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Rosetta
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Variables | |
| ocstream | cout (std::cout) |
| Wrapper around std::cout. More... | |
| ocstream | cerr (std::cerr) |
| Wrapper around std::cerr. More... | |
| ocstream | clog (std::clog) |
| Wrapper around std::clog. More... | |
| ocstream utility::io::oc::cerr | ( | std::cerr | ) |
Wrapper around std::cerr.
Referenced by add_constraints(), append_sequence_to_pose(), DummyMover::apply(), RotateSAXS::apply(), ConstraintMinimizer::apply(), RDF_Mover::apply(), PBPotentialMover::apply(), CustomMover::apply(), utility::io::mpi_stream::basic_mpi_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::basic_mpi_streambuf(), calc_ddg(), 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(), PoseWrap::check(), check_lengths(), protocols::jumping::SpecificJumpSetup::clean_jump_sample(), myspace::collect_silent(), correct_rama(), utility::file::create_blank_file(), create_starting_template(), utility::tag::Tag::die_for_unaccessed_options(), utility::excn::Exception::display(), utility::excn::UserCorrectableIssue::display(), do_work(), doit(), dump_multivec(), dumpcgo(), utility::exit_handler(), pointGroupHit::expand(), fa_refine_and_design(), utility::file::file_size(), find_centerest_residue(), find_disulfides(), find_hppatches_distance(), find_hppatches_nb_graph(), myspace::get_data_index(), get_interface_score(), get_nodes(), basic::thread_manager::RosettaThreadManager::get_rosetta_thread_index(), get_tasks_from_command_line(), gpu_score_test(), utility::file::gunzip(), utility::file::gzip(), handle_assert_failure(), basic::options::int2afteroption(), basic::options::intafteroption(), numeric::fourier::kiss_dct(), numeric::fourier::kiss_fftr(), numeric::fourier::kiss_fftri(), numeric::fourier::kiss_idct(), TNM::load_normal_modes(), numeric::geometry::hashing::SixDOffsetTree::lookup(), main(), make_helix(), mg_pdbstats_test(), Mode::Mode(), utility::options::mpi_safe_std_err(), MSA_design_main(), my_main(), myasserteq(), ObjexxFCL::internal::ObserverGraph::ObserverGraph(), utility::io::izstream::open(), RTminOptMultifunc::operator()(), utility::options::OptionCollection::operator()(), ObjexxFCL::operator>>(), utility::options::OptionCollection::operator[](), output_packstat_pdb(), ConstraintConfig::pick_sequence(), polar_pdbstats_test(), SequenceCoords::print(), print_ddgs(), utility::options::Option::print_error_message(), print_passed(), print_vals(), print_verbose_ddgs(), rand_Vec_condition(), myspace::read_contact(), DisulfEposDatabase::read_data_file(), read_ddg_file(), read_frags(), numeric::interpolation::Histogram< X, Y >::read_from_db(), read_list_pose_range(), read_master_pose_range(), read_rigid_body_settings(), basic::options::real2afteroption(), basic::options::real3afteroption(), basic::options::realafteroption(), referenceRDC(), relax_test(), repack_test(), RosettaJob::request_job_from_server(), numeric::fourier::kiss_dct_state::resize(), numeric::fourier::kiss_fftr_state::resize(), CloudArchiveManagerWrapper::restore_batchlist(), RosettaJob::return_results_to_server(), rhiju_pdbstats(), MPI_Refinement_Launcher::run(), RosettaBackend::run(), run(), core::pack::annealer::FixbbSimAnnealer::run(), run_trace(), basic::TracerImpl::safe_output(), utility::save_crash_report_to_console(), utility::save_crash_report_to_file(), select_residues_for_evaluation(), numeric::interpolation::Histogram< X, Y >::set_params(), ThisApplication::setup(), NativeEnsemble::show_footer(), NativeEnsemble::show_progress(), basic::show_time(), numeric::sin_cos_range(), numeric::geometry::hashing::SixDOffsetTree::sum_radius(), basic::ComparingTracer::t_flush(), test(), test_ddg(), test_deriv_pose(), test_fake_silent(), test_gpu_speed(), test_gradient(), test_int(), test_known_value(), test_PCA_eigen(), test_real(), test_suck_res(), test_Vec(), test_vs_dots(), boost::throw_exception(), use_backrub(), utility::options::ResidueChainVectorOption::value_of(), utility::options::ResidueChainVectorOption::values_of(), numeric::expression_parser::ASTPrinter::visit(), visualize(), protocols::moves::SimpleCstMover::write(), write_checkpoint(), OutputManager::write_footer(), and OutputManager::write_progress().
