subloop_histogram Namespace Reference

Functions
def	pivots_from_line (line)
def	key_from_pivots (pivots)

Variables
	parser = argparse.ArgumentParser()
	arguments = parser.parse_args()
	path = os.path.join(arguments.input)
dictionary	pivots_to_keys = {}
dictionary	keys_to_pivots = {}
	iterator = itertools.combinations(range(1, 13), 2)
list	combos = [tuple(x) for x in iterator if x[0] + 1 != x[1]]
	length_key = lambda x: x[1] - x[0]
	key = key_from_pivots(pivots)
	lengths = map(length_key, combos)
	num_combos = len(pivots_to_keys)
list	histograms = [[] for x in range(num_combos)]
def	pivots = pivots_from_line(line)
	axes = subplot(111)
	twin = axes.twiny()
	top_labels
	top_label_locations
	bottom_labels
	bottom_label_locations
	x
	artists = axes.boxplot(histograms)
	black = tango.black
	color
	linewidth
	solid_capstyle
	linestyle
	marker
	markersize
	coordinates = zip(box.get_xdata(), box.get_ydata())
	polygon = plt.Polygon(coordinates, facecolor=tango.brown[0])
float	xpadding = 0.02 * num_combos
	size
	rotation
	ymin
	ymax
float	ypadding = 0.03 * ymax
	dpi

Function Documentation

key_from_pivots()

def subloop_histogram.key_from_pivots

(

pivots

)

References basic::database.open().

pivots_from_line()

def subloop_histogram.pivots_from_line

(

line

)

References enumerate_junctions.int.

Variable Documentation

arguments

subloop_histogram.arguments = parser.parse_args()

artists

subloop_histogram.artists = axes.boxplot(histograms)

axes

subloop_histogram.axes = subplot(111)

Referenced by pointGroupHit.as_string(), pointGroupHit.axis(), percent_subangstrom.compare_benchmarks(), pointGroupHit.construct_from_basis(), get_euler_axes(), get_zn_axes(), pointGroupHit.pointGroupHit(), run(), pointGroupHit.show(), and pointGroupHit.transform().

black

subloop_histogram.black = tango.black

Referenced by utility::graph.breadth_first_visit_prune(), utility::graph.depth_first_visit_sort_impl(), and ui::widgets::PoseEditor.on_pause_toggled().

bottom_label_locations

subloop_histogram.bottom_label_locations

bottom_labels

subloop_histogram.bottom_labels

color

subloop_histogram.color

combos

list subloop_histogram.combos = [tuple(x) for x in iterator if x[0] + 1 != x[1]]

coordinates

subloop_histogram.coordinates = zip(box.get_xdata(), box.get_ydata())

dpi

subloop_histogram.dpi

histograms

list subloop_histogram.histograms = [[] for x in range(num_combos)]

iterator

subloop_histogram.iterator = itertools.combinations(range(1, 13), 2)

