erraser_single_res_analysis Namespace Reference

Functions
def	find_chi_angle_std_pdb
def	syn_anti_check
def	extract_info

Variables
tuple	file_path = os.path.split( os.path.abspath(__file__) )
tuple	prefix = parse_options( sys.argv, 'prefix', '' )
tuple	res = parse_options( sys.argv, 'res', '' )
tuple	outfile = parse_options( sys.argv, 'out', 'erraser_single_res.analysis' )
list	data = []
tuple	pdb_list = sorted( glob.glob( prefix + '_*.pdb') )
int	pdb_id = 0
int	start_min_score = 0
string	name = 'start_min'
tuple	out = open(outfile, 'w')
string	score = '%9.1f'

Function Documentation

def erraser_single_res_analysis.extract_info	(		pdb,
			res,
			name
	)

References basic::options::OptionKeys::stepwise.enumerate, find_chi_angle_std_pdb(), fmt.join(), basic::database.open(), erraser_util.phenix_rna_validate(), erraser_util.subprocess_call(), and syn_anti_check().

def erraser_single_res_analysis.find_chi_angle_std_pdb	(		input_pdb,
			res_find
	)

References measure_params.compute_torsion(), ObjexxFCL.len(), basic::database.open(), and binder.replace().

Referenced by extract_info().

def erraser_single_res_analysis.syn_anti_check

(

chi

)

Referenced by extract_info().

Variable Documentation

list erraser_single_res_analysis.data = []

Referenced by analyze_base_pair_test(), MetalSiteFinderMover.apply(), correct_dunbrack(), correct_rama(), utility.exit(), utility::thread::SharedThreadLocalData< T >.get(), utility::io.get_lines_from_file_data(), SVC_Q.get_Q(), ONE_CLASS_Q.get_Q(), SVR_Q.get_Q(), basic.get_usage_from_procfilesystem(), numeric::nls.lm_lmdif(), numeric::nls.lmmin(), main(), processRegions(), read_rama_map_file(), numeric.read_tensor_from_file(), binder.relevant_include(), basic::mpi.request_data_from_head_node(), rna_features_from_pose(), rna_score_test(), basic::mpi.send_data_to_head_node(), basic::options.start_files(), utility.swap4_aligned(), and Cache.swap_index().

tuple erraser_single_res_analysis.file_path = os.path.split( os.path.abspath(__file__) )

string erraser_single_res_analysis.name = 'start_min'

tuple erraser_single_res_analysis.out = open(outfile, 'w')

Referenced by add_rosetta_options_0(), add_rosetta_options_13(), add_rosetta_options_6(), add_rosetta_options_7(), calc_rama_scores(), calc_scores(), numeric::AgglomerativeHierarchicalClusterer.cluster(), basic::ComparingTracer.ComparingTracer(), convert(), numeric::alignment.coordinate_array_broadcast_rmsd(), numeric::alignment.coordinate_array_rmsd(), numeric::alignment.coordinate_array_superimpose(), utility::file.create_blank_file(), numeric::geometry::hashing::xyzStripeHash.debug_pdb(), supercharge.design_supercharge(), dump_table(), fmt::internal.format_system_error(), fmt.format_system_error(), go_main(), utility::file.gunzip(), harvest_motifs(), numeric::alignment.indexed_coordinate_array_broadcast_rmsd(), interface_residue_ddg(), is_interface_residue(), main(), nucleobase_probe_score_test(), utility::io::izstream.open(), utility::io::ozstream.open(), utility::io::ozstream.open_append(), numeric::kinematic_closure.operator<<(), numeric::kdtree.operator<<(), basic::resource_manager.operator<<(), numeric.operator<<(), basic::sampling::orientations.operator<<(), utility::tag.operator<<(), output_packstat_pdb(), output_results(), print_pep_csts(), register_options(), reverse_convert(), rna_sequence_recovery_metrics(), run(), ScoreFragmentSetMover.run(), run_pep_prep(), RunPepSpec(), utility::tag::Tag.setOption(), setup_mask(), basic::resource_manager::locator::FileSystemResourceLocator.show(), basic::TracerToFile.TracerToFile(), fmt::internal::ArgFormatterBase< ArgFormatter< Char >, Char, FormatSpec >.visit_char(), fmt::BasicWriter< Char >.write_double(), fmt::BasicWriter< Char >.write_str(), numeric.write_tensor_to_file(), numeric.write_tensor_to_file_without_json(), basic::resource_manager.write_type< bool >(), and utility::io.write_vector().

tuple erraser_single_res_analysis.outfile = parse_options( sys.argv, 'out', 'erraser_single_res.analysis' )

Referenced by correct_dunbrack(), correct_rama(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), filter_combine_long_loop(), graft_pdb(), harvest_motifs(), main(), make_fragments(), mg_modeler_test(), output_results(), output_superimposed_pdb(), Prepare(), rhiju_pdbstats(), rna_build_helix_test(), rna_design_test(), rna_thread_test(), FragmentAssemblyMover.run(), and swa_rna_cluster().

int erraser_single_res_analysis.pdb_id = 0

tuple erraser_single_res_analysis.pdb_list = sorted( glob.glob( prefix + '_*.pdb') )

Referenced by add_rosetta_options_11(), and rhiju_pdbstats().

tuple erraser_single_res_analysis.prefix = parse_options( sys.argv, 'prefix', '' )

Referenced by add_rosetta_options_0(), add_rosetta_options_10(), add_rosetta_options_11(), add_rosetta_options_14(), add_rosetta_options_5(), add_rosetta_options_6(), add_rosetta_options_8(), add_rosetta_options_9(), binder.begins_with(), binder.ends_with(), binder.function_pointer_type(), main(), numeric::kinematic_closure.operator<<(), processRegions(), report_and_dump(), retag(), sequence_tolerance_main(), binder.update_source_file(), and fmt::BasicWriter< Char >.write_int().

tuple erraser_single_res_analysis.res = parse_options( sys.argv, 'res', '' )

string erraser_single_res_analysis.score = '%9.1f'

Referenced by UBQ_GTPase_disulfide_Mover.analyze_and_filter(), UBQ_E2Mover.analyze_and_filter(), calculate_average_residue_scores(), CAtrace.CAtrace(), do_color_by_score(), helix_from_sequence(), main(), myMC.myMC(), numeric::interpolation.polycubic_interpolation(), basic::options.process(), read_silent_input_as_library(), myMC.roll(), SolutionRescoreMover.run(), basic::svd::SVD_Solver.run_score_svd_on_matrix(), basic::svd::SVD_Solver.run_score_svd_without_solving(), save_per_residue_scores(), and numeric::VoxelGrid< typename >.SetupGrid().

list erraser_single_res_analysis.start_min_score = 0