| ocstream utility::io::oc::clog | ( | std::clog | ) |
Wrapper around std::clog.
| ocstream utility::io::oc::cout | ( | std::cout | ) |
Wrapper around std::cout.
Referenced by utility::Inline_File_Provider::add_input_file(), add_virtual_res(), utility::signals::PausableSignalHub< ReturnType, Signal >::after_send(), ala_ct(), align_pdbs(), align_pdbs_function(), align_pose_general(), ThisApplication::analyze_tree(), numeric::deriv::angle_p1_deriv(), CartPerturber::apply(), EnvToolMover::apply(), RDCToolMover::apply(), Protocol_MolecularDynamics::apply(), GunnTest::apply(), PrintFeatures::apply(), MinTestMover::apply(), GraftDesignCDRs::apply(), SuperDeviationMover::apply(), InteractionDistMinimizer::apply(), SpartaSuperDeviationMover::apply(), StatefulMover::apply(), PhProtocol::apply(), DesignGlycansProtocol::apply(), GlycomutagenesisProtocol::apply(), LoopHash_Analyze::apply(), TestJD2Mover::apply(), RDCScoreMover::apply(), PairDistance::apply(), FoldTreeOutputter::apply(), InterfaceStrandFinderMover::apply(), CustomMover::apply(), RDF_Mover::apply(), HolesTrainingDataMover::apply(), A3BPeptideBuilder::apply(), CovalentPeptidomimeticCreator::apply(), TriazoleCreator::apply(), ComputeSAXSSpectrum::apply(), PrintPDDF::apply(), SetupMover::apply(), HotspotPlacementMover::apply(), LoopHashRelax_Sampler::apply(), protocols::moves::FragCaptureMover::apply(), IdentifyCDRClusters::apply(), DockGlycansProtocol::apply(), GlycanClashCheckMover::apply(), HDmakerMover::apply(), xtal_water_bunsat::apply(), FastThreadingMover::apply(), Designer::apply(), MPFindInterfaceTestMover::apply(), MPframeworkTest1Mover::apply(), Benchmark::apply(), ScTrials::apply(), MembraneSfxnMover::apply(), MembraneDockingxMover::apply(), MPFoldingMover::apply(), LoadMembraneMover::apply(), ExemplarMover::apply(), protocols::moves::SimpleCstMover::apply(), complex_interface_optimize::apply(), compute_Irmsd::apply(), HBondReporter::apply(), protocols::abinitio::ShowViolation::apply(), apply_all_frags(), apply_angle_set(), apply_filter_base_stack_direction(), apply_mask(), apply_south_syn_to_dinucleotide_pose(), aro_pack_pdbstats_from_pose(), assign_rigid_body_settings_to_clusters_test(), atom_types_test(), atom_vdw_test(), automorph_rmsd(), backrub_min_test(), backrub_protocol(), utility::py::Base::Base(), base_doublet_rmsd_test(), base_pair_to_base_pair_test(), benzene_pair_score_test(), bk_test2(), blosum_score_alignment(), build_next_nucleotide_test(), build_toy_pose(), cal_score(), calc_B_values(), calc_c3_rmsd(), calc_rmsd_test(), calculate_distances(), calculate_pairwise_RMSD(), calculate_percent_hydrophobic_stats(), calculate_sasa(), calculate_theoretical_RNA_length(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), basic::TracerImpl::calculate_visibility(), calpha_pdb_superimpose_pose(), capri_t033_loop_test(), capri_t033_trim_dock_test(), centroid_rescore_test(), ch_o_pdbstats_from_pose(), chain_rmsd(), Tensor::check(), check_alignment_RMSD_cutoff(), myspace::check_clash(), check_clash(), check_structures(), chi_stats_test(), choose_centroids(), CL::CL(), numeric::geometry::hashing::xyzStripeHash::clash_amount(), MyCI1B::clone(), cluster_rigid_body_settings_test(), cluster_rotamers(), cluster_silent_file_data(), cluster_test(), coarse_rb_test(), coarse_to_full_test(), collect_stats(), color_by_lj_base_RNA_test(), color_by_lj_test(), compare_dna_energies(), compare_energies(), compare_gpu_result_against_cpu(), compare_text_