Referenced by HolesTrainingDataMover.apply(), MySlideMover.apply(), MetalSiteFinderMover.apply(), SwapElementsMover1.apply(), SwapElementsMover2.apply(), ConstraintConfig.apply_dcsts(), apply_filter_base_stack_direction(), bind_T60_pybind11(), calc_outputCoordCsts(), calc_rmsf_and_avrg(), calc_scores(), 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(), ClashCheck.clash_check(), ClashCheck.clash_check_trimer(), cluster_rigid_body_settings_test(), numeric::Calculator.compute(), VecContains.convert(), cxdock_design(), density_grid_search(), utility::graph.depth_first_visit_sort_impl(), protocols::abinitio::JumpSpecificAbrelax.do_rerun(), dock(), dostuff(), TCDock.dump_pdb(), dump_unique_atoms(), expand_chi_for_silent_structs(), extract_pdbs_test(), extract_replica(), fillPoseAndDataList(), filterAllAlignments(), filterNonCore(), myspace.find_best_projection(), find_hppatches_distance(), find_hppatches_nb_graph(), rosetta_binders.fixedsizearray_add_on_binder(), protocols::abinitio::JumpSpecificAbrelax.fold(), formatter< T, Char, enable_if_t< detail::type_constant< T, Char >::value !=detail::type::custom_type > >.format(), dynamic_formatter< Char >.format(), SetupHotspotMover.generate_csts(), generate_partial_threads(), generateRankedAlignments(), get_area(), get_ddg(), get_deriv(), get_opte_data(), get_pose_by_id(), get_unalignedLoopsMapped(), harvest_scores(), input_alignmentsMapped(), utility::Inline_File_Provider.is_black_listed_file(), is_cut(), rosetta_binders.list_add_on_binder(), main(), make_frag_set(), make_frag_set_9mers(), make_move_map(), makerots(), minimize_poses(), my_main(), MyRotMover.MyRotMover(), MyTransMover.MyTransMover(), optimize_weights(), output_caAtomsToConstraint(), parse_position(), pep_scan_analysis(), ThisApplication.pick_frags(), ObjexxFCL::internal::ObserverGraph.pop(), PoseWrap.PoseWrap(), JDmover.print_features(), processChild(), processChildren(), processChildrenIntensification(), Bola.random_move(), RDF_Mover.RDF_Mover(), read_library_simple(), read_library_w_simpose(), read_silent_input_as_library(), refresh_cutpoints(), utility::signals::BufferedSignalHub< ReturnType, Signal >.release_buffer(), utility::keys::KeyLookup< K >.remove(), utility::Inline_File_Provider.remove_input_file(), removeConstraintsNearGap(), report(), myspace::DataClass.report_by_aa(), ConstraintConfig.reset_csts(), reverse_doublet_test(), rna_fullatom_minimize_silent_test(), rna_lores_score_silent_test(), run(), ScoreFragmentSetMover.run(), FragmentAssemblyMover.run(), ConsensusFragmentMover.run(), SolutionRescoreMover.run(), RunPepSpec(), rosetta_binders.set_add_on_binder(), setup_loops_fragment_libraries_with_ss(), XMLprinterMover.setup_tf(), setup_tf(), DomainDescription.sheet_match(), ThisApplication.show_cuts(), ThisApplication.show_jumps(), sicdock_thread_num(), sicfast(), simple_opte_test(), smooth_motif_column(), split_silent_file_data(), stat_output(), SymmSilentFileTest(), test(), detail.vformat_to(), vprintf(), detail.write(), detail.write_bytes(), detail.write_char(), detail.write_float(), write_for_resnum(), detail.write_int(), detail.write_nonfinite(), detail.write_ptr(), RDF_Mover.write_R_data_file(), and CL.~CL().

key

def subloop_histogram.key = key_from_pivots(pivots)

