|
Rosetta
|
An object for reading/writing a simple xml-like language. More...
#include <utility/tag/Tag.hh>#include <iostream>#include <cstdio>#include <utility/string_util.hh>#include <utility/exit.hh>#include <utility/excn/Exceptions.hh>#include <string>#include <sstream>#include <boost/spirit/home/classic/attribute.hpp>#include <boost/spirit/home/classic/core/composite/actions.hpp>#include <boost/spirit/home/classic/core/composite/alternative.hpp>#include <boost/spirit/home/classic/core/composite/kleene_star.hpp>#include <boost/spirit/home/classic/core/composite/optional.hpp>#include <boost/spirit/home/classic/core/composite/positive.hpp>#include <boost/spirit/home/classic/core/composite/sequence.hpp>#include <boost/spirit/home/classic/core/non_terminal/grammar.hpp>#include <boost/spirit/home/classic/core/non_terminal/rule.hpp>#include <boost/spirit/home/classic/iterator/position_iterator.hpp>#include <boost/spirit/home/classic/phoenix/binders.hpp>#include <boost/spirit/home/classic/utility/functor_parser.hpp>Namespaces | |
| boost | |
| utility | |
| unresizable vector whose size is known at compile time, which may be allocated on the stack, and which indexes from 0. | |
| utility::tag | |
Functions | |
| void | boost::throw_exception (std::exception const &) |
| template<> | |
| std::string | utility::tag::Tag::getOption< std::string > (std::string const &key, char const *default_as_string_literal) const |
| Special-casing the string literal version for string options. In this case, there shouldn't be an error thrown. A string literal should be allowed to set the default value for a string. More... | |
| template<> | |
| platform::Size | utility::tag::Tag::getOption< platform::Size > (std::string const &key, int const default_int) const |
| Special-casing to ensure that 0 gets interpreted as Size(0) rather than nullptr. More... | |
| std::ostream & | utility::tag::operator<< (std::ostream &out, Tag const &tag) |
| std::ostream & | utility::tag::operator<< (std::ostream &out, TagCOP const &tag_ptr) |
An object for reading/writing a simple xml-like language.
Reads simple xml-like files, such as:
<loop_design> <params max_cycles=100 > <loop begin=A:10 end=A:15 length=5-6/>> </loop_design>
When read into a tag, the following code would be valid: std::ifstream fin; fin.open("loop_design.tag") TagCOP tag = Tag::create( fin ); runtime_assert( tag->getName() == "loop_design" ); int max_cycles = tag->getTag("params")->getOption<int>("max_cycles");
Files must obey the following grammar:
top := !xml_schema_tag misc* tag misc* xml_schema_tag := <?xml (char - '?')* '?>' misc := comment_tag | (char - '<') comment_tag := '' tag := leaf_tag | branch_tag leaf_tag := '<' name options* '/>' option := name '=' ( name | quote | squote ) name := (alnum | '_' | '-' | '.' | '*' | ',' )+ quote := '"' (alnum - '"')* '"' squote := '\'' (alnum - '\'')* '\'' branch_tag := '<' name options* '>' ( tag | misc )* '</' name '>' *whitespace allowed between all tokens
Less complex than XML, also: no need to quote options, and text outside of tags is ignored. Implemented with the boost spirit library.
To debug the schema: 1) uncomment this:
#define BOOST_SPIRIT_DEBUG
2) add in the definition function below
BOOST_SPIRIT_DEBUG_NODE(rule_name);
for each rule defined.
NOTE: As of r53105, Rosetta doesn't compile with line 162 in boost_1_46_1/boost/spirit/home/debug/debug_node.hpp when BOOST_SPIRIT_DEBUG is enabled.
| rule<Scanner,tag_closure::context_t> branch_tag |
| rule<Scanner,string_closure::context_t> close_tag |
| rule<Scanner> comment_tag |
| functor_parser<error_report_parser> error_report_p |
| vector< file_position > errors |
Referenced by main().
| rule<Scanner,name_and_options_closure::context_t> leaf_tag |
| rule<Scanner> misc |
| rule<Scanner,string_closure::context_t> name |
Referenced by binder::add_relevant_include_for_decl(), RDF_Mover::apply(), CaToAllAtom::apply(), basic_format_context< OutputIt, Char >::arg(), arg(), basic_format_context< OutputIt, Char >::arg_id(), binder::bind_enum(), PerformanceBenchmark::execute(), PerformanceBenchmark::executeOneBenchmark(), basic_format_args< Context >::get(), basic_format_args< Context >::get_id(), PerformanceBenchmark::getOneReport(), detail::handle_dynamic_spec(), binder::is_banned_symbol(), binder::is_bindable(), binder::is_const_overload(), binder::is_python_builtin(), main(), A3BHbsCreatorMover::make_a3b_pose(), binder::mangle_type_name(), pid(), HBondReporter::pose_name(), binder::python_class_name(), binder::Config::read(), setup_loops_fragment_libraries_with_ss(), test_cofactor(), traceCAs(), utility::file::trytry_ifstream_open(), utility::file::trytry_ofstream_open(), and zf_test().