files(), compute_intrinsic_deviation(), connectivity_test(), SetOfClusters::consolidate(), constraint_set_slice(), myspace::Scheduler::control_schedule(), converged(), convert(), convert_to_coarse_test(), convert_to_native_test(), copy_rotamerized_torsions(), copy_virtual_variant_type(), correlation(), create_base_pair_step_database_test(), utility::file::create_blank_file(), create_bp_jump_database_test(), create_cs_rosetta_rna_scorefxn(), MyCI1B_Creator::create_energy_method(), create_ensemble(), create_rna_benchmark_test(), create_rna_vall_torsions_test(), create_scorefxn(), create_starting_template(), cs_rosetta_rna_pdb(), cst_relax_test(), define_states_test(), delete_test(), delta_chi_correction_test(), design_test(), devel_main(), dinucleotide_test(), disp_symmop(), GlycomutagenesisProtocol::disulfide_treatment(), diversify_sam_loop_test(), dna_chain_check(), dna_coupled_rotamer_design_test(), dna_deriv_test(), dna_deriv_test_old(), dna_design_test(), dna_dr_loop_test(), dna_geometry(), dna_io_test(), dna_nbr_radii_test(), dna_specificity_test(), dna_stats(), dna_test(), do_oom(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), do_the_match(), do_two(), do_work(), dock(), InterfaceStrandFinderMover::dock_strands(), dostuff(), double_helix_test(), TCDock::dump_onecomp(), dump_pose(), TCDock::dump_top_hits(), dump_unique_atoms(), each_aa_test(), easy_target_test(), entropy_calculate_test(), env_sugar_test(), erraser_monte_carlo(), DisulfideBondEnergy::evaluate(), myspace::evaluate_and_write(), extract_pdbs_test(), extract_replica(), fa_cenpack_pdbstats_from_pose(), fa_scorefxn_test(), feed_rms_and_clash_scores_to_database(), figure_out_best_alpha_beta_gamma(), figure_out_fold_tree(), figure_out_icoord_test(), figure_out_secstruct(), figure_out_stems(), figure_out_which_sequence_is_template(), BuildFullModel::fill_and_sample_full_model(), fill_chainTORS_info(), filter_combine_long_loop(), filterAlignment(), filterAllAlignments(), filterNonCore(), basic::TracerImpl::final_stream(), myspace::find_best_projection(), ElecDensMinPackMinReporter::find_flips(), finely_sample_base_pair_test(), fixbb_design(), utility::py::Base::foo_int(), utility::py::Base::foo_string(), utility::py::Base::foo_value(), utility::py::Base::foo_value_sp(), StatefulMover::fresh_instance(), full_length_rmsd_over_reside_list_general(), TCDock::gather_hits(), gather_info_all_repeats(), gather_repeats(), gen_fold_tree_for_nbr_segments(), general_initialize(), PosePyObserver::generalEvent(), generate_disulfide_conformations(), get_angle_sets(), get_basepair_atoms(), get_cys_rts(), get_ddG(), get_disordered_regions(), get_euler_axes(), get_exclid(), get_frag_rmsd(), get_fragment_sets(), get_hb_srbb_score(), get_hbond_rotation_samples(), get_input_res(), get_min_frag_rmsd(), get_movable_jumps(), get_obligated_rna_pairings(), get_omgphipsi_bins(), get_opte_data(), utility::Inline_File_Provider::get_ostream(), get_pose_energy_breakdown(), get_reflection_axis(), get_residue_xyz_list(), myspace::get_resmap(), get_resmap(), get_rmsd(), get_RNAring_sasa(), get_rsrpl(), get_sc(), get_silent_file_tags(), utility::Inline_File_Provider::get_sstream(), get_subpose(), get_working_directory(), glu_ct(), gpu_refold_test(), graft_pdb(), graphics_main(), grid_matcher(), utility::file::gunzip(), utility::file::gzip(), hard_minimize(), harvest_motifs_one(), harvest_scores(), hbond_stats(), HBondedPairIterator::HBondedPairIterator(), helix_ST(), hermann_phase_two(), hermann_phase_two_minimize(), hessian_estimate(), homolog_finder(), idealize_tf_pose(), utility::SimulateMPI::incoming_message_queue_is_empty(), TCDock::init(), initialize_for_grid_matcher(), initialize_free_and_fixed(), input_torsion_M_v_lists(), basic::options::int2afteroption(), basic::options::intafteroption(), interface_repack_test(), intra_dna_stats(), is_cluster_member(), is_interface_heavyatom(), numeric::kdtree::is_legal_greater_than(), numeric::kdtree::is_legal_less_than(), is_locked(), is_new_cluster_center_rotamer(), is_new_cluster_center_second_stage(), is_new_cluster_center_xyz(), is_nonempty_input_silent_file(), iterative_optE(), juke_sam_test(), TCDock::justone(), KIC_loop_close(), apps::pilot::KicSandbox::KicSandbox(), kono_sarai_stats(), kono_sarai_zscore(), largest_cluster(), lariat_modeling(), ligand_rmsd(), ligrot_test(), lk_ball_wtd_deriv_test(), utility::options::OptionCollection::load(), utility::options::OptionCollection::load_options_from_stream(), loop_closure_test(), loop_modeling_test(), loop_rebuilding_test(), luxr_setup(), main(), make_motif_task(), make_two_trimers(), manual_copy(), map_sec(), MC_run(), measure_sequence_recovery(), methane_pair_score_test(), mg_hires_pdbstats_from_pose(), mg_modeler_test(), mg_pdbstats_from_pose(), mg_pdbstats_test(), minimize_and_score(), minimize_helix(), minimize_pdb(), minimize_poses(), minimize_protocol(), minimize_test(), minimize_to_close(), minimize_with_constraints(), minimizer_test(), mismatch_test(), mm_pack_test(), modeler_closure_test(), modeler_map_test(), modelSSLoop(), modify_foldtree(), morph_pdbs_test(), motif_dna_packer_design(), motif_scan(), MSA_design_main(), multimodel_gdt(), multiple_variant_type_test(), mutate_residue(), mutate_residues_wrapper(), my_main(), myasserteq(), MyCI1B::MyCI1B(), new_sc(), not1_loop_test(), not1_test(), not_main(), nucleobase_probe_score_test(), o2prime_packer(), one_chain_MC_sampling(), one_chain_ST_MC(), utility::io::ozstream::open_append(), StatefulMover::operator=(), opt_bicelle_params(), opt_double_vesicle_params(), OPT_KEY(), opt_vesicle_params(), optimize_weights(), basic::options::optional_positive_intafteroption(), utility::SimulateMPI::outgoing_message_queue_is_empty(), output_angles(), output_chainTORS(), output_chi_stats(), output_minipose_coords_test(), output_packstat_pdb(), output_score(), output_single_motif(), output_strand1_strand2_info(), output_stuff(), output_sugar_internal_dof(), output_superimposed_pdb(), pack_interface(), pack_o2prime(), pack_rotamers_test(), packRotamers(), parse_pathway_test(), parse_sequence(), pass_VDW_replusion_screen_fast(), pass_VDW_replusion_screen_slow(), pdb_little_motif_test(), pdb_scoring(), pdb_to_silent_file(), pdb_to_silent_file_simple(), pep_energies_analysis(), pep_phipsi_analysis(), pep_scan_analysis(), peptide_plane_test(), peptide_plane_test_OLD(), performMinimization(), perturb_and_rescore(), place_waters_and_minimize(), polar_pdbstats_from_pose(), polar_pdbstats_test(), pose2frags(), post_rebuild_bulge_assembly(), TCDock::precompute_intra(), predict_chem_map_test(), prepare_full_length_start_model(), prepare_start_model(), prepare_threaded_model(), basic::sampling::orientations::QuaternionGrid::print(), utility::graph::DirectedNode::print(), print_all_torsions_test(), print_debug_information(), print_dm(), print_energies(), PepMinMover::print_energy(), JDmover::print_features(), print_graph(), PhDocking