Referenced by utility::keys::ClassKeyMap< K, T, C >.activate(), utility::keys::ClassKeyVector< K, T, C >.activate(), utility::keys::ClassKeyMap< K, T, C >.activated_index(), utility::keys::ClassKeyVector< K, T, C >.activated_index(), utility::keys::ClassKeyMap< K, T, C >.active(), utility::keys::ClassKeyVector< K, T, C >.active(), utility::keys::KeyVector< K, T >.active(), utility::keys::SmallKeyMap< K, T >.active(), utility::keys::SmallKeyVector< K, T >.active(), utility::options::OptionCollection.add(), ui::task::Node.add(), utility::keys::ClassKeyMap< K, T, C >.add(), utility::keys::ClassKeyVector< K, T, C >.add(), utility::keys::KeyVector< K, T >.add(), utility::keys::SmallKeyMap< K, T >.add(), utility::keys::SmallKeyVector< K, T >.add(), utility::factory::Factory< P >.add(), basic::database::schema_generator::Schema.add_foreign_key(), utility::thread::MutableCache< K, V >.add_if_missing(), utility::keys::ClassKeyMap< K, T, C >.add_key(), utility::keys::ClassKeyVector< K, T, C >.add_key(), utility::keys::KeyVector< K, T >.add_key(), utility::keys::SmallKeyMap< K, T >.add_key(), utility::keys::SmallKeyVector< K, T >.add_key(), utility::options::OptionCollection.add_relevant(), InteractionDistMinimizer.apply(), CustomMover.apply(), utility::keys::ClassKeyMap< K, T, C >.assign(), utility::keys::SmallKeyMap< K, T >.assign(), utility::keys::ClassKeyVector< K, T, C >.assign(), utility::keys::KeyVector< K, T >.assign(), utility::keys::SmallKeyVector< K, T >.assign(), utility::keys::UserKey< O, S, C >.assign_Key(), utility::keys::AutoKey< O, S, C >.assign_Key(), utility::keys::ClassKeyVector< K, T, C >.at(), utility::keys::KeyVector< K, T >.at(), utility::keys::SmallKeyVector< K, T >.at(), utility::keys::AutoKey< O, S, C >.AutoKey(), binder.bind_member_functions_for_call_back(), calculate_hydrophobic_accessible_surface_area(), 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(), utility::options::OptionCollection.check_key(), utility::options::OptionCollection.check_specs(), utility::options::OptionCollection.check_values(), utility::keys::UserKey< O, S, C >.comparable(), utility::keys::AutoKey< O, S, C >.comparable(), utility::factory::Factory< P >.create(), dist(), utility::keys::UserKey< O, S, C >.equals(), utility::keys::AutoKey< O, S, C >.equals(), utility::keys::ClassKeyMap< K, T, C >.find(), utility::keys::ClassKeyVector< K, T, C >.find(), utility::keys::KeyVector< K, T >.find(), utility::keys::SmallKeyMap< K, T >.find(), utility::keys::SmallKeyVector< K, T >.find(), utility::options::OptionCollection.find_key_cl(), numeric.find_nearest_value(), build.generate_rosetta_cmake_files(), update_ui_project.generate_rosetta_libraries_project_files(), utility::thread::MutableCache< K, V >.get(), get_env_var(), basic::options.get_option(), utility::tag::Tag.getOption(), utility::options::OptionCollection.has(), utility::thread::MutableCache< K, V >.has(), utility::factory::Factory< P >.has(), utility::keys::ClassKeyMap< K, T, C >.has(), utility::keys::ClassKeyVector< K, T, C >.has(), utility::keys::KeyVector< K, T >.has(), utility::keys::SmallKeyMap< K, T >.has(), utility::keys::SmallKeyVector< K, T >.has(), utility::tag::Tag.hasOption(), utility::keys::ClassKeyMap< K, T, C >.inactive(), utility::keys::ClassKeyVector< K, T, C >.inactive(), utility::keys::KeyVector< K, T >.inactive(), utility::keys::SmallKeyMap< K, T >.inactive(), utility::keys::SmallKeyVector< K, T >.inactive(), utility::keys::ClassKeyMap< K, T, C >.index(), utility::keys::ClassKeyVector< K, T, C >.index(), utility::keys::SmallKeyMap< K, T >.index(), utility::keys::SmallKeyVector< K, T >.index(), utility::options::OptionCollection.is_relevant(), ui::task::Node.leaf(), utility::keys::UserKey< O, S, C >.less_than(), utility::keys::AutoKey< O, S, C >.less_than(), utility::options::OptionCollection.operator()(), utility::keys::ClassKeyMap< K, T, C >.operator()(), utility::keys::ClassKeyVector< K, T, C >.operator()(), utility::keys::KeyVector< K, T >.operator()(), utility::keys::SmallKeyMap< K, T >.operator()(), utility::keys::SmallKeyVector< K, T >.operator()(), utility::options.operator+(), utility::keys::AutoKey< O, S, C >.operator=(), utility::keys::Key.operator=(), utility::options::AnyOptionKey.operator=(), utility::options::AnyVectorOptionKey.operator=(), utility::options::BooleanOptionKey.operator=(), utility::options::BooleanVectorOptionKey.operator=(), utility::options::FileOptionKey.operator=(), utility::options::FileVectorOptionKey.operator=(), utility::options::IntegerOptionKey.operator=(), utility::options::IntegerVectorOptionKey.operator=(), utility::options::OptionKey.operator=(), utility::options::PathOptionKey.operator=(), utility::options::PathVectorOptionKey.operator=(), utility::options::RealOptionKey.operator=(), utility::options::RealVectorOptionKey.operator=(), utility::options::ResidueChainVectorOptionKey.operator=(), utility::options::ScalarOptionKey.operator=(), utility::options::StringOptionKey.operator=(), utility::options::StringVectorOptionKey.operator=(), utility::options::VectorOptionKey.operator=(), utility::keys::UserKey< O, S, C >.operator=(), utility::options::OptionCollection.operator[](), utility::keys::ClassKeyMap< K, T, C >.operator[](), utility::keys::ClassKeyVector< K, T, C >.operator[](), utility::keys::KeyVector< K, T >.operator[](), utility::keys::SmallKeyMap< K, T >.operator[](), utility::keys::SmallKeyVector< K, T >.operator[](), utility::tag::Tag.operator[](), utility::options::OptionCollection.option(), parse_pdb_pos(), read_fold_tree_from_file(), numeric::interpolation::Histogram< X, Y >.read_from_db(), read_NACCESS_asa_file(), utility::factory::Registrant< P >.Registrant(), utility::factory::Factory< P >.remove(), core::pack::annealer::FixbbSimAnnealer.run(), basic::Report.set(), basic::Reporter.set(), basic::options.set_option(), utility::options::OptionCollection.set_option_value_cl(), utility::options::OptionCollection.set_option_value_file(), numeric::interpolation::Histogram< X, Y >.set_params(), utility::tag::Tag.setAccessed(), utility::tag::Tag.setOption(), utility::options::OptionCollection.show_all(), utility::options::OptionCollection.show_all_hier(), utility::options::OptionCollection.show_help(), utility::options::OptionCollection.show_help_hier(), utility::options::OptionCollection.show_inaccessed_user_options(), utility::options::OptionCollection.show_option_help(), utility::options::OptionCollection.show_option_help_hier(), utility::options::OptionCollection.show_table_text(), utility::options::OptionCollection.show_table_Wiki(), utility::options::OptionCollection.show_user(), utility::tag.Tag::getOption< platform::Size >(), utility::tag.Tag::getOption< std::string >(), ui::task::Node.update_from_json(), and utility::keys::UserKey< O, S, C >.UserKey().

