Functions
def	smart_int (string)

def	setup_hook ()

Variables
dictionary	name_abbreviations

dictionary	names = name_abbreviations.keys()

string	default_name = 'sandbox'

string	closure_moves = 'naive', 'balanced',

string	sampling_moves = 'uniform', 'rama', 'walking', 'vicinity'

string	breadth_moves = 'uniform', 'omega', 'rama'

string	score_functions = 'rama', 'off'

string	default_closure_move = 'naive'

string	default_sampling_move = 'uniform'

string	default_breadth_move = 'omega'

string	default_score_function = 'off'

string	default_structure = 'structures/linear/6.symmetry.pdb'

dictionary	default_pivots

string	command = 'git', 'rev-parse', '--show-toplevel'

	output = check_output(command, stderr=devnull)

	rosetta_path = output.strip()

	rosetta_subpath = lambda subpath: os.path.join(rosetta_path, subpath)

	parser = argparse.ArgumentParser()

	default

	action

	dest

	choices

	type

	int

	nargs

	smart_int

	float

	job = scripting.Job()

	arguments = parser.parse_args()

	background

	overwrite

	foreground

	hook

	dry_run

	pivots

	pdb_string

	pivot_string

Function Documentation

◆ setup_hook()

def run_backbone.setup_hook ( )

References rosetta_subpath.

◆ smart_int()

def run_backbone.smart_int ( string )

 Convert the given string to an integer.  Metric suffixes, if they are 
present, will be properly translated.

References ObjexxFCL.get(), int, and smart_int.

Variable Documentation

◆ action

run_backbone.action

◆ arguments

run_backbone.arguments = parser.parse_args()

◆ background

run_backbone.background

◆ breadth_moