirit::Semantic_actions< Value_type, Iter_type >.new_int(), new_sc(), newer_sc(), ObjexxFCL::format.nl_if(), ui::util::TreeNodeModel< T >::Node.node_index(), ui::task::PNode.node_index(), utility::graph::DisjointSets.nodes_in_set(), non_chain_coords(), ObjexxFCL::ChunkVector< T >.non_preserving_resize(), ObjexxFCL::Chunk< T >.non_preserving_resize(), normalize_info(), normalize_res_freqs(), not1_loop_test(), not1_test(), nucleobase_probe_score_test(), numeric::MultiDimensionalHistogram.num_bins(), num_nbrs(), utility::json_spirit.obj_to_map(), octree_test(), ObjexxFCL::IndexRange.offset(), ObjexxFCL::StaticIndexRange.offset(), MainWindow.on_button_run_minimizer_clicked(), detail::fixed_handler.on_digit(), detail::int_writer< OutputIt, Char, UInt >.on_num(), MainWindow.on_presets_comboBox_currentIndexChanged(), one_chain_MC_sampling(), one_chain_ST_MC(), ONE_CLASS_Q.ONE_CLASS_Q(), oneChainPose(), utility::io::izstream.open_ifstream(), ObjexxFCL.operator!=(), ObjexxFCL::byte.operator&=(), ObjexxFCL::ubyte.operator&=(), formatter< TupleT, Char, enable_if_t< fmt::is_tuple_like< TupleT >::value > >::format_each< FormatContext >.operator()(), CheeseFunction.operator()(), RTminOptMultifunc.operator()(), numeric::Polynomial_1d.operator()(), SimpleComparison.operator()(), HitCmp.operator()(), utility::keys::ClassKeyMap< K, T, C >.operator()(), utility::keys::SmallKeyMap< K, T >.operator()(), numeric::VoxelArray< _Float, _Value >.operator()(), numeric::xyzTriple< T >.operator()(), numeric::xyzVector< T >.operator()(), ObjexxFCL::FArray1< T >.operator()(), ObjexxFCL::FArray1A< T >.operator()(), ObjexxFCL::FArray1D< T >.operator()(), ObjexxFCL::FArray1P< T >.operator()(), utility::keys::Key2Vector< K >.operator()(), utility::keys::Key3Vector< K >.operator()(), utility::keys::Key4Vector< K >.operator()(), numeric::xyzMatrix< T >.operator()(), utility::json_spirit::Value_impl< Config >::Variant_converter_visitor.operator()(), ObjexxFCL::KeyFArray1D< T >.operator()(), numeric::interpolation::InterpolatedPotential< N >.operator()(), ObjexxFCL::ChunkVector< T >.operator()(), ObjexxFCL::Fstring.operator()(), numeric::MathNTensor< T, N >.operator()(), numeric::interpolation::TempStruct< T, N >.operator()(), numeric.operator*(), numeric::MathMatrix< T >.operator*=(), ObjexxFCL::FArray2< T >.operator*=(), ObjexxFCL::Dimension.operator*=(), ObjexxFCL::byte.operator*=(), ObjexxFCL::CArray< T >.operator*=(), ObjexxFCL::CArrayP< T >.operator*=(), ObjexxFCL::FArray< T >.operator*=(), ObjexxFCL::Chunk< T >.operator*=(), ObjexxFCL::ChunkVector< T >.operator*=(), ObjexxFCL::ubyte.operator*=(), operator+(), utility::BitSet< B >.operator+=(), utility::BitVector< B >.operator+=(), ObjexxFCL::CArray< T >.operator+=(), ObjexxFCL::CArrayP< T >.operator+=(), ObjexxFCL::Chunk< T >.operator+=(), ObjexxFCL::ChunkVector< T >.operator+=(), ObjexxFCL::FArray< T >.operator+=(), ObjexxFCL::Dimension.operator+=(), ObjexxFCL::byte.operator+=(), ObjexxFCL::ubyte.operator+=(), utility::BitSet< B >.operator-=(), utility::BitVector< B >.operator-=(), ObjexxFCL::CArray< T >.operator-=(), ObjexxFCL::CArrayP< T >.operator-=(), ObjexxFCL::Chunk< T >.operator-=(), ObjexxFCL::ChunkVector< T >.operator-=(), ObjexxFCL::FArray< T >.operator-=(), ObjexxFCL::Dimension.operator-=(), ObjexxFCL::byte.operator-=(), ObjexxFCL::ubyte.operator-=(), ObjexxFCL::Dimension.operator/=(), ObjexxFCL::byte.operator/=(), ObjexxFCL::CArray< T >.operator/=(), ObjexxFCL::CArrayP< T >.operator/=(), ObjexxFCL::FArray< T >.operator/=(), ObjexxFCL::Chunk< T >.operator/=(), ObjexxFCL::ChunkVector< T >.operator/=(), ObjexxFCL::ubyte.operator/=(), ObjexxFCL.operator<(), utility.operator<<(), operator<<(), numeric::kinematic_closure.operator<<(), numeric.operator<<(), ObjexxFCL.operator<<(), detail::bigint.operator<<=(), ObjexxFCL.operator<=(), detail::fill_t< Char >.operator=(), ObjexxFCL::CArray< T >.operator=(), ObjexxFCL::CArrayP< T >.operator=(), ObjexxFCL::Chunk< T >.operator=(), ObjexxFCL::ChunkVector< T >.operator=(), basic::datacache::DataCache< Data >.operator=(), ObjexxFCL::FArray< T >.operator=(), ObjexxFCL::Dimension.operator=(), utility::keys::ClassKeyMap< K, T, C >.operator=(), utility::keys::SmallKeyMap< K, T >.operator=(), ObjexxFCL::byte.operator=(), basic::svd::SVD_Solver.operator=(), utility::tag::Tag.operator=(), ObjexxFCL::ubyte.operator=(), utility::keys::ClassKeyVector< K, T, C >.operator=(), utility::keys::KeyVector< K, T >.operator=(), utility::keys::SmallKeyVector< K, T >.operator=(), ObjexxFCL.operator==(), ObjexxFCL.operator>(), ObjexxFCL.operator>=(), operator>>(), utility::BitSet< B >.operator[](), utility::BitVector< B >.operator[](), utility::keys::ClassKeyMap< K, T, C >.operator[](), utility::keys::ClassKeyVector< K, T, C >.operator[](), utility::keys::SmallKeyMap< K, T >.operator[](), utility::keys::SmallKeyVector< K, T >.operator[](), utility::vectorL< L, T, A >.operator[](), utility::vectorL< L, bool, A >.operator[](), numeric::xyzTriple< T >.operator[](), numeric::xyzVector< T >.operator[](), utility::keys::Key2Vector< K >.operator[](), utility::keys::Key3Vector< K >.operator[](), utility::keys::Key4Vector< K >.operator[](), SphereSampler.operator[](), ObjexxFCL::CArray< T >.operator[](), ObjexxFCL::CArrayP< T >.operator[](), ObjexxFCL::Chunk< T >.operator[](), ObjexxFCL::ChunkVector< T >.operator[](), ObjexxFCL::Cstring.operator[](), ObjexxFCL::FArray< T >.operator[](), ObjexxFCL::FArray1D< T >.operator[](), ObjexxFCL::FArray2D< T >.operator[](), ObjexxFCL::FArray3D< T >.operator[](), ObjexxFCL::FArray4D< T >.operator[](), ObjexxFCL::FArray5D< T >.operator[](), ObjexxFCL::FArray6D< T >.operator[](), ObjexxFCL::Fstring.operator[](), ObjexxFCL::KeyFArray1D< T >.operator[](), ObjexxFCL::KeyFArray2D< T >.operator[](), ObjexxFCL::KeyFArray3D< T >.operator[](), ObjexxFCL::KeyFArray4D< T >.operator[](), ObjexxFCL::KeyFArray5D< T >.operator[](), ObjexxFCL::KeyFArray6D< T >.operator[](), utility::small_vectorL< T, L, BUFFER_SIZE >.operator[](), ObjexxFCL::byte.operator^=(), ObjexxFCL::ubyte.operator^=(), utility::BitSet< B >.operator|=(), utility::BitVector< B >.operator|=(), ObjexxFCL::byte.operator|=(), ObjexxFCL::ubyte.operator|=(), optimize_weights(), basic::sampling::orientations::QuatSet.Orientation(), utility::json_spirit::Generator< Value_type, Ostream_type >.output(), utility::xsd_util.output_all_tag_options(), output_angles(), utility::json_spirit::Generator< Value_type, Ostream_type >.output_array_or_obj(), output_backbone_stats(), output_benchmark_stuff(), output_canonical_base_pair_steps(), output_centroid_stats(), output_chainTORS(), output_chi_stats(), utility::json_spirit::Generator< Value_type, Ostream_type >.output_composite_item(), output_constraints(), output_constraints_for_full_length(), output_contact_info(), output_csts(), output_distance_matrix(), output_general_base_pair_steps(), output_interface_graphviz(), output_minipose_coords_test(), output_native_ss_info(), output_packstat(), output_packstat_pdb(), output_PCA(), output_pdb(), output_results(), output_ss_info(), output_strand1_strand2_info(), output_struct_type(), output_stuff(), output_sugar_geometry_parameters(), output_sugar_internal_dof(), output_torsion_list(), output_torsion_M_v_lists(), output_torsions(), ScoreFragmentSetMover.overlap_score(), overlay_bb_bondangles(), apps::public1::scenarios::chemically_conjugated_docking.pack_extra_bodies(), pack_interface(), pack_it(), pack_o2prime(), pack_phosphates(), pack_sidechains(), ui::network::BowmanModel.parent(), SphereNode.parent(), parse_chains(), ConstraintConfig.parse_config_file(), parse_extra_atom_list(), parse_into_stub(), parse_nonstandard_angles(), parse_nonstandard_bondlengths(), parse_pathway_test(), parse_pdb_pos(), parse_resfile(), parse_resfiles(), ConstraintConfig.parse_residues(), ui::viewers.parse_score_file(), parse_ss_regions(), abbinding.partners_from_info(), passes_quality_check(), path_distance_OK(), SphereSample.pdb_from_level(), pdb_little_motif_test(), pdbslice(), peek(), pep_phipsi_analysis(), pep_rmsd_analysis(), pep_scan_analysis(), PerformanceBenchmark.PerformanceBenchmark(), numeric::random::mt19937_RG.period_certification(), permutate(), basic::sampling::orientations::Permute.Permute(), perturb_and_rescore(), perturb_bb_and_relax(), UniformPerturber.perturb_chain(), phosphate_stats(), pick_normal_sampling(), ConstraintConfig.pick_sequence(), place_sf4(), place_waters_and_minimize(), place_zns(), plot_scoreterm(), numeric::kinematic_closure.point_value16(), numeric::kinematic_closure.point_value2(), numeric::kinematic_closure.point_value4(), numeric::kinematic_closure.point_value6(), numeric::kinematic_closure.point_value8(), points_in_triangle(), polar_pdbstats_from_pose(), pose2bin(), pose2frags(), pose_cbcount(), pose_from_posedata(), myspace.pose_from_scratch(), pose_list_compare(), pose_pos_from_pdb_pos(), PoseWrap.PoseWrap(), posewrap_from_command_line(), positions_incompatible_with_task(), power_set(), TCDock.precompute_intra(), predict_chem_map_test(), predict_disorder(), utility::options::OptionCollection.prefix(), Prepare(), prepare_full_length_start_model(), prepare_start_model(), prepare_threaded_model(), numeric.principal_components_and_eigenvalues(), numeric.principal_components_and_eigenvalues_ndimensions(), basic::sampling::orientations::QuaternionGrid.print(), basic::sampling::orientations::QuatSet.Print(), basic::database::schema_generator::Index.print(), basic::database::schema_generator::ForeignKey.print(), basic::database::schema_generator::UniqueConstraint.print(), MPInterfaceStatistics.print_aa_statistics(), print_base_centroid_atoms(), print_ddgs(), JDmover.print_features(), print_hb_counts(), print_hbonds_test(), print_motifs(), print_movemap(), print_passed(), print_pep_analysis(), print_pep_csts(), numeric.print_probabilities(), print_res_freqs(), print_res_ids(), DesignGlycansProtocol.print_sequences(), print_torsions_check(), print_verbose_ddgs(), printbits(), printbits16(), printbits32(), printBondAngles(), printEnergies(), numeric::kinematic_closure.printTranspose(), DisulfideBondEnergy.probability(), DockFragmentsMover.process_fragfile(), process_pose(), process_ss_str(), process_the_pose(), processChildren(), processChildrenIntensification(), proclose_test(), numeric.product(), basic.prof_show(), numeric::geometry.projection_area(), proline_rama_pdbstats_from_pose(), prune_away_cnl(), utility::factory::Factory< P >.ptr_registry_transfer(), basic::sampling::orientations.QuatDBMetatada_cmpcover(), basic::sampling::orientations.QuatDBMetatada_cmpradius(), basic::sampling::orientations.QuatDBMetatada_cmpsize(), basic::sampling::orientations::QuaternionGrid.quaternion(), basic::sampling::orientations::QuaternionGrid.QuaternionGrid(), quick_score_test(), numeric::linear_algebra.qzhes(), numeric::linear_algebra.qzit(), numeric::linear_algebra.qzval(), numeric::linear_algebra.qzvec(), myspace.ramp_repack_min(), rand_Vec(), Bola.random_close_phipsi_from_rama(), Bola.random_move(), Bola.random_nonclashing_move(), numeric::random.random_permutation(), numeric::IntervalSet< T >.random_point(), numeric::random::WeightedSampler.random_sample(), random_torsions(), randomly_open_pose_loop(), rb_test(), RDF_Mover.RDF_Mover(), ObjexxFCL.read_binary(), read_complex_type(), read_covalent_connections_file(), read_distances(), read_ERMS(), read_fragdata(), read_frags(), read_input_weights(), read_PCAfile(), read_pdbs(), read_rama_map_file(), read_rigid_body_settings(), read_silent_input_as_library(), read_soft_segment_file(), read_sphere(), SphereSample.read_sphere_data(), numeric.read_tensor_from_file(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.real_eigenvalues(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.real_eigenvectors(), real_test_GA(), reavrg(), rebuild_test(), rebuild_trimmed_loops(), Solver.reconstruct_gradient(), zinc_stats::ZincStatisticGenerator.recursively_model_rotamer_chis(), refine(), refine_pose(), Bola.refold(), refold_first(), refold_ros(), refold_second(), register_options(), relax_cenrot_pose(), relax_test(), relax_with_restraints_on_constres(), relaxloop(), utility::signals::BufferedSignalHub< ReturnType, Signal >.release_buffer(), utility::keys::KeyLookup< K >.remove(), remove_all_virtual_residues(), remove_dashes(), remove_drift(), utility::signals::SignalHub< ReturnType, Signal >.remove_invalid(), remove_membrane_residue(), numeric::UniformRotationSampler.remove_redundant(), numeric::VoxelGrid< T >.RemoveObjects(), reorder_foldtree(), reorient_to_base_pair_coordinate_system(), HbondZinc.repack(), HbondZincBackbone.repack(), repack(), repack_all(), repack_cluster(), repack_iface(), repack_test(), binder.replace(), numeric::MathMatrix< T >.replace_col(), numeric::MathNTensor< T, N >.replace_layer(), replace_nat_seq(), binder.replace_reverse(), PoseWrap.replace_scattach_res(), replace_string(), replace_torsion_angles(), report(), report_and_dump(), myspace::DataClass.report_by_aa(), GlycanClashCheckMover.report_data(), myspace.report_data(), FragMonteCarlo.report_score(), basic::sampling::orientations::QuaternionGridManager.request_by_radius(), basic::sampling::orientations::QuaternionGridManager.request_by_size(), rescale_phosphate_charges(), rescore(), rescore_test(), ObjexxFCL::Chunk< T >.reserve(), ui::ui_protocols::helical_bundle::HelicalBundleDialogueWidget.reset_controls_dependent_on_other_helix(), numeric::MultiDimensionalHistogram.reset_counts(), ConstraintConfig.reset_csts(), HubDenovo.reset_hub(), numeric::geometry.residual_squared_of_points_to_plane(), ConstraintConfig.residue_names_from_sequence(), numeric::VoxelArray< _Float, _Value >.resize(), numeric::fourier::kiss_fft_state.resize(), numeric::fourier::kiss_dct_state.resize(), numeric::fourier::kiss_fftr_state.resize(), ObjexxFCL::Chunk< T >.resize(), ObjexxFCL::CArray< T >.resize(), ObjexxFCL::CArrayP< T >.resize(), ObjexxFCL::ChunkVector< T >.resize(), numeric::fourier::kiss_fftnd_state.resize(), numeric::fourier::kiss_fftndr_state.resize(), numeric::MultiDimensionalHistogram.resize_counts(), numeric::random::mt19937_RG.restoreState(), PerturbStruct.revert_muations(), ObjexxFCL::Cstring.right_justify(), ObjexxFCL::Fstring.right_justify(), ObjexxFCL::FArray2< T >.right_multiply_by_transpose(), MinPackMin.rigid_body_minimization(), DisulfEposDatabase.rms(), numeric::model_quality.rms_fit(), PoseWrap.rms_to_orig_subsubs(), numeric::model_quality.rms_wrapper_slow_and_correct(), rmsd_compute(), abbinding.rmsd_frmk_chothia_num_ab(), rmsd_over_base(), numeric::model_quality.rmsfitca2(), numeric::model_quality.rmsfitca3(), rna_backbone_rebuild_test(), rna_build_helix_test_precompute(), rna_chain_closure_test(), rna_close_chainbreaks_test(), rna_design_gap_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_test(), rna_o2prime_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), rna_sequence_recovery_metrics(), rna_stack_pdbstats_from_pose(), rna_suitename(), rna_superimpose_and_graft_test(), rna_torsion_check_test(), rotamerize_rna_test(), rotamerize_structure(), Link.rotate(), rotate_into_nucleobase_frame(), numeric::kinematic_closure.rotateX(), numeric::kinematic_closure::radians.rotateX(), numeric::kinematic_closure.rotateY(), numeric::kinematic_closure::radians.rotateY(), numeric::kinematic_closure.rotateZ(), numeric::kinematic_closure::radians.rotateZ(), RotSel.RotSel(), round(), numeric::xyzMatrix< T >.row(), ui::network::BowmanModel.rowCount(), numeric::model_quality.rsym_evector(), numeric::model_quality.rsym_rotation(), numeric::xyzTransform< T >.rt6(), protocols::abinitio::CustomAbinitio.run(), DomainAssemblerNDocker.run(), TryScoreFilter.run(), run(), MPI_Refinement_Launcher.run(), TCDock.run(), DockFragmentsMover.run(), FragmentAssemblyMover.run(), ConsensusFragmentMover.run(), ui::task::FunctorSequence.run(), FragMonteCarlo.run(), DesignBenchmark.run(), DockingBenchmark< dock, TScale >.run(), LigandDockBenchmark.run(), MinimizerBenchmark< sft, TScale >.run(), OptionCollectionBenchmark.run(), PDB_IOBenchmark.run(), ScoreBenchmark.run(), ScoreEachBenchmark.run(), ShearMoverBenchmark.run(), SmallMoverBenchmark.run(), XMLParseBenchmark.run(), run_3bpy(), run_diiron_glu(), run_hd(), run_hh(), run_m8(), run_mc(), run_parallel_docking(), run_pep_prep(), basic::svd::SVD_Solver.run_score_svd_on_matrix(), basic::svd::SVD_Solver.run_score_svd_without_solving(), run_sf4h(), run_trace(), run_tyr_his(), run_zn2his(), RunPepSpec(), ChallengeMover.sample(), SphereSample.sample(), SphereSample.sample1(), SphereSample.sample2(), SphereSample.sample3(), SphereSample.sample4(), SphereSample.sample5(), SphereSample.sample6(), SphereSample.sample7(), sample_near_current_torsion(), sample_near_suite_torsion(), sample_rama_test(), sample_rna_dofs_new(), sample_trp_test(), SamplingManager.SamplingManager(), SphereSample.sanity_check(), numeric::geometry::hashing::xyzStripeHash.sanity_check(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.sanity_check(), sasa_separation(), numeric::VoxelArray< _Float, _Value >.save(), save_contact_info(), save_ss_info(), numeric::random::mt19937_RG.saveState(), A3BHbsCreatorMover.scan(), myspace.scan_Evalue(), scan_hbond_jumps(), scmove_residue(), FragmentAssemblyMover.score(), score12_plot_test(), CapriTotalEnergy.score_experimental_constraints(), numeric::kinematic_closure.scpn(), numeric::kinematic_closure::radians.scpn(), search_other_atoms(), search_translations(), select_loop_residues(), select_residues_for_evaluation(), select_string(), Solver.select_working_set(), separation(), sequence_tolerance_main(), sequence_tolerance_mf_main(), set_all_loop_dihedrals_to_180(), set_basic_dock_options(), protocols::antibody::design::AntibodyDesignMoverGenerator.set_cdr_range(), protocols::antibody::design::AntibodyDesignMoverGenerator.set_cdrs(), set_chain_end_fold_tree(), ObjexxFCL::FArray2< T >.set_diagonal(), protocols::moves::SimpleCstMover.set_distmax(), protocols::moves::SimpleCstMover.set_distmin(), ui::ui_protocols::helical_bundle::HelicalBundleDialogueWidget.set_everything_except_delta_omega0_copies_helix1(), MinTestMover.set_foldtree_for_variable_movement(), set_fullatom_flag_test(), ui::ui_protocols::helical_bundle::HelicalBundleDialogueWidget.set_helix_index(), set_ideal_geometry(), basic::Emitter.set_indent(), numeric::interpolation::Histogram< X, Y >.set_interpolator(), basic::svd::SVD_Solver.set_matrix_A(), set_pattern(), myspace::Scheduler.set_pertscale(), Link.set_phi(), Link.set_phi_psi(), set_pose_conformation(), utility::sql_database::DatabaseSessionManager.set_postgres_schema_search_path(), Link.set_psi(), PoseWrap.set_root_atomno(), set_sc_repacking(), set_secstruct_from_psipred_ss2(), set_torsion_and_align(), numeric::MathMatrix< T >.set_unit(), set_up_covalent_connections(), set_up_pose(), HECTMover.set_up_taskfactory(), numeric::MathNTensor< T, N >.set_value(), basic::svd::SVD_Solver.set_vector_b(), utility::graph::DisjointSets.sets(), numeric::random::mt19937_RG.setSeed(), MinimizerBenchmark< sft, TScale >.setUp(), setup_align_atom_map(), setup_alignment_map(), setup_atom_id_map(), setup_atom_number(), setup_backbone_atoms(), setup_bonded_protein_rna_pose(), setup_CA_constraints(), setup_ca_constraints(), setup_capri_data(), setup_coord_csts(), setup_design_res(), setup_dinucleotide_pose(), setup_domain_list(), setup_double_helix_pose(), setup_favor_native(), nacl_rosetta::RosettaInstance.setup_file_handler(), protocols::abinitio::JumpSpecificAbrelax.setup_fold(), abbinding.setup_foldtree(), PhDocking.setup_foldtree(), setup_for_folding(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_general_min_foldtree(), setup_heavy_atoms(), zinc2_homodimer_setup.setup_homodimer(), setup_hydrophobic_cbetas(), protocols::abinitio::JumpSpecificAbrelax.setup_jumps(), BBG_Cyclic_Mover.setup_locker(), setup_loops_fragment_libraries_with_ss(), setup_loops_from_mapping(), CrystFFTDock.setup_maps(), setup_mask(), zinc2_homodimer_design.setup_metalsite(), zinc1_homodimer_design.setup_metalsite_constraints(), CalcIrms.setup_native(), setup_one_chain_pose(), setup_per_residue_rmsd_atom_map(), numeric::fourier::SHT.setup_Pmls(), TryScoreFilter.setup_pose(), setup_pose(), setup_pose_with_loop(), setup_repeat_symminfo(), setup_rhiju_fold_tree(), setup_rmsd_atom_map(), CapriTotalEnergy.setup_rna_atoms_for_pose(), setup_rna_base_pair_constraints(), setup_rna_chainbreak_constraints(), setup_sam_constraints(), setup_sam_constraints_for_t033(), setup_secstruct(), setup_secstruct_dssp(), apps::pilot::SampleSecondaryStructureAlignmentMover.setup_startree(), setup_symmetric_dimer(), basic.setup_tag2string(), zinc1_homodimer_design.setup_taskfactory(), zinc2_homodimer_design.setup_taskfactory_scorefunction_movers(), setup_two_base_pair_pose(), setup_two_base_pair_pose_with_chainbreak(), numeric::fourier::SHT.setup_Wig(), setup_zf_pose(), numeric::random.sformat_idxof(), numeric::fourier::SHT.sharm_invTransform(), numeric::fourier::SHT.sharm_transform(), DomainDescription.sheet_match(), shift_angles(), shift_center_and_PCA(), show(), pointGroupHit.show(), numeric::Polynomial_1d.show(), utility::options::OptionCollection.show_accessed_options(), utility::options.show_accessed_options_T(), utility::options::OptionCollection.show_all(), utility::options::OptionCollection.show_all_hier(), show_clashes(), ConstraintConfig.show_cst_grids(), utility::options::OptionCollection.show_help(), utility::options::OptionCollection.show_help_hier(), utility::options::OptionCollection.show_inaccessed_user_options(), show_intrachain_energies(), show_protein_DNA_interactions(), show_rasmol_hbonds(), show_residue_hbonds(), ConstraintConfig.show_sequence(), utility::options::OptionCollection.show_table_text(), utility::options::OptionCollection.show_table_Wiki(), utility::options::OptionCollection.show_unused_options(), utility::options.show_unused_options_T(), utility::options::OptionCollection.show_user(), ObjexxFCL::Chunk< T >.shrink(), sic_fast_x(), sicdock_thread_num(), sicfast(), sidechain_sample(), sidechain_sasa(), sigmoid_train(), simple_centroid_test(), simple_frag_test(), simple_loop_modeling_test(), simple_minimization(), simple_opte_test(), simple_packing(), simple_rotamer_recovery(), simple_rotamer_test(), protocols::moves::SimpleCstMover.SimpleCstMover(), simulate_ERMS(), numeric::kinematic_closure.sincos(), numeric::kinematic_closure::radians.sincos(), single_position_motif_scan(), single_sasa_calc(), slice_ellipsoid_envelope(), slice_pdb(), utility::keys::SmallKeyMap< K, T >.SmallKeyMap(), numeric::fourier::SHT.so3_correlate(), numeric::fourier::SHT.so3CombineCoef(), Solver.Solve(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), numeric::kinematic_closure.solve_sturm(), utility::keys::ClassKeyVector< K, T, C >.sort(), sort_mine(), sortclusterlist(), spanfile_for_each_chain(), spec_test(), numeric::fourier::SHT.sph_standardize(), sphere_coverage(), SphereSampler.SphereSampler(), spinner_test(), numeric::interpolation::spline.spline_second_derivative(), utility.split(), binder.split(), utility.split_by_newlines(), utility.split_to_list(), utility.split_to_set(), detail::bigint.square(), PoseWrap.ss(), ConstraintConfig.ssstr(), utility::Inline_File_Provider.standardise_filename(), numeric::MultiDimensionalHistogram.start(), start_file_test(), basic::options.start_files(), numeric::fourier::kiss_fftnd_state.states(), myspace.stdev(), stepwise_template_test(), store_energies(), storeposedata(), utility.string2float(), utility.string2int(), utility.string2Real(), utility.string2Size(), utility.string_split(), utility.string_split_multi_delim(), utility.string_split_simple(), utility.string_to_sha1(), strip_termini(), HubDenovo.stupid_ddg(), ui::task::TaskSyncer_TaskStrategy.subscribe(), utility::json_spirit.substitute_esc_chars(), detail::bigint.subtract_aligned(), utility::options::OptionCollection.suffix(), sum(), numeric::geometry::hashing::SixDOffsetTree.sum_radius(), superimpose_pose(), superimpose_tmalign(), basic::svd::SVD_Solver.svbksb(), SVC_Q.SVC_Q(), basic::svd::SVD_Solver.SVD_Solver(), basic::svd::SVD_Solver.svdcmp(), numeric::linear_algebra.svdcmp(), svm_binary_svc_probability(), svm_check_parameter(), svm_cross_validation(), svm_free_model_content(), svm_get_labels(), svm_get_sv_indices(), svm_group_classes(), svm_load_model(), svm_predict_probability(), svm_predict_values(), svm_save_model(), svm_svr_probability(), svm_train(), svm_train_one(), ObjexxFCL::format.SW(), utility.swap4_aligned(), TCDock.swap_axis(), numeric::MathMatrix< T >.swap_cols(), Cache.swap_index(), Solver.swap_index(), Kernel.swap_index(), SVC_Q.swap_index(), ONE_CLASS_Q.swap_index(), SVR_Q.swap_index(), ui::task::Task.swap_jobs(), numeric::MathMatrix< T >.swap_rows(), swapalignmentvector(), swapchains(), PoseWrap.switch_to_cen(), switch_to_cen(), PoseWrap.switch_to_fa(), switch_to_fa(), symm_self_rep(), SymmAbRelaxTest(), ObjexxFCL::FArray2< T >.symmetric(), symmetrize_map(), Spacegroup.symmop(), SymRBMover.SymRBMover(), basic::ComparingTracer.t_flush(), basic::database.table_exists(), basic::database::schema_generator::Schema.table_schema_statements(), PoseWrap.tag(), tar_motif_test(), target_constraints(), HDdesignMover.task_constraint_setup(), TCDock.TCDock(), binder.template_specialization(), test(), test_actcoord(), test_bridgeObjects(), numeric::kinematic_closure.test_bridgeObjects(), myspace::GraftTester.test_cart_graft(), numeric::kinematic_closure.test_chainParams(), numeric::kinematic_closure.test_chainTORS(), numeric::kinematic_closure.test_chainXYZ(), test_chunk(), test_cofactor(), test_deriv(), test_deriv_pose(), numeric::kinematic_closure.test_dixon(), test_dunbrack_io(), numeric::kinematic_closure.test_frame(), FunctorTest.test_functor_async_sequence(), FunctorTest.test_functor_sequence(), test_GA(), test_gb(), test_gpu_inlining(), test_gpu_speed(), InterfaceFeaturesTests.test_interfaces(), test_k_square(), test_kc(), test_kc2(), test_known_value(), test_lh_counts(), myspace.test_loophash(), myspace.test_MD(), test_membrane_chain(), test_membrane_conformation(), test_membrane_fold_tree(), myspace.test_NMrelaxer(), test_NMrelaxer(), test_pack14(), test_Random(), myspace::GraftTester.test_rb_min_graft(), test_refold(), test_replicate_xform(), InterfaceFeaturesTests.test_reporter(), numeric::kinematic_closure.test_rotateX(), test_suck_res(), test_sugar(), FunctorTest.test_task_upload(), test_Vec(), test_vs_dots(), testone(), tf_specificity_test(), utility::json_spirit.throw_error(), numeric::kinematic_closure::radians.to_degrees(), ObjexxFCL::FArray2< T >.to_diag(), ObjexxFCL::FArray2< T >.to_identity(), to_integer(), numeric::kinematic_closure::radians.to_radians(), numeric::kinematic_closure.torsion(), numeric::kinematic_closure::radians.torsion(), torsion2big_bin_string(), torsion2decoy(), torsion2id(), torsion2pdb(), torsion_convert(), traceCAs(), TracerDiskSpaceTest(), numeric::interpolation::spline::CubicSpline.train(), numeric::interpolation::spline::PolycubicSpline< N >.train(), pointGroupHit.transform(), transforms_equiv(), transmit_additional_info(), numeric::MathMatrix< T >.transpose(), ObjexxFCL::FArray2< T >.transpose(), ObjexxFCL.transposed(), traverse_for_hbonds(), numeric::kinematic_closure::radians.triaxialCoefficients(), numeric::kinematic_closure.triaxialCoefficients(), utility::options::OptionCollection.trim(), trim_and_add_jump_data(), trim_back_t033_pose(), trim_dock_rebuild_relax_test(), trim_pdb(), utility::options::OptionCollection.trimmed(), utility::file.trytry_ifstream_open(), utility::file.trytry_ofstream_open(), two_base_pairs_via_loop_closure_test(), twoChainPose(), unbound_protein_minimization(), numeric::UniformRotationSampler.UniformRotationSampler(), ObjexxFCL.unique(), ObjexxFCL.uniqued(), unsatisfied_buried_polars(), up_jump_tree(), Solver.update_alpha_status(), update_backbone(), update_constraints(), ui::ui_protocols::helical_bundle::HelicalBundleDialogueWidget.update_control_dependencies_given_helix_to_be_removed(), numeric::random::WeightedSampler.update_cumulative_distribution(), PoseWrap.update_designable_packable(), MainWindow.update_helix_indices(), MainWindow.update_later_helix_dependencies(), update_nucleoside(), MainWindow.update_residue_selector(), update_system(), update_torsion_set(), ui::task::TaskSubmit.update_ui_from_task(), FragMonteCarlo.updated_covered_rsds(), updateSSAtoms(), ObjexxFCL::Cstring.uppercase(), ObjexxFCL::Fstring.uppercase(), ObjexxFCL.uppercase(), ObjexxFCL.uppercased(), use_backrub(), use_in_rmsd(), use_in_rmsd_offset(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.utility_vector_binder(), numeric::MathNTensor< T, N >.value(), utility::options::ResidueChainVectorOption.values_of(), vary_geometry_backbone(), vary_geometry_RNA(), vary_geometry_sidechains(), vdw_stats(), vecs2vv(), numeric::geometry.vector_normal_to_ring_plane_of_best_fit(), numeric::kinematic_closure.vectorDiff(), numeric::kinematic_closure.vectorsEqual(), viewer_main(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.visit(), numeric::geometry::hashing::xyzStripeHash.visit(), numeric::geometry::hashing::xyzStripeHash.visit_lax(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.visit_lax(), visualize(), numeric::VoxelArray< _Float, _Value >.VoxelArray(), vv2vecs(), wait_for_gdb(), water_test(), water_test_fixed_O(), basic::sampling::orientations::QuaternionGrid.weight(), basic::sampling::orientations::QuatSet.Weight(), weights(), PoseWrap.which_sub(), which_subsub(), PoseWrap.which_subsub(), numeric::fourier::SO3coeffs.wignerSynthesis(), numeric::fourier::SO3coeffs.wignerSynthesisDiffSign(), numeric::fourier::SO3coeffs.wignerSynthesisSameSign(), utility::options::OptionCollection.wrapped(), wriggle_test(), protocols::moves::SimpleCstMover.write(), PBPotentialMover.write_APBS_config(), write_base_pair_step_to_silent_struct(), ObjexxFCL.write_binary(), write_cluster_frags(), write_distances(), write_output_files(), RDF_Mover.write_R_data_file(), basic::Emitter.write_raw(), write_schema_to_db(), SampleTiltProtocol.write_score_to_outfiles(), basic::database::insert_statement_generator::InsertGenerator.write_to_database_sequential(), MatchSet.write_to_file(), write_to_restype_file(), CrystFFTDock.writeMRC(), xform_rsd_gl2(), rosetta_binders.xyzMatrix_add_on_binder(), rosetta_binders.xyzVector_add_on_binder(), zero_occ_for_deleted_atoms(), zf_relax_test(), zif268_test(), ZincMinimize.zn_min_pack(), CL.~CL(), SphereSample.~SphereSample(), and basic::TracerImpl.~TracerImpl().