| rule<Scanner,name_and_options_closure::context_t> name_and_options |
| rule<Scanner,string_closure::context_t> name_or_quote |
| rule<Scanner,name_and_options_closure::context_t> open_tag |
| rule<Scanner,option_closure::context_t> option |
Referenced by TCDock::__dock_base__(), myspace::Scheduler::accept_and_report(), protocols::abinitio::JumpSpecificAbrelax::add_constraints(), add_constraints(), add_rosetta_options_0(), add_user_constraints(), adjust_ref_weights(), align_pdbs(), alignment_atoms_in_res(), analyze_base_pair_test(), analyze_interface_test(), ThisApplication::analyze_tree(), anglestats_local(), protocols::abinitio::ApplicationContext::ApplicationContext(), ConstraintToolMover::apply(), RDCToolMover::apply(), DougsDockDesignMinimizeMagicMover::apply(), PeptoidRotamerRecoverer::apply(), CartRefineWrapperMover::apply(), CenRelaxMover::apply(), dsRNA_grow::apply(), MirrorSymmTest::apply(), TestMMOP::apply(), ConstraintMinimizer::apply(), PhProtocol::apply(), LoopHash_Analyze::apply(), PairDistance::apply(), PickBAB::apply(), DeleteSegments::apply(), ElecDensMinPackMinMover::apply(), FloppyTailMover::apply(), HECTMover::apply(), UBQ_E2Mover::apply(), PepMinMover::apply(), SymFixbbMover::apply(), InterfaceStrandFinderMover::apply(), HolesTrainingDataMover::apply(), apps::pilot::CustomStarTreeMover::apply(), apps::pilot::SampleSecondaryStructureAlignmentMover::apply(), A3BHbsCreatorMover::apply(), A3BHbsDockDesignMinimizeMover::apply(), CovalentPeptidomimeticCreator::apply(), MikeLinkerMover::apply(), TrizaolamerDockDesignMinimizeMover::apply(), JDmover::apply(), FaSolReporter::apply(), MinTestMover::apply(), LigandDockingHbondsReporter::apply(), LDConverterMover::apply(), LoopHashRelax_Sampler::apply(), Foldptn::apply(), MinPackMinMover::apply(), MinCenrotMover::apply(), CenRotRelaxMover::apply(), HbsDesignMover::apply(), OopDesignMover::apply(), PeptoidDesignMover::apply(), RNA_ScoreMover::apply(), ExposedStrandMover::apply(), HDdesignMover::apply(), HDmakerMover::apply(), UBQ_GTPase_disulfide_Mover::apply(), SmoothFragRepackMover::apply(), RescoreCenrot::apply(), RepackMinCenrotMover::apply(), MPFindInterfaceTestMover::apply(), CrystDesign::apply(), CrystRelax::apply(), CrystCluster::apply(), CrystFFTDock::apply(), MPFoldingMover::apply(), ViewMembraneProteinMover::apply(), CenRotCanonicalMover::apply(), CenRotRBRelaxMover::apply(), CenRotDockingMover::apply(), MPDomainAssembly::apply(), Minimize::apply(), ExemplarMover::apply(), NCMinimize::apply(), protocols::abinitio::ShowViolation::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), apply_south_syn_to_dinucleotide_pose(), assign_rigid_body_settings_to_clusters_test(), attach_abego_pools(), backrub_protocol(), base_pair_to_base_pair_test(), benchmark_contacts(), benzene_pair_score_test(), bp_score_calibrate(), brute_force_matcher(), build_full_model_test(), build_helix_test(), build_next_nucleotide_test(), build_template(), BuildFullModel::BuildFullModel(), byres_analysis(), bzip_test(), CA_cst_generator(), calc_dist(), calc_rama_scores(), calc_rms_test(), calc_rmsd_test(), calc_rmsf_and_avrg(), PairDistance::calc_rsd_sasa(), calc_scores(), CalcCdrRms::CalcCdrRms(), CalcsTestMover::CalcsTestMover(), calculate_pairwise_RMSD(), calculate_sasa(), capri15_relax(), capri_t033_centroid_trim_dock_test(), capri_t033_loop_test(), capri_t033_trim_dock_test(), cen_fold(), CenRotCanonicalMover::CenRotCanonicalMover(), CenRotDockingMover::CenRotDockingMover(), CenRotRBRelaxMover::CenRotRBRelaxMover(), CenRotRelaxMover::CenRotRelaxMover(), centroid_rescore_test(), check_contact(), protocols::abinitio::JumpSpecificAbrelax::check_filters(), check_hydrophobic_contact(), check_quality_of_cluster_frags(), check_required_options(), PoseWrap::check_scattach_res(), check_steric_overlap(), chi_stats_test(), protocols::abinitio::JumpSpecificAbrelax::close_loops(), cluster_outfile_test(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), cluster_rotamers(), cluster_rotamers_wrapper(), cluster_silent_file_data(), cluster_test(), coarse_frag_test(), coarse_rna_denovo_test(), coarse_to_full_test(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), color_by_lj_test(), compare_chi1_2_angles(), compare_frags(), compare_frags_pose(), compare_residues_and_chi1_2_angles(), StepWiseJobQueen::complete_larval_job_maturation(), compute_folding_energies(), compute_intrinsic_deviation(), compute_min_mean_rmsd_frag(), connectivity_test(), convert_to_coarse_test(), convert_to_native_test(), copy_rotamerized_torsions(), correct_dunbrack(), correct_rama(), count_bb_dihedrals(), count_contacts(), create_and_score_fragments(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_loop(), create_random_pose(), create_rna_benchmark_test(), create_rna_vall_torsions_test(), create_scorefxn(), CrystDesign::CrystDesign(), CrystFFTDock::CrystFFTDock(), cst_relax_test(), basic::database::db_partition_from_options(), utility::options::ScalarOption_T_< K, T >::default_to(), utility::options::VectorOption_T_< K, T >::default_to(), define_movemap_extending_chain(), define_states_test(), A3BHbsCreatorMover::delete_extra_residues(), DeleteSegments::DeleteSegments(), delta_chi_correction_test(), densityTools(), derive(), design(), design_cluster(), CrystDesign::design_cycle(), design_homodimer(), design_test(), designloop(), determine_residues_to_rebuild(), devel_main(), RTminOptMultifunc::dfunc(), utility::tag::Tag::die_for_unaccessed_options(), dinucleotide_test(), dist_matrix_test(), distribute_jobs(), diversify_sam_loop_test(), dna_dr_loop_test(), dna_specificity_test(), dna_stats(), do_clustering(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), do_erraser2(), do_initial_checks(), A3BHbsCreatorMover::do_mc(), do_postload_checks(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), CrystDesign::do_reversion(), ChallengeMover::do_rigid_body_moves(), do_rtmin(), do_the_match(), dock(), doit(), doit_refine(), DomainAssemblerNDocker::DomainAssemblerNDocker(), dostuff(), double_helix_test(), drrafter_error_estimation(), RDCToolMover::dump_averages(), dump_insert_pdb_and_remodel_blueprint(), TCDock::dump_onecomp(), TCDock::dump_pdb(), PoseWrap::dump_pdb(), TCDock::dump_top_hits(), basic::DynamicProfileThis::DynamicProfileThis(), easy_loop_model_test(), easy_target_test(), endo_test(), entropy_calculate_test(), env_sugar_test(), erraser2_test(), erraser_monte_carlo(), myspace::evaluate_and_write(), ExposedStrandMover::ExposedStrandMover(), extract_pdbs_test(), fa_refine_and_design(), figure_out_icoord_test(), files_for_openMM_test(), BuildFullModel::fill_and_sample_full_model(), fill_designable_set(), fill_input_poses_based_on_possible_checkpoints(), fillPoseAndDataList(), filter_combine_long_loop(), find_close_motifs(), find_close_parents(), ElecDensMinPackMinReporter::find_flips(), finely_sample_base_pair_test(), fit_centroid_to_the_best_rot(), protocols::abinitio::JumpSpecificAbrelax::fold(), Foldptn::Foldptn(), frag_extract_test(), FragmentAssemblyMover::FragmentAssemblyMover(), basic::database::full_cache_name(), basic::database::full_name(), ga_main(), TCDock::gather_hits(), gen_pep_bb_frag(), gen_pep_bb_frag_old(), gen_pep_bb_rama(), gen_pep_bb_sequential(), general_initialize(), protocols::abinitio::JumpSpecificAbrelax::generate_scorefxn(), generateRankedAlignments(), get_backbone_rotamers(), get_best_rotamer_index(), get_bin_size(), get_contacts(), basic::database::get_db_session(), get_env_bin_number(), get_exclid(), get_fixed_res(), get_fragments(), get_info_test(), get_input_res(), CrystDesign::get_interface_residues(), get_min_frag_rmsd(), CrystDesign::get_neighbor_residues(), get_pose_energy_breakdown(), get_res_data_ss(), get_rmsd(), get_rotamer_type_index(), get_rsrpl(), get_silent_file_tags(), get_stepwise_score_function(), get_tasks_from_command_line(), go(), protocols::jd2::RECONMPIJobDistributor::go(), protocols::jd2::RECONMPIJobDistributor::go_hardcoded(), gpu_refold_test(), graft_pdb(), graphics_main(), grid_matcher(), GunnTest::GunnTest(), HDdesignMover::HDdesignMover(), HDmakerMover::HDmakerMover(), helix_ST(), hermann_phase_two(), hermann_phase_two_minimize(), hessian_estimate(), homolog_finder(), idealize_tf_pose(), import_and_dump_pdb(), TCDock::init(), MPInterfaceStatistics::init_from_cmd(), TestQuickRelaxMover::init_from_cmd(), MPDomainAssembly::init_from_cmd(), HECTAllMover::init_on_new_input(), HECTUBQMover::init_on_new_input(), FloppyTailMover::init_on_new_input(), abbinding::init_options(), PhDocking::init_options(), SampleTiltProtocol::init_options(), PhProtocol::init_options(), initialize_base_pair(), protocols::abinitio::JumpSpecificAbrelax::initialize_constraint_forest(), initialize_native_pose(), initialize_peptide(), ChallengeMover::initialize_pose(), initialize_rigid_body_sampler(), initialize_sequence_mask(), input_alignments(), input_alignmentsMapped(), insert_chunk(), protocols::abinitio::JumpSpecificAbrelax::insert_template_frags(), interface_repack_test(), InterfaceStrandFinderMover::InterfaceStrandFinderMover(), juke_sam_test(), apps::pilot::KicSandbox::KicSandbox(), kinclose(), lariat_modeling(), ligand_dock_main_jd1(), load_checkpoint(), load_coords(), load_models(), LocalRmsd::LocalRmsd(), loop_closure_test(), loop_modeling_test(), loop_rebuilding_test(), luxr_setup(), luxr_test(), main(), apps::pilot::frankdt::main(), make_1mer_frags(), BuildFullModel::make_built_residues_virtual(), make_disulfides(), make_fragments(), make_pose(), match_main(), MC_run(), measure_sequence_recovery(), methane_pair_score_test(), mg_modeler_test(), mg_pdbstats_test(), TCDock::min_termini_dis(), TCDock::min_termini_proj(), Minimize::Minimize(), minimize_and_score(), minimize_pdb(), minimize_poses(), minimize_protocol(), minimize_test(), minimizer_test(), MinPackMinMover::MinPackMinMover(), mismatch_test(), protocols::antibody::model_cdrs(), modeler_closure_test(), modeler_map_test(), morph_pdbs_test(), motif_scan(), MSA_design(), MSA_design_main(), multiple_variant_type_test(), apps::pilot::MultiTemplateAlignChunkMover::MultiTemplateAlignChunkMover(), multivec2sf(), mutate_random_residue(), mutate_residues_wrapper(), my_main(), MyScoreMover::MyScoreMover(), not1_loop_test(), not1_test(), nucleobase_probe_score_test(), o2prime_packer(), obtain_start_pose(), ui::ui_protocols::helical_bundle::HelicalBundleDialogueWidget::on_radioButton_custom_helix_clicked(), one_chain_MC_sampling(), one_chain_ST_MC(), utility::options::AnyOption< T >::operator=(), utility::options::AnyVectorOption< T >::operator=(), utility::options::Option::operator=(), utility::options::ScalarOption_T_< K, T >::operator=(), utility::options::VectorOption_T_< K, T >::operator=(), OPT_KEY(), output_csts(), output_minipose_coords_test(), output_packstat(), output_packstat_pdb(), output_results(), output_single_motif(), output_strand1_strand2_info(), output_stuff(), OutputManager::OutputManager(), pack_interface(), pack_phosphates(), pack_polar_hydrogens(), packmin_unbound_pep(), PairDistance::PairDistance(), basic::database::parse_database_connection(), parse_extra_atom_list(), HECTMover::parse_options(), parse_pathway_test(), parse_pdb_pos(), pdb_little_motif_test(), pdb_scoring(), pdb_to_silent_file(), pdb_to_silent_file_simple(), pdbstats_test(), pep_phipsi_analysis(), pep_rmsd_analysis(), pep_scan_analysis(), PepMinMover::PepMinMover(), peptide_plane_test(), ThisApplication::pick_frags(), PickBAB::PickBAB(), PickSSE::PickSSE(), polar_pdbstats_test(), pose_from_posedata(), PoseWrap::PoseWrap(), posewrap_from_command_line(), post_rebuild_bulge_assembly(), predict_chem_map_test(), Prepare(), prepare_start_model(), print_all_torsions_test(), print_hbonds_test(), print_internal_coord_test(), print_pep_analysis(), print_pep_csts(), print_secstruct_test(), SuperDeviationMover::print_stats(), SpartaSuperDeviationMover::print_stats(), protocols::abinitio::JumpSpecificAbrelax::process_decoy(), process_for_motifs(), process_the_pose(), processChild(), processChildren(), processChildrenIntensification(), basic::prof_reset(), basic::prof_show(), protein_helix_test(), protocols_main(), pymol_struct_type_test(), quick_score_test(), Bola::random_nonclashing_move(), rb_entropy_test(), read_in_flexible_regions(), read_input_weights(), read_native_pose(), read_pose(), read_soft_segment_file(), read_structures(), read_thickness(), read_write(), rebuild_centroid_test(), rebuild_test(), rebuild_trimmed_loops(), recover_clustered_frags(), refine_fa_pep_bb(), register_calcs(), register_options(), MPInterfaceStatistics::register_options(), TestQuickRelaxMover::register_options(), SampleTiltProtocol::register_options(), DockGlycansProtocol::register_options(), MPDomainAssembly::register_options(), register_options_broker(), protocols::abinitio::JumpSpecificAbrelax::relax(), relax_cenrot_pose(), relax_test(), relaxloop(), A3BHbsCreatorMover::repack(), repack_cluster(), repack_minimize_test(), repack_step(), repack_test(), report(), res_lvl_analysis(), resample_full_model_test(), rescore_pose(), rescore_test(), reverse_doublet_test(), reverse_rbs_test(), apps::pilot::SampleSecondaryStructureAlignmentMover::revert_loops_to_original(), rhiju_pdbstats(), rna_assemble_all_combinations_test(), rna_assemble_test(), rna_backbone_rebuild_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_chain_closure_test(), rna_close_chainbreaks_test(), rna_close_loop_test(), rna_denovo(), rna_denovo_legacy(), rna_design_gap_test(), rna_design_test(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_idealize_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_o2prime_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), rna_resample_test(), rna_sample_virtual_sugar(), RNA_ScoreMover::RNA_ScoreMover(), rna_stats_test(), rna_suitename(), rna_superimpose_and_graft_test(), rna_thread_test(), rna_torsion_check_test(), RotamerAnalysis(), rotamerize_rna_test(), RotateSAXS::RotateSAXS(), run(), DomainAssemblerNDocker::run(), protocols::abinitio::JumpSpecificAbrelax::run(), MPI_Refinement_Launcher::run(), MPI_LoopHash_Launcher::run(), protocols::abinitio::Application::run(), ThisApplication::run(), TCDock::run(), DockFragmentsMover::run(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), OptionCollectionBenchmark::run(), myspace::Scheduler::run_combine(), run_hd(), run_hh(), myspace::Scheduler::run_LHeval(), run_mc(), myspace::Scheduler::run_md(), myspace::Scheduler::run_NM_evalmodes(), run_pep_prep(), RunPepSpec(), basic::database::safely_read_from_database(), sample_new_base_in_two_base_pair_pose(), sample_rama_test(), sample_state_to_state(), sample_trp_test(), sample_trp_tyr_test(), SamplingManager::SamplingManager(), Sasa::Sasa(), sasa_test(), save_cluster_tree_lite(), saxs_energy(), utility::options::ScalarOption_T_< K, T >::ScalarOption_T_(), A3BHbsCreatorMover::scan(), scan_hbond_jumps(), myspace::Scheduler::Scheduler(), scmove_residue(), score12_plot_test(), score_and_minimize(), score_clustered_frags(), score_folded_residues(), screen_phosphates(), search_translations(), sequence_tolerance_main(), sequence_tolerance_mf_main(), GlycomutagenesisProtocol::set_commandline_options(), DockGlycansProtocol::set_commandline_options(), myspace::Scheduler::set_default_parameters(), set_ideal_geometry(), set_loop_conformation(), set_pep_csts(), set_secstruct_from_psipred_ss2(), set_up_engine(), set_up_pose(), HECTMover::set_up_taskfactory(), protocols::abinitio::JumpSpecificAbrelax::setup(), protocols::abinitio::Application::setup(), ThisApplication::setup(), setup_align_atom_map(), setup_CA_constraints(), setup_ca_constraints(), setup_copy_DOF_input(), setup_design_res(), setup_dinucleotide_pose(), setup_double_helix_pose(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), setup_for_folding(), protocols::abinitio::JumpSpecificAbrelax::setup_fragments(), protocols::abinitio::JumpSpecificAbrelax::setup_jumps(), myspace::Scheduler::setup_LHsampler(), setup_loops_fragment_libraries_with_ss(), CrystFFTDock::setup_maps(), setup_mask(), CalcIrms::setup_native(), setup_one_chain_pose(), TryScoreFilter::setup_pose(), setup_pose(), setup_pose_setup_class(), setup_pose_with_loop(), setup_rna_base_pair_constraints(), setup_rna_working_parameters(), apps::pilot::SampleSecondaryStructureAlignmentMover::setup_startree(), zinc1_homodimer_design::setup_taskfactory(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), protocols::abinitio::JumpSpecificAbrelax::setup_templates(), XMLprinterMover::setup_tf(), setup_tf(), setup_two_base_pair_pose(), setup_two_base_pair_pose_with_chainbreak(), sf2multivec(), shift_center_and_PCA(), ConstraintToolMover::show_cstset(), simple_frag_test(), simple_loop_modeling_test(), simple_opte_test(), simple_rotamer_recovery(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), small_min_test(), SmoothFragRepackMover::SmoothFragRepackMover(), spanfile_from_pdb(), spinner_test(), split_fa_dun(), ss_ds_ts_assign_test(), stepwise_monte_carlo_legacy(), stepwise_template_test(), storeposedata(), sugar_geometry_RNA_test(), superimpose(), superimpose_pdb(), swa_rna_cluster(), swa_rna_sample(), PoseWrap::switch_to_cen(), HDdesignMover::sym_repack_minimize(), SymFixbbMover::SymFixbbMover(), SymmAbRelaxTest(), SymmSilentFileTest(), tar_motif_test(), HDdesignMover::task_constraint_setup(), TCDock::TCDock(), TCDock::termini_score(), test(), test_function(), test_kc(), test_kc2(), test_NMmin(), test_NMrelaxer(), tf_specificity_test(), thermal_sampler(), torsion2decoy(), torsion2pdb(), transform_pose(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), TryScoreFilter::TryScoreFilter(), two_base_pairs_test(), two_base_pairs_via_loop_closure_test(), HECTMover::ubq_constraints(), update_system(), use_backrub(), use_in_rmsd(), use_in_rmsd_offset(), user_overwrites_options(), utility::options::VectorOption_T_< K, T >::VectorOption_T_(), water_test(), write_checkpoint(), write_cluster_frags(), write_for_resnum(), NativeEnsemble::write_job_to_db(), XMLprinterMover::XMLprinterMover(), zf_relax_test(), zf_test(), zif268_test(), ZincMinimize::zn_min_pack(), and basic::DynamicProfileThis::~DynamicProfileThis().
| rule<Scanner,options_closure::context_t> options |
Referenced by utility::options::OptionCollection::add_built_in_options(), adjust_ref_weights(), Protocol_MolecularDynamics::apply(), CustomMover::apply(), MyScoreMover::apply(), MinTestMover::apply(), Benchmark::apply(), ScTrials::apply(), Minimize::apply(), NCMinimize::apply(), backrub_protocol(), BacksideHbondFinderMover::BacksideHbondFinderMover(), build_helix_test(), build_next_nucleotide_test(), calc_rama_scores(), calc_scores(), ccd_test(), StepWiseJobQueen::complete_larval_job_maturation(), configure_master_mover(), CrystDesign::design_cycle(), dinucleotide_test(), dna_chain_check(), dna_deriv_test_old(), dna_stats(), do_color_by_score(), CrystDesign::do_reversion(), erraser_monte_carlo(), utility::xsd_util::generate_human_readable_summary(), get_loop_scorefxn(), get_loop_scorefxn_old(), CrystDesign::greedy_revert_unsats(), hard_minimize(), hermann_phase_two_minimize(), homolog_finder(), idealize_tf_pose(), intra_dna_stats(), juke_sam_test(), lk_ball_wtd_deriv_test(), utility::options::OptionCollection::load(), main(), make_etable(), MC_run(), minimize_helix(), minimize_pdb(), minimize_poses(), minimize_protocol(), minimize_test(), minimize_with_constraints(), minimizer_test(), my_main(), not1_loop_test(), SSM_energies::optimization_loop(), optimize_weights(), parse_pathway_test(), place_waters_and_minimize(), post_rebuild_bulge_assembly(), real_test_GA(), rebuild_test(), repack_test(), resample_full_model_test(), rna_close_chainbreaks_test(), rna_design_gap_test(), rna_design_test(), rna_fullatom_minimize_test(), rna_fullatom_score_test(), rotamerize_rna_test(), ConsensusFragmentMover::run(), MinimizerBenchmark< sft, TScale >::run(), utility::set_options_string(), utility::tag::Tag::setOptions(), simple_opte_test(), stepwise_lores_test(), stepwise_monte_carlo_legacy(), stepwise_template_test(), test_NMmin(), thermal_sampler(), and zf_relax_test().
| rule<Scanner,string_closure::context_t> quote |
| rule<Scanner,string_closure::context_t> squote |
| rule<Scanner,tag_closure::context_t> tag |
Referenced by numeric::interpolation::spline::SplineGenerator::add_boundary_function(), add_protocols(), utility::tag::Tag::addTag(), analyze_base_pair_test(), GraftDesignCDRs::apply(), SuperDeviationMover::apply(), SpartaSuperDeviationMover::apply(), HolesTrainingDataMover::apply(), PBPotentialMover::apply(), MyScoreMover::apply(), RNA_ScoreMover::apply(), apply_all_frags(), base_pair_to_base_pair_test(), build_full_model_test(), build_next_nucleotide_test(), byres_analysis(), calc_scores(), calculate_distances(), capri_t033_centroid_trim_dock_test(), CAtrace::CAtrace(), check_structures(), protocols::abinitio::JumpSpecificAbrelax::close_loops(), Cluster::Cluster(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), cluster_rotamers(), myspace::collect_silent(), collect_stats(), convert_silent_file_to_pose_data_list(), count_contacts(), utility::tag::Tag::create(), cxdock_design(), design_hits(), design_test(), dinucleotide_test(), distribute_jobs(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), do_the_match(), dock(), doit(), dostuff(), drrafter_error_estimation(), dump_ddg_pdb(), dump_efactor_pdb(), dump_energy_kinemage(), dump_insert_pdb_and_remodel_blueprint(), dump_pose(), dump_residue_kinemage(), dump_table(), basic::DynamicProfileThis::DynamicProfileThis(), expand_chi_for_silent_structs(), extract_pdbs_test(), extract_replica(), figure_out_stems(), BuildFullModel::fill_and_sample_full_model(), utility::find_gemmi_column(), FragID::FragID(), get_contacts(), get_file_name(), basic::mpi::MessageListenerFactory::get_listener(), SequenceProfileDB::get_next_profile(), utility::get_resnum_and_chain_from_one_tag(), utility::get_resnum_and_segid(), utility::get_resnum_and_segid_from_one_tag(), get_rmsd(), get_RNA_binding_residues(), get_tag(), get_tag_from_pdb_filename(), go_main(), harvest_motifs(), harvest_motifs_one(), ik_his_clamp(), insert_chunk(), numeric::RocCurve::insert_point(), protocols::abinitio::JumpSpecificAbrelax::insert_template_frags(), intra_dna_stats(), basic::mpi::listener_tag_to_name(), main(), utility::make_segtag_with_dashes(), utility::make_tag(), utility::make_tag_with_dashes(), mg_modeler_test(), minimize_poses(), modeler_map_test(), morph_pdbs_test(), my_main(), utility::tag::operator<<(), utility::tag::Tag::operator=(), output_benchmark_stuff(), output_centroid_silent_struct(), output_contact_info(), output_to_silent(), basic::database::parse_database_connection(), basic::resource_manager::locator::DatabaseResourceLocator::parse_my_tag(), basic::resource_manager::locator::FileSystemResourceLocator::parse_my_tag(), parse_pathway_test(), FixbbJobQueen::parse_sfxns_and_taskops(), pdb_to_silent_file(), pdb_to_silent_file_simple(), ThisApplication::pick_frags(), pose2frags(), SuperDeviationMover::print_stats(), SpartaSuperDeviationMover::print_stats(), protocols::abinitio::JumpSpecificAbrelax::process_decoy(), process_the_pose(), basic::prof_show(), basic::prof_start_function_body(), basic::prof_stop_function_body(), utility::tag::Tag::read(), read_embeddings(), read_membrane(), read_parameters(), read_penalties(), basic::resource_manager::ResourceManager::read_resources_tags(), receive_string_from_node(), protocols::abinitio::JumpSpecificAbrelax::relax(), basic::gpu::Timer::Report(), report(), FragMonteCarlo::report_results(), rescore(), rescore_pose(), rescore_test(), CloudArchiveManagerWrapper::restore_batchlist(), reverse_doublet_test(), rna_assemble_test(), rna_backbone_rebuild_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_features_from_pose(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_lores_score_silent_test(), rna_protein_rb_test(), RotamerAnalysis(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), myspace::Scheduler::run_combine(), run_diiron_glu(), run_m8(), run_tyr_his(), run_zn2his(), sample_rama_test(), sample_trp_test(), sample_trp_tyr_test(), myspace::DataClass::scan_Evalue(), myspace::DataClass::scan_Evalue_and_write(), score12_plot_test(), score_and_minimize(), search_translations(), send_string_to_node(), setup_capri_data(), setup_roc_curve(), show_accuracy_report(), sicdock_thread_num(), single_position_motif_scan(), SpacegroupHit::SpacegroupHit(), tag_from_pose(), test(), tf_specificity_test(), basic::gpu::Timer::Timer(), SpacegroupHit::to_string(), transmit_silent_struct(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), wriggle_test(), utility::tag::Tag::write(), PBPotentialMover::write_APBS_config(), and NativeEnsemble::write_stats_to_db().
| rule<Scanner> top |
Referenced by ConstraintToolMover::apply(), utility::options::OptionCollection::find_key_cl(), utility::options::OptionCollection::find_key_file(), utility::options::OptionCollection::load_option_cl(), utility::options::OptionCollection::load_option_file(), main(), OPT_KEY(), setup_tf(), and detail::write_exponent().
| member1 value |
Referenced by utility::json_spirit::Config_vector< String >::add(), utility::json_spirit::Config_map< String >::add(), protocols::moves::SimpleCstMover::add_distmax(), protocols::moves::SimpleCstMover::add_distmin(), utility::json_spirit::Semantic_actions< Value_type, Iter_type >::add_first(), utility::thread::MutableCache< K, V >::add_if_missing(), utility::json_spirit::add_posn_iter_and_read_range_or_throw(), utility::tag::XMLSchemaRestriction::add_restriction(), numeric::CalculatorParser::add_symbol(), utility::json_spirit::Semantic_actions< Value_type, Iter_type >::add_to_current(), UBQ_E2Mover::analyze_and_filter(), UBQ_GTPase_disulfide_Mover::analyze_and_filter(), analyze_base_pair_test(), AnchorFinderMover::AnchorFinderMover(), APDBCMover::APDBCMover(), AssignClusterToolMover::apply(), zinc1_homodimer_setup::apply(), DougsDockDesignMinimizeMagicMover::apply(), PeptoidRotamerRecoverer::apply(), HemeReplace::apply(), InverseRotlibDumpMover::apply(), FloppyTailMover::apply(), HECTMover::apply(), UBQ_E2Mover::apply(), PepMinMover::apply(), IAMover::apply(), SymFixbbMover::apply(), InterfaceStrandFinderMover::apply(), A3BHbsCreatorMover::apply(), A3BHbsDockDesignMinimizeMover::apply(), CovalentPeptidomimeticCreator::apply(), MikeLinkerMover::apply(), TrizaolamerDockDesignMinimizeMover::apply(), LDConverterMover::apply(), HotspotPlacementMover::apply(), MinPackMinMover::apply(), APDBCMover::apply(), AnchorFinderMover::apply(), HbsDesignMover::apply(), OopDesignMover::apply(), PeptoidDesignMover::apply(), HDdesignMover::apply(), UBQ_GTPase_disulfide_Mover::apply(), MetalSiteFinderMover::apply(), ZincSiteEvaluator::apply(), HBondReporter::apply(), hbs_creator::apply(), utility::as_char(), utility::keys::ClassKeyVector< K, T, C >::assign(), utility::keys::KeyVector< K, T >::assign(), utility::keys::SmallKeyVector< K, T >::assign(), ObjexxFCL::CArray< T >::assign(), ObjexxFCL::CArrayP< T >::assign(), ObjexxFCL::Chunk< T >::assign(), ObjexxFCL::ChunkVector< T >::assign(), utility::keys::ClassKeyMap< K, T, C >::assign(), utility::keys::SmallKeyMap< K, T >::assign(), IAMover::assign_IA_mover(), numeric::MultiDimensionalHistogram::bin_index(), PyCallBack_Mammal_1_t::Breathe(), PyCallBack_Dog_1_t::Breathe(), BuildFullModel::BuildFullModel(), byres_analysis(), ObjexxFCL::Chunk< T >::Chunk(), ObjexxFCL::ChunkVector< T >::ChunkVector(), numeric::clamp(), FixbbJobQueen::complete_larval_job_maturation(), detail::const_check(), detail::count_named_args(), ObjexxFCL::cube(), numeric::interpolation::spline::PolycubicSpline< N >::dFdxi(), numeric::do_add_symbol(), do_erraser2(), A3BHbsCreatorMover::do_mc(), do_options_checks(), formatter< std::chrono::duration< Rep, Period >, Char >::do_parse(), PyCallBack_Animal_1_t::Eat(), PyCallBack_Mammal_1_t::Eat(), PyCallBack_Dog_1_t::Eat(), numeric::Polynomial_1d::eval(), PyCallBack_A2::f(), PyCallBack_A3::f(), numeric::interpolation::spline::PolycubicSpline< N >::F(), PyCallBack_Base::f_v(), PyCallBack_Derived::f_v(), PyCallBack_Delete::f_v(), PyCallBack_Base::f_v_2(), PyCallBack_Derived::f_v_2(), PyCallBack_Delete::f_v_2(), PyCallBack_X::f_v_2(), detail::fallback_format(), BuildFullModel::fill_and_sample_full_model(), fill_input_poses_based_on_possible_checkpoints(), zinc2_homodimer_setup::filter_clashes(), zinc2_homodimer_setup::filter_metal_geom(), utility::find_closest(), find_middle_of_vector(), detail::first(), FloppyTailMover::FloppyTailMover(), PyCallBack_Base::foo(), PyCallBack_n1_A::foo(), PyCallBack_n1_n2_A::foo(), PyCallBack_Base::foo_int(), PyCallBack_Base::foo_protected(), PyCallBack_Derived::foo_protected(), PyCallBack_Delete::foo_protected(), PyCallBack_X::foo_protected(), PyCallBack_Base::foo_sring(), PyCallBack_Base::foo_sring_r(), PyCallBack_Base::foo_void(), PyCallBack_Base::foo_void_pure(), formatter< arg_join< It, Sentinel, Char >, Char >::format(), formatter< detail::bigint >::format(), format(), printf_formatter< T >::format(), formatter< tuple_arg_join< Char, T... >, Char >::format(), formatter< tuple_arg_join< Char, T... >, Char >::format_args(), detail::format_decimal(), detail::format_duration_value(), detail::format_float(), format_int::format_signed(), format_int::format_unsigned(), detail::format_value(), utility::fractional_rank(), utility::gemmi_add_row(), utility::json_spirit::Generator< Value_type, Ostream_type >::Generator(), detail::locale_ref::get(), basic::datacache::HierarchicalDataMap::get(), detail::get_dynamic_spec(), utility::json_spirit::get_int(), utility::json_spirit::get_mArray(), utility::json_spirit::get_mObject(), utility::get_num_digits(), basic::options::get_option(), utility::json_spirit::get_real(), get_res_data_ss(), get_rsrpl(), utility::json_spirit::get_string(), utility::json_spirit::get_string_or_empty(), utility::json_spirit::internal_::get_value(), go_main(), HbondZinc::graft_match(), HbondZincBackbone::graft_match(), graphics_main(), rosetta_binders::has_insertion_operator(), utility::type_traits::has_insertion_operator(), utility::heap::heap_up(), HECTMover::HECTMover(), HemeReplace::HemeReplace(), numeric::hsv_to_rgb(), UBQ_E2Mover::init_on_new_input(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), AbInitio_MPI::init_on_new_input(), HECTAllMover::init_on_new_input(), FloppyTailMover::init_on_new_input(), HemeBindingMover::initialize_from_options(), utility::keys::SmallKeyVector< K, T >::insert(), utility::keys::ClassKeyVector< K, T, C >::insert(), utility::keys::KeyVector< K, T >::insert(), utility::keys::ClassKeyMap< K, T, C >::insert(), utility::keys::SmallKeyMap< K, T >::insert(), utility::options::Option::is_group(), numeric::kdtree::is_legal_greater_than(), numeric::kdtree::is_legal_kdtree_below_node(), numeric::kdtree::is_legal_less_than(), detail::is_supported_floating_point(), PyCallBack_Animal_1_t::isDog(), PyCallBack_Mammal_1_t::isDog(), PyCallBack_Dog_1_t::isDog(), Kernel::kernel_precomputed(), numeric::VoxelArray< _Float, _Value >::load(), detail::locale_ref::locale_ref(), LoopBuild_main(), main(), apps::pilot::frankdt::main(), make_args_checked(), HECTMover::make_frags(), detail::arg_mapper< Context >::map(), numeric::MathTensor< T >::MathTensor(), ObjexxFCL::max(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::maybe_has_equal_operator(), numeric::mean(), measure_sequence_recovery(), ObjexxFCL::min(), detail::bigint::multiply(), my_main(), ObjexxFCL::Chunk< T >::non_preserving_resize(), NonceHistogram::NonceHistogram(), detail::normalize(), ui::network::FloatArgument::on_value_changed(), ui::network::IntegerArgument::on_value_changed(), ui::network::PathArgument::operator QString(), detail::arg_converter< T, Context >::operator()(), numeric::Polynomial_1d::operator()(), detail::width_checker< ErrorHandler >::operator()(), detail::precision_checker< ErrorHandler >::operator()(), detail::printf_precision_handler::operator()(), detail::printf_width_handler< Char >::operator()(), printf_arg_formatter< OutputIt, Char >::operator()(), ObjexxFCL::operator*(), ObjexxFCL::Chunk< T >::operator*=(), ObjexxFCL::ChunkVector< T >::operator*=(), ObjexxFCL::operator+(), ObjexxFCL::Chunk< T >::operator+=(), ObjexxFCL::ChunkVector< T >::operator+=(), ObjexxFCL::operator-(), ObjexxFCL::Chunk< T >::operator-=(), ObjexxFCL::ChunkVector< T >::operator-=(), ObjexxFCL::operator/(), ObjexxFCL::Chunk< T >::operator/=(), ObjexxFCL::ChunkVector< T >::operator/=(), PyCallBack_A4::operator=(), ObjexxFCL::Chunk< T >::operator=(), ObjexxFCL::ChunkVector< T >::operator=(), utility::keys::ClassKeyVector< K, T, C >::operator=(), utility::keys::KeyVector< K, T >::operator=(), utility::keys::SmallKeyVector< K, T >::operator=(), utility::json_spirit::Generator< Value_type, Ostream_type >::output(), utility::json_spirit::Generator< Value_type, Ostream_type >::output_int(), basic_printf_context< OutputIt, Char >::parse_header(), detail::parse_nonnegative_int(), HECTMover::parse_options(), numeric::EulerAngles< T >::phi(), numeric::EulerAngles< T >::phi_degrees(), numeric::EulerAngles< T >::phi_radians(), ObjexxFCL::pow(), basic::options::pre_tracer_process(), utility::libsvm::Svm_rosetta::predict(), utility::libsvm::Svm_rosetta::predict_probability(), processRegions(), detail::promote_float(), numeric::EulerAngles< T >::psi(), numeric::EulerAngles< T >::psi_degrees(), numeric::EulerAngles< T >::psi_radians(), detail::dynamic_arg_list::push(), detail::buffer< T >::push_back(), dynamic_format_arg_store< Context >::push_back(), ObjexxFCL::Chunk< T >::push_back(), ObjexxFCL::ChunkVector< T >::push_back(), utility::keys::ClassKeyVector< K, T, C >::push_back(), utility::keys::KeyVector< K, T >::push_back(), utility::keys::SmallKeyVector< K, T >::push_back(), numeric::interpolation::Histogram< X, Y >::read_from_db(), read_in_extension(), APDBCMover::read_in_insert_loop_info(), utility::json_spirit::read_mArray(), basic::read_metric_value_scalar(), basic::read_metric_value_vector1(), utility::json_spirit::read_mObject(), utility::json_spirit::Stream_reader< Istream_type, Value_type >::read_next(), utility::json_spirit::Stream_reader_thrower< Istream_type, Value_type >::read_next(), utility::json_spirit::read_range(), utility::json_spirit::read_range_or_throw(), utility::json_spirit::read_stream(), utility::json_spirit::read_stream_or_throw(), utility::json_spirit::read_string(), utility::json_spirit::read_string_or_throw(), numeric::read_tensor_from_file(), basic::options::realafteroption(), numeric::MultiDimensionalHistogram::record(), register_metrics(), ObjexxFCL::ChunkVector< T >::reshape(), utility::keys::ClassKeyVector< K, T, C >::resize(), utility::keys::KeyVector< K, T >::resize(), utility::keys::SmallKeyVector< K, T >::resize(), ObjexxFCL::Chunk< T >::resize(), ObjexxFCL::ChunkVector< T >::resize(), rna_denovo(), rna_design_test(), rna_fullatom_minimize_test(), safe_duration_cast::safe_float_conversion(), numeric::VoxelArray< _Float, _Value >::save(), A3BHbsCreatorMover::scan(), numeric::expression_parser::ArithmeticScanner::scan_literal(), Mode::set(), basic::Report::set(), basic::Reporter::set(), basic::datacache::HierarchicalDataMap::set(), NativeEnsemble::set_algorithm(), NativeEnsemble::set_description(), protocols::moves::SimpleCstMover::set_distmax(), protocols::moves::SimpleCstMover::set_distmin(), NativeEnsemble::set_dump_frequency(), set_file_output(), NativeEnsemble::set_input_file(), NativeEnsemble::set_iterations(), myspace::Scheduler::set_maxiter(), utility::SimulateMPI::set_mpi_rank(), basic::options::set_option(), utility::options::OptionCollection::set_option_value_file(), numeric::interpolation::Histogram< X, Y >::set_params(), NativeEnsemble::set_quiet(), ui::ui_protocols::helical_bundle::HelicalBundleDialogueWidget::set_real_subwidget(), NativeEnsemble::set_temperature(), numeric::expression_parser::LiteralExpression::set_value(), numeric::expression_parser::VariableExpression::set_value(), ui::task::FileTableModel::setData(), utility::tag::Tag::setOption(), zinc1_homodimer_design::setup_metalsite_constraints(), setup_roc_curve(), zinc1_homodimer_design::setup_scorefunctions(), HemeReplace::setup_task_factory(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), detail::snprintf_float(), ObjexxFCL::square(), StatefulMover::StatefulMover(), HDdesignMover::sym_repack_minimize(), ui::task::Task::syncing_progress(), ui::task::Task::syncing_progress_advance(), test(), numeric::EulerAngles< T >::theta(), numeric::EulerAngles< T >::theta_degrees(), numeric::EulerAngles< T >::theta_radians(), detail::to_ascii(), detail::to_nonnegative_int(), to_string(), detail::to_unsigned(), to_wstring(), HECTMover::ubq_constraints(), UBQ_E2Mover::UBQ_E2Mover(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::utility_vector_binder(), detail::arg_formatter_base< OutputIt, Char, ErrorHandler >::write(), detail::write(), detail::write_char(), utility::json_spirit::write_stream(), utility::json_spirit::write_string(), numeric::write_tensor_to_file(), writeYamlValue(), and zinc2_homodimer_setup::zinc2_homodimer_setup().
| rule<Scanner> xml_schema_tag |
1.9.1