bin_torsions Namespace Reference

Functions
def	parse_arguments ()
def	parse_iterations (arguments)
def	key_from_torsion (torsion, index)
def	torsion_from_key (key)
def	load_histograms (arguments)
def	load_histograms_from_npz (arguments)
def	load_torsions_from_npz (arguments)
def	load_torsions_from_dat (arguments)
def	generate_histograms (arguments, all_torsions)
def	find_title (arguments)
def	find_y_limits (arguments, axes)
def	find_pivots (arguments)
def	bin_histograms (arguments, key, all_bins, all_counts, warning_messages)
def	plot_histograms (arguments, all_bins, all_counts, ks_test, index)
def	plot_score_function (arguments)

Variables
	figure = plt.figure()
def	arguments = parse_arguments()
	job
	bins
	counts
	ks_test
	output
	dpi

Function Documentation

bin_histograms()

def bin_torsions.bin_histograms	(		arguments,
			key,
			all_bins,
			all_counts,
			warning_messages
	)

 Return bins and counts for the given key, where the number of bins is
adjusted to best match the value specified by the '--bins' argument.  This
is necessary because the same number of bins (720) are always cached, but
the user may want a coarser view of the data. 

References ObjexxFCL.abs(), run_backbone.float, ObjexxFCL.len(), range, and sum().

Referenced by plot_histograms().

find_pivots()

def bin_torsions.find_pivots

(

arguments

)

References enumerate_junctions.int, key_from_torsion(), basic::database.open(), and binder.split().

Referenced by plot_histograms().

find_title()

def bin_torsions.find_title

(

arguments

)

References join(), basic::database.open(), binder.split(), and ObjexxFCL.strip().

Referenced by plot_histograms().

find_y_limits()

def bin_torsions.find_y_limits	(		arguments,
			axes
	)

References run_backbone.float, basic::database.open(), and binder.split().

Referenced by plot_histograms().

generate_histograms()

def bin_torsions.generate_histograms	(		arguments,
			all_torsions
	)

References basic::database.open().

Referenced by load_histograms().

key_from_torsion()

def bin_torsions.key_from_torsion	(		torsion,
			index
	)

 Return a simple string representing the given torsion angle.  A handful
of command line options expect arguments in this format. 

References str().

Referenced by find_pivots(), and load_torsions_from_dat().

load_histograms()

def bin_torsions.load_histograms

(

arguments

)

 Return two dictionaries holding the bins and the counts, respectively,
for each torsion.  Much effort has been made to optimize this function by
caching intermediate results. 

References generate_histograms(), load_histograms_from_npz(), load_torsions_from_dat(), and load_torsions_from_npz().

load_histograms_from_npz()

def bin_torsions.load_histograms_from_npz

(

arguments

)

References basic::database.open().

Referenced by load_histograms().

load_torsions_from_dat()

def bin_torsions.load_torsions_from_dat

(

arguments

)

References basic::options::OptionKeys::stepwise.enumerate, run_backbone.float, enumerate_junctions.int, key_from_torsion(), basic::database.open(), parse_iterations(), and binder.split().

Referenced by load_histograms().

load_torsions_from_npz()

def bin_torsions.load_torsions_from_npz

(

arguments

)

Referenced by load_histograms().

parse_arguments()

def bin_torsions.parse_arguments

(

)

parse_iterations()

def bin_torsions.parse_iterations

(

arguments

)

 Return the number of iterations that need to be read off disk. 

References basic::database.open(), and binder.split().

Referenced by load_torsions_from_dat().

plot_histograms()

def bin_torsions.plot_histograms	(		arguments,
			all_bins,
			all_counts,
			ks_test,
			index
	)

References bin_histograms(), find_pivots(), find_title(), find_y_limits(), pyrosetta.tests.distributed.test_dask.format, ObjexxFCL.len(), range, set(), str(), and torsion_from_key().

plot_score_function()

def bin_torsions.plot_score_function

(

arguments

)

References basic::options::OptionKeys::stepwise.enumerate, run_backbone.float, enumerate_junctions.int, ObjexxFCL.len(), basic::database.open(), and sum().

torsion_from_key()

def bin_torsions.torsion_from_key

(

key

)

 Return a (torsion, index) tuple represented by this key. 

Referenced by plot_histograms().