::print_hbonds(), PhProtocol::print_hbonds(), print_hbonds_test(), print_internal_coord_test(), print_internal_coordinates(), print_matrix_to_file(), print_pdb_info(), numeric::RocCurve::print_roc_curve(), print_scores(), print_secstruct_test(), DesignGlycansProtocol::print_sequences(), SuperDeviationMover::print_stats(), print_surface_score_by_res(), print_torsions_check(), numeric::kdtree::print_tree(), print_vals(), print_vector(), printbits16(), printbits32(), printBondAngles(), printEnergies(), numeric::kinematic_closure::printMatrix(), printScoreTermsPose(), numeric::kinematic_closure::printTranspose(), numeric::kinematic_closure::printVector(), process_file_list(), process_for_motifs(), process_pose(), processChild(), processChildren(), processChildrenIntensification(), proclose_test(), proline_rama_pdbstats_from_pose(), protein_helix_test(), protocols_main(), pymol(), CloudArchiveManagerWrapper::queue_batch(), quick_score_test(), Bola::random_close_phipsi_from_rama(), rb_entropy_test(), rb_test(), RBSegmentRelax_test(), read_alignment_fasta_file(), read_list_file(), read_list_pose_range(), read_master_pose_range(), read_occupancy_data(), read_pdbs(), numeric::read_tensor_from_file(), readFile(), basic::options::real2afteroption(), basic::options::real3afteroption(), basic::options::realafteroption(), rebuild_centroid_test(), rebuild_test(), DisulfideBondEnergy::rebuildAndDetectDisulfideBond(), DockGlycansProtocol::record_pose_metrics(), StatefulMover::reinitialize_for_each_job(), StatefulMover::reinitialize_for_new_input(), relax_test(), repack_minimize_test(), repack_test(), basic::gpu::Timer::Report(), report(), myspace::DataClass::report_by_aa(), myspace::report_data(), MyFeaturesReporter::report_features(), RosettaJob::request_job_from_server(), res_type_score(), resample_full_model_test(), utility::io::mpi_stream::basic_mpi_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::reset_state(), CapriTwoBodyEnergy::residue_pair_energy(), retrieve_rms_and_clash_scores_from_gpu(), RosettaJob::return_results_to_server(), reverse_convert(), rhiju_pack(), rhiju_pdbstats(), rna_backbone_rebuild_test(), rna_build_helix_test_precompute(), rna_chain_closure_test(), rna_close_chainbreaks_test(), rna_denovo(), rna_denovo_legacy(), rna_denovo_test(), rna_design_test(), rna_features_from_pose(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_motif_test(), rna_o2prime_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), rna_sequence_recovery_metrics(), rna_stack_pdbstats_from_pose(), rna_suitename(), rna_thread_test(), rna_torsion_check_test(), rotamer_trials_test(), rotamerize(), rotamerize_rna_test(), rotateUntilCys(), numeric::model_quality::rsym_evector(), RosettaBackend::run(), protocols::abinitio::Application::run(), run(), TCDock::run(), ui::network::B::run(), core::pack::annealer::FixbbSimAnnealer::run(), ui::network::BowmanThread::run(), HubDenovo::run(), run_mc(), myspace::Scheduler::run_md(), run_parallel_docking(), run_sandbox(), run_test(), RunPepSpec(), sample_new_base_in_two_base_pair_pose(), sample_rama_test(), sample_rna_dofs_new(), sample_torsions(), sample_trp_tyr_test(), sasa_test(), myspace::scan_contact(), scan_Evalue(), myspace::scan_Evalue(), scan_rotamer(), scheme_score(), score12_plot_test(), score_pdb(), score_rnp(), MyCI1B_Creator::score_types_for_method(), scoring_test(), utility::py::OverloadTest::self_pure_test_virtual_p(), utility::py::OverloadTest::self_pure_test_virtual_ref(), utility::py::OverloadTest::self_test_virtual_p(), utility::py::OverloadTest::self_test_virtual_ref(), basic::TracerImpl::set_default_final_stream(), PoseAndData::set_file_name(), set_fullatom_flag_test(), utility::options::OptionCollection::set_option_value_cl(), utility::options::OptionCollection::set_option_value_file(), set_temp_based_on_ens_diversity(), basic::TracerImpl::set_tracer_options(), setup_CA_constraints(), setup_ca_constraints(), setup_copy_DOF_input(), setup_dinucleotide_pose(), setup_docking_ft_with_randomization(), setup_double_helix_pose(), abbinding::setup_foldtree(), setup_fragment_mover(), protocols::abinitio::JumpSpecificAbrelax::setup_jumps(), setup_mask(), setup_pert_foldtree(), A3BHbsDockDesignMinimizeMover::setup_pert_foldtree(), DougsDockDesignMinimizeMagicMover::setup_pert_foldtree(), HotspotPlacementMover::setup_pert_foldtree_byres(), setup_pose_setup_class(), setup_rhiju_fold_tree(), setup_rna_base_pair_constraints(), setup_rna_minimizer(), setup_two_base_pair_pose(), setup_two_base_pair_pose_with_chainbreak(), setup_VDW_rep_atom_map_list(), shear_moves_test(), pointGroupHit::show(), show(), show_allowed_residue_types(), show_clashes(), show_intrachain_energies(), show_pairing_info(), show_protein_DNA_interactions(), show_residue_hbonds(), show_residue_residue_clashes(), sicdock_thread_num(), simple_centroid_test(), simple_dna_test(), simple_loop_modeling_test(), simple_opte_test(), simple_relax(), numeric::sin_cos_range(), single_position_motif_scan(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), small_moves_test(), spec_test(), SphereSampler::SphereSampler(), spinner_test(), ss_test(), start_file_test(), stat_output(), StatefulMover::StatefulMover(), stepwise_template_test(), basic::options::stringafteroption(), sugar_frag_RNA_test(), sugar_geometry_RNA_test(), superimpose_pdb(), svm_load_model(), swa_rna_cluster(), swa_rna_sample(), sweep_params_from_match_constraint_file(), SymmAbRelaxTest(), SymmDataTest(), SymmSilentFileTest(), utility::sys_sleep(), DisulfideBondEnergy::tabulate(), tar_motif_test(), TCDock::TCDock(), test(), test_actcoord(), myspace::test_bbgauss(), numeric::kinematic_closure::test_bondangle(), test_bridgeObjects(), test_cofactor(), test_ddg(), test_deriv(), test_deriv_pose(), numeric::kinematic_closure::test_dixon(), numeric::kinematic_closure::test_eucDistance(), test_fake_silent(), test_find_neighbors(), test_function(), test_gb(), test_gpu_speed(), test_kc2(), test_lh_counts(), test_membrane_scoring_lowres(), test_NM(), test_NMmin(), test_NMrelaxer(), test_PCA_eigen(), test_protein_rna(), test_rama(), test_refold(), test_replicate_xform(), test_scorefxn_io(), numeric::kinematic_closure::test_scpn(), test_sugar(), numeric::kinematic_closure::test_torsion(), tf_specificity_test(), torsion2decoy(), basic::options::truefalseoption(), two_base_pairs_test(), two_base_pairs_via_loop_closure_test(), tyr_ct(), SamplingManager::update(), CovalentPeptidomimeticCreator::update_hydrogens(), utility::py::Value::Value(), vary_geometry_backbone(), vary_geometry_sidechains(), visualize(), vsasa_bunsats(), wriggle_test(), protocols::moves::SimpleCstMover::write(), write_base_pair_step_to_silent_struct(), OutputManager::write_header(), write_parameters_to_std_out(), zf_relax_test(), zf_test(), zif268_test(), utility::options::OptionCollection::~OptionCollection(), PosePyObserver::~PosePyObserver(), and utility::py::Value::~Value().
1.9.1