References N, test.T008_Serialization::oss, docking::s, and predPRE::t.
Referenced by PyMOL-Rosetta-relay-client.Matrix::__init__(), PyMOL-RosettaServer.Matrix::__init__(), pyrosetta.bindings.pose.ResidueLabelAccessor::__str__(), pyrosetta.bindings.pose.PoseScoreAccessor::__str__(), test.Workshop9_my_shapes.PhiNByXDegreesMover::__str__(), utility::excn::Exception::add_msg(), PyMOL-Rosetta-relay-client::add_point(), PyMOL-RosettaServer::add_point(), pyrosetta.PyMOLRosettaServer::add_point(), ConstraintConfig::add_sym_cst(), pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider::append_to_fragment_store(), Hit::apply(), ConstraintConfig::apply_dcsts(), ObjexxFCL::DynamicIndexRange::assign(), ObjexxFCL::StaticIndexRange::assign(), ObjexxFCL::DynamicIndexRange::assign_no_notify(), base_name(), bind_T60_pybind11(), calc_c3_rmsd(), calc_rama_scores(), pyrosetta.toolbox.cleaning::cleanCRYS(), compute_intrinsic_deviation(), PyMOL-Rosetta-relay-client::connect_points(), PyMOL-RosettaServer::connect_points(), pyrosetta.PyMOLRosettaServer::connect_points(), mp_ddG::convert_array_to_str(), detail::copy(), ObjexxFCL::Fstring::copy(), utility::copy_to_cstr_buffer(), utility::file::create_temp_filename(), cxdock_design(), helpers::database_arguments(), pyrosetta.bindings.pose::display_secstruct(), dock(), pyrosetta.toolbox.atom_pair_energy::dump_atom_pair_energy_table(), pyrosetta.toolbox.atom_pair_energy::dump_residue_pair_energies(), dump_unique_atoms(), dynamic_bitset_to_hex_string(), utility::json_spirit::erase_and_extract_exponent(), erraser_wrapper::erraser_minimize(), erraser_util::extract_pdb(), mutant_modeler::figure_out_WT_seq(), basic::datacache::WriteableCacheableMap::find(), sidechain_cst_3::find_CA(), utility::json_spirit::find_first_non_zero(), basic_printf_context< OutputIt, Char >::format(), format(), detail::fallback_formatter< T, Char, enable_if_t< is_streamable< T, Char >::value > >::format(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >::format_localized(), build::generate_bindings(), pyrosetta.toolbox.generate_resfile::generate_resfile_from_pose(), demo.D050_Packer_task::generate_resfile_from_pose(), utility::io::icstream::get(), utility::io::izstream::get(), mutant_modeler.MutantModeler::get_command_lines(), pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider::get_fragment_store(), mutant_modeler.MutantModeler::get_high_res_command_lines(), mutant_modeler.MutantModeler::get_med_res_command_lines(), util::get_surrounding_res(), options_class.Option::getCName(), options_class.Option::getDoxygenRow(), options_class::getMarkdownPage(), options_class.Option::getMarkdownRow(), options_class.Option::getWikiTableRow(), DRRAFTER_util::graph_from_ss(), utility::options::has_non_ascii(), ObjexxFCL::format::I(), basic::options::int2afteroption(), int2str(), int2string(), basic::options::intafteroption(), demo.D090_Ala_scan::interface_ddG(), interface_residue_ddg(), is_in_list(), is_interface_residue(), isUnique(), basic::options::key(), bin_torsions::key_from_torsion(), pyrosetta.toolbox.load_ligand::load_from_pubchem(), ObjexxFCL::main(), mp_ddG::main(), options::main(), combine_ContactMaps::main(), arls_impl::main(), sidechain_cst_3::main(), main(), PyMOL-Rosetta-relay-client::make_axis(), PyMOL-RosettaServer::make_axis(), pyrosetta.PyMOLRosettaServer::make_axis(), PyMOL-Rosetta-relay-client::make_data(), PyMOL-RosettaServer::make_data(), pyrosetta.PyMOLRosettaServer::make_data(), make_fragments(), mutant_modeler.MutantModeler::make_high_res_subsets_and_cmd_lines(), submit_jobs::make_job_files_and_submit(), utility::options::non_ascii_pos(), ObjexxFCL::DynamicIndexRange::operator=(), ObjexxFCL::StaticIndexRange::operator=(), basic::datacache::WriteableCacheableMap::operator[](), basic::options::optional_positive_intafteroption(), utility::json_spirit::Generator< Value_type, Ostream_type >::output(), pyrosetta.toolbox.py_jobdistributor::output_scorefile(), pyrosetta.toolbox.load_ligand::params_from_pubchem(), ConstraintConfig::parse_config_file(), parse_numbers(), DRRAFTER_util::parse_tag(), util::parse_tag(), erraser_util::pdb2rosetta(), bin_torsions::plot_histograms(), HBondReporter::pose_name(), demo.D020_Pose_scoring::pose_scoring(), demo.D010_Pose_structure::pose_structure(), basic::TracerImpl::prepend_channel_name(), utility::excn::Exception::prepend_to_msg(), mp_ddG::print_ddG_breakdown(), ObjexxFCL::process_file(), PyMOL-Rosetta-relay-client.PR_PyMOLServer::process_packet(), PyMOL-RosettaServer.PR_PyMOLServer::process_packet(), pyrosetta.PyMOLRosettaServer.PR_PyMOLServer::process_packet(), pymol(), CL::q1d(), CL::q2d(), CL::q3d(), utility::io::icstream::read(), utility::io::izstream::read(), utility::tag::Tag::read(), read_sphere(), utility::io::icstream::readsome(), utility::io::izstream::readsome(), basic::options::real2afteroption(), basic::options::real3afteroption(), basic::options::realafteroption(), receive_string_from_node(), recover_clustered_frags(), utility::json_spirit::remove_trailing(), PyMOL-Rosetta-relay-client::rescale_cartesian(), PyMOL-RosettaServer::rescale_cartesian(), pyrosetta.PyMOLRosettaServer::rescale_cartesian(), ConstraintConfig::residue_names_from_sequence(), pyrosetta.bindings.energies::residue_pair_energies_array(), erraser_util::rna_rosetta_ready_set(), erraser_util::rosetta2phenix_merge_back(), job_manager.DeleteJob::run(), HubDenovo::run(), run(), run_hd(), run_hh(), demo.D070_Refinement::sample_refinement(), demo.D080_Loop_modeling::sample_single_loop_modeling(), demo.D090_Ala_scan::scanning(), erraser_wrapper::seq_rebuild_new(), pyrosetta::Set(), utility::options::VectorOption::set_value(), setargs(), CL::setargs(), submit_jobs::setup_out_dir(), ConstraintConfig::show_cst_grids(), SphereSampler::SphereSampler(), split_string(), pyrosetta.toolbox.py_jobdistributor.PyJobDistributor::start_decoy(), detail::strftime(), utility::tag::string_contains_gt_lt_or_ampersand(), basic::options::stringafteroption(), erraser_wrapper::SWA_rebuild_erraser(), basic::basic_otstream< CharT, Traits >::basic_tstringbuf< _CharT, _Traits >::sync(), basic::MemTracerImpl::t_flush(), basic::PyTracer::t_flush(), basic::TracerImpl::t_flush(), tag_from_pose(), TEST(), test_refold(), testone(), tokenize_string(), basic::options::truefalseoption(), ObjexxFCL::DynamicIndexRange::u(), ObjexxFCL::StaticIndexRange::u(), ObjexxFCL::DynamicIndexRange::u_no_notify(), pyrosetta::Vector1(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::write(), zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::write(), utility::io::ocstream::write(), utility::io::ozstream::write(), write_cluster_frags(), write_distances(), detail::write_nonfinite(), and write_output_files().
