closure_error Namespace Reference

Functions
def	backbone_filter (model, atom, position)
def	distance (coordinates)

Variables
	parser = argparse.ArgumentParser()
	type
	action
	int
	default
	arguments = parser.parse_args()
	output = os.path.join(arguments.job, 'pivots.dat')
	first_pivot = None
	line = file.readline().strip()
	third_pivot = int(line.split()[-1])
	directory = os.path.join(arguments.job, 'trajectory')
	paths = os.listdir(directory)
	count = len(paths)
	models = arange(count)
	error = zeros(count)
	reference = None
	path = os.path.join(directory, subpath)
	model = biophysics.Model(path)
	coordinates = model.coordinates
	solutions = file.readlines()
	dpi

Function Documentation

backbone_filter()

def closure_error.backbone_filter	(		model,
			atom,
			position
	)

distance()

def closure_error.distance

(

coordinates

)

Variable Documentation

action

closure_error.action

arguments

closure_error.arguments = parser.parse_args()

coordinates

closure_error.coordinates = model.coordinates

count

closure_error.count = len(paths)

default

closure_error.default

directory

closure_error.directory = os.path.join(arguments.job, 'trajectory')

Referenced by main().

dpi

closure_error.dpi

error

closure_error.error = zeros(count)

Referenced by utility::tag::XMLValidationOutput.add_error(), check_silent_error(), utility::options::OptionCollection.check_specs(), utility::options::OptionCollection.check_values(), DockFragmentsMover.cluster_frags(), basic::database.db_partition_from_options(), utility::tag.handle_structured_xml_error(), utility::options::VectorOption_T_< K, T >.legal_check(), utility::options::VectorOption_T_< K, T >.legal_default_check(), utility::options::ScalarOption_T_< K, T >.legal_default_report(), utility::options::VectorOption_T_< K, T >.legal_default_report(), utility::options::ScalarOption_T_< K, T >.legal_limits_report(), utility::options::VectorOption_T_< K, T >.legal_limits_report(), utility::options::ScalarOption_T_< K, T >.legal_report(), utility::options::VectorOption_T_< K, T >.legal_report(), utility::options::VectorOption_T_< K, T >.legal_size_report(), main(), numeric::linear_algebra.minimum_bounding_ellipse(), multiclass_probability(), numeric::expression_parser::ArithmeticASTExpression.parse(), numeric::expression_parser::ArithmeticASTFunction.parse(), numeric::expression_parser::ArithmeticASTTerm.parse(), numeric::expression_parser::ArithmeticASTFactor.parse(), numeric::expression_parser::ArithmeticASTOrClause.parse(), numeric::expression_parser::ArithmeticASTAndClause.parse(), numeric::expression_parser::ArithmeticASTValue.parse(), utility::tag::Tag.read(), read_silent_input_as_library(), utility::tag.recurse_through_tree(), RosettaJob.request_job_from_server(), nacl_rosetta::RosettaURLFileHandler.return_file_callback(), RosettaJob.return_results_to_server(), basic::database.safely_prepare_statement(), numeric::expression_parser::ArithmeticScanner.scan_identifier(), utility::options::ScalarOption_T_< K, T >.specified_report(), and utility::options::VectorOption_T_< K, T >.specified_report().

first_pivot

closure_error.first_pivot = None

Referenced by devel_main(), and protocols_main().

int

closure_error.int

line

closure_error.line = file.readline().strip()

model

closure_error.model = biophysics.Model(path)

Referenced by ui::task::TaskView.action_output_open(), ui::task::TaskView.action_output_save_as(), compute_windowed_rmsd(), cost(), describe_move(), ui::task::TaskView.index_to_file(), main(), ui::task::TaskSubmit.on_files_clicked(), svm_check_probability_model(), svm_get_labels(), svm_get_nr_class(), svm_get_nr_sv(), svm_get_sv_indices(), svm_get_svm_type(), svm_get_svr_probability(), svm_load_model(), svm_predict(), svm_predict_probability(), svm_predict_values(), svm_save_model(), svm_train(), ui::task::TaskView.TaskView(), and ui::task::TaskView.update_ui_file_list_from_task().

models

closure_error.models = arange(count)

Referenced by assign_models(), check_lengths(), choose_centroids(), dist(), load_models(), main(), multimodel_gdt(), select_residues_for_evaluation(), write_distances(), and write_output_files().

output

closure_error.output = os.path.join(arguments.job, 'pivots.dat')

parser

closure_error.parser = argparse.ArgumentParser()

path

closure_error.path = os.path.join(directory, subpath)

Referenced by utility::graph::RingEdgeAnnotationVisitor< Graph, EdgeMap, PathMap >.back_edge(), determine_output_name(), utility::file.file_delete(), utility::file.file_exists(), utility.filename(), basic::resource_manager::locator::FileSystemResourceLocator.FileSystemResourceLocator(), basic::database.find_database_path(), protocols::abinitio::JumpSpecificAbrelax.fold(), basic::database.full_cache_name(), utility::file.is_directory(), main(), out::path.mmtf(), mutate_and_score_RNP(), my_main(), binder.namespace_from_named_decl(), binder.operator<<(), basic::database.parse_database_connection(), basic::resource_manager::locator::FileSystemResourceLocator.parse_my_tag(), utility.pathname(), basic::options.process(), scheme_score(), ui::config.set_pdb_viewer_path(), utility::graph::RingDetection< Graph >.SetupAdjacencyVector(), stepwise_monte_carlo_legacy(), utility::graph::RingEdgeAnnotationVisitor< Graph, EdgeMap, PathMap >.tree_edge(), and binder.update_source_file().

paths

closure_error.paths = os.listdir(directory)

Referenced by basic::resource_manager::locator::FileSystemResourceLocator.parse_my_tag().

reference

closure_error.reference = None

Referenced by PyCallBack_Mammal_1_t.Breathe(), PyCallBack_Dog_1_t.Breathe(), check_lengths(), compute_windowed_rmsd(), PyCallBack_Animal_1_t.Eat(), PyCallBack_Mammal_1_t.Eat(), PyCallBack_Dog_1_t.Eat(), PyCallBack_A2.f(), PyCallBack_A3.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(), 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(), PyCallBack_Animal_1_t.isDog(), PyCallBack_Mammal_1_t.isDog(), PyCallBack_Dog_1_t.isDog(), main(), and PyCallBack_A4.operator=().

solutions

closure_error.solutions = file.readlines()

Referenced by devel_main(), main(), ClosureMover.naive_apply(), pick_correct_solution(), pick_pathological_solution(), and pick_random_solution().

third_pivot

closure_error.third_pivot = int(line.split()[-1])

Referenced by devel_main(), and protocols_main().

type

closure_error.type