Variable Documentation

arguments

def bin_torsions.arguments = parse_arguments()

Referenced by ui::task.open_file_viewer().

bins

bin_torsions.bins

Referenced by numeric::geometry::hashing::SixDCoordinateBinner.bin6(), numeric::interpolation::spline::PolycubicSpline< N >.dFdxi(), numeric::interpolation::spline::PolycubicSpline< N >.F(), numeric::interpolation::InterpolatedPotential< N >.get_indices(), numeric::interpolation.polycubic_interpolation(), and numeric::VoxelGrid< T >.SetupGrid().

counts

bin_torsions.counts

Referenced by ClosabilityScore.closability_score(), count_subset(), gather_ss_pct(), apps::pilot::HelixMover.get_helix_centers(), numeric::histograms::TwoDHistogram< key1, key2 >.insert_data(), numeric::histograms::OneDHistogram< key1 >.insert_data(), numeric::histograms::OneDHistogram< key1 >.lookup_counts(), numeric::histograms::TwoDHistogram< key1, key2 >.lookup_counts(), main(), nsat(), print_hb_counts(), symmetrize_map(), and RDF_Mover.write_R_data_file().

dpi

bin_torsions.dpi

figure

bin_torsions.figure = plt.figure()

Referenced by gaussian-sampling.plot_correlation(), gaussian-sampling.plot_histogram(), and gaussian-sampling.plot_trajectory().

job

bin_torsions.job

Referenced by ui::task::Task.add_job(), MPInterfaceStatistics.add_to_scorefile(), CalcIrms.apply(), abbinding.apply(), PhDocking.apply(), GlycomutagenesisProtocol.apply(), CustomMover.apply(), DockGlycansProtocol.apply(), HemaggTrimer.apply(), MotifDock.apply(), CalcCdrRms.apply(), PackingAngle.apply(), RescoreCenrot.apply(), MPFindInterfaceTestMover.apply(), TestQuickRelaxMover.apply(), compute_Irmsd.apply(), run_score_patchdock_hotspot.apply(), run_score_hotspot.apply(), ui::task::Task.delete_job(), protocols::abinitio::JumpSpecificAbrelax.do_distributed_rerun(), erraser2_test(), protocols::abinitio::JumpSpecificAbrelax.fold(), main(), my_main(), ui::task::TaskSubmit.on_add_job_clicked(), InterfaceDDGBindJobInputter.pose_from_job(), DockGlycansProtocol.record_pose_metrics(), ui::task::Task.rename_job(), ui::task::Task.task_data(), ui::task::TaskView.TaskView(), and ui::task::TaskSubmit.update_ui_from_task().

ks_test

bin_torsions.ks_test

output

bin_torsions.output

Referenced by GraftDesignCDRs.apply(), FindOptimalHydrophobicThk.apply(), IdentifyCDRClusters.apply(), HBondReporter.apply(), numeric::Calculator.compute(), cone_cen_nc_calculator(), cone_FA_nc_anyatom_calculator(), cone_FA_nc_calculator(), cone_FA_nc_calculator_amide(), numeric.FArray_to_vector_of_xyzvectors(), ui::task::TaskSyncer_NodeStrategy.files_topology_updated(), ElecDensMinPackMinReporter.find_flips(), Foldptn.Foldptn(), detail.format_value(), gpu_score_test(), SampleTiltProtocol.init_options(), main(), match_main(), numeric.operator<<(), opt_bicelle_params(), opt_double_vesicle_params(), opt_vesicle_params(), output_all_repeats(), zinc_stats::ZincStatisticGenerator.output_file(), output_sasa(), PairDistance.PairDistance(), PickBAB.PickBAB(), predict_ss(), Features.print_features(), ElecDensMinPackMinReporter.print_flips(), print_rot_vector(), zinc_stats::ZincStatisticGenerator.recursively_model_rotamer_chis(), SampleTiltProtocol.register_options(), Sasa.Sasa(), save_per_residue_scores(), utility::tag::XMLValidatorImpl.set_schema(), DesignGlycansProtocol.show(), GlycomutagenesisProtocol.show(), DockGlycansProtocol.show(), GlycanClashCheckMover.show(), sphere_cen_nc_calculator(), sphere_FA_nc_anyatom_calculator(), sphere_FA_nc_calculator(), ui::task::TaskSyncer_TaskStrategy.subscribe(), test_gpu_speed(), utility::tag.test_if_schema_is_valid(), test_k_square(), utility::tag::XMLValidatorImpl.validate_xml_against_schema(), utility::tag.validate_xml_against_xsd(), numeric.vector_of_xyzvectors_to_FArray(), detail::cf.vformat_to(), viewer_main(), and numeric.xyzmatrix_to_FArray().