keys_to_pivots

dictionary subloop_histogram.keys_to_pivots = {}

length_key

subloop_histogram.length_key = lambda x: x[1] - x[0]

lengths

subloop_histogram.lengths = map(length_key, combos)

linestyle

subloop_histogram.linestyle

linewidth

subloop_histogram.linewidth

marker

subloop_histogram.marker

markersize

subloop_histogram.markersize

num_combos

subloop_histogram.num_combos = len(pivots_to_keys)

parser

subloop_histogram.parser = argparse.ArgumentParser()

path

subloop_histogram.path = os.path.join(arguments.input)

pivots

def subloop_histogram.pivots = pivots_from_line(line)

pivots_to_keys

dictionary subloop_histogram.pivots_to_keys = {}

polygon

subloop_histogram.polygon = plt.Polygon(coordinates, facecolor=tango.brown[0])

Referenced by inside_polygon().

rotation

subloop_histogram.rotation

size

subloop_histogram.size

Referenced by pyrosetta.bindings.pose.PoseResidueAccessor.__len__(), protocols::abinitio::JumpSpecificAbrelax.add_constraints(), binder.add_relevant_includes(), MPInterfaceStatistics.add_to_scorefile(), ClusterCycDisulf.align_clusters(), analyze_poses_for_convergence(), detail::buffer< Container::value_type >.append(), PeptoidRotamerRecoverer.apply(), khSandbox.apply(), KHSandbox.apply(), LoopHash_Analyze.apply(), apps::pilot::CustomFragmentMover.apply(), MPDomainAssembly.apply(), ScoreFunctionFingerprintMover.apply(), apply_mask(), detail::bigint.assign(), utility::small_vectorL< T, L, BUFFER_SIZE >.at(), bind_std_array(), bind_std_forward_list(), bind_std_stl_vector(), bind_std_stl_vector_1(), bind_T20_template_variadic(), binder::ClassBinder.bind_with(), blosum_score_alignment(), buns_stats(), calc_dist(), calculate_hASA_by_type_and_attractiveE(), calculate_hASA_by_type_and_exposure(), basic::TracerImpl.calculate_tracer_level(), cen_fold(), myspace.check_clash(), ClashCheck.clash_check(), MatchSet.clash_check(), detail.code_point_index(), detail.count_code_points(), CL.cpu2gpu(), create_pseudo_commandline(), do_event_prediction(), basic::thread_manager::RosettaThreadManager.do_multistage_work_vector_in_threads(), dock(), dump_sequences(), TCDock.dump_top_hits(), utility::vectorL< L, T, A >.erase_index(), utility::vectorL< L, bool, A >.erase_index(), figure_out_stems(), filter_frags(), fit_helix_in_map(), detail::iterator_buffer< OutputIt, T, Traits >.flush(), formatter< std::tm, Char >.format(), detail.format_decimal(), detail.format_float(), formatstr(), basic::database.full_name(), detail.fwrite_fully(), gen_pep_bb_frag(), gen_pep_bb_frag_old(), gen_pep_bb_sequential(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.GeneralizedEigenSolver(), get_contacts(), get_filename(), get_options_from_options_collection(), get_tasks_from_command_line(), binder.get_type_dependencies(), basic.get_usage_from_procfilesystem(), binder::Context.global_insertion_operator(), CL.gpu2cpu(), utility::vectorL< L, T, A >.has(), utility::vectorL< L, bool, A >.has(), HBondedPairIterator.HBondedPairIterator(), basic::TracerImpl.in(), HBondedPairIterator.increment(), utility::vector1< bool, A >.index(), utility::vector1< T, A >.index(), utility::vectorL< L, T, A >.index_of(), myspace::GraftTester.init(), numeric::random::mt19937_RG.init_by_array(), numeric::IntervalSet< T >.is_inside(), is_new_cluster_center_xyz(), binder.is_std_function_bindable(), numeric::IntervalSet< T >.length(), utility::graph::RingDetection< Graph >.LengthOfSmallestCycleWithVertex(), detail::buffer_traits.limit(), detail::fixed_buffer_traits.limit(), load_bb_torsions_into_vector(), main(), apps::pilot::frankdt.main(), make_disulfides(), utility.make_segtag_with_dashes(), CL.makeROmem(), CL.makeRWmem(), makesplitwork_3bpy(), CL.makeWOmem(), mask_out_loop(), MC_run(), numeric::statistics.mean(), numeric::MultiDimensionalHistogram.mean_squared_error(), protocols::abinitio::JumpSpecificAbrelax.multi_fast_relax(), apps::pilot::MultiTemplateAlignChunkMover.MultiTemplateAlignChunkMover(), Mutate1Randomizer.mutate(), mutate_and_score_RNP(), mutate_to_sequence(), my_main(), obtain_start_pose(), detail::int_writer< OutputIt, Char, UInt >.on_num(), detail::format_handler< OutputIt, Char, Context >.on_text(), detail::utf8_to_utf16.operator wstring_view(), numeric::kdtree::CompareKDPoints.operator()(), numeric.operator<<(), detail::fill_t< Char >.operator=(), operator>>(), utility::vectorL< L, T, A >.operator[](), utility::vectorL< L, bool, A >.operator[](), utility::small_vectorL< T, L, BUFFER_SIZE >.operator[](), output_PCA(), ConstraintConfig.parse_config_file(), parse_nonstandard_angles(), parse_nonstandard_bondlengths(), parse_resfiles(), perturb_bb_and_relax(), ThisApplication.pick_frags(), apps::pilot::MultiTemplateAlignChunkMover.pick_random_template(), ChallengeMover.pick_random_template(), PoseWrap.PoseWrap(), posewrap_from_command_line(), post_rebuild_bulge_assembly(), power_set(), prepare_full_length_start_model(), numeric.principal_components_and_eigenvalues_ndimensions(), print_debug_information(), print_verbose_ddgs(), myspace.project(), numeric::IntervalSet< T >.push_back(), numeric::IntervalSet< T >.random_point(), read_alignment_fasta_file(), read_complex_type(), detail.reserve(), run(), TCDock.run(), run_parallel_docking(), RunPepSpec(), sasa_separation(), scan_Evalue(), myspace.scan_Evalue(), scheme_score(), select_residues_for_evaluation(), separation(), sequence_tolerance_main(), sequence_tolerance_mf_main(), utility::graph::ArrayPool< T >.set_array_size(), set_basic_dock_options(), utility::graph::ArrayPool< T >.set_block_size(), set_up_engine(), ThisApplication.setup(), setup_alignment_map(), setup_pdbnames_next_round(), numeric::fourier::SHT.setup_Pmls(), ConstraintConfig.show_cst_grids(), utility::vectorL< L, T, A >.shrink(), utility::vectorL< L, bool, A >.shrink(), sicdock_thread_num(), simple_loop_modeling_test(), detail.snprintf_float(), SphereGrinder(), numeric::statistics.std_dev_with_provided_mean(), storeposedata(), detail::utf8_to_utf16.str(), format_int.str(), target_constraints(), binder.template_specialization(), test(), test_actcoord(), myspace::GraftTester.test_cart_graft(), myspace::GraftTester.test_rb_min_graft(), detail.to_pointer(), to_string(), utility::vectorL< L, T, A >.u(), utility::vectorL< L, bool, A >.u(), use_in_rmsd(), use_in_rmsd_offset(), validate_dunbrack_binaries(), vfprintf(), detail::arg_formatter_base< OutputIt, Char, ErrorHandler >.write(), detail.write(), detail.write_buffer(), detail.write_float(), detail::write_int_data< Char >.write_int_data(), detail.write_nonfinite(), detail.write_padded(), detail.write_ptr(), and CL.zero_gpu_mem().

solid_capstyle

subloop_histogram.solid_capstyle

top_label_locations

subloop_histogram.top_label_locations

top_labels

subloop_histogram.top_labels

twin

subloop_histogram.twin = axes.twiny()

x

subloop_histogram.x

xpadding

float subloop_histogram.xpadding = 0.02 * num_combos

ymax

subloop_histogram.ymax

Referenced by CrystFFTDock.resample_maps_and_get_self().

ymin

subloop_histogram.ymin

ypadding

float subloop_histogram.ypadding = 0.03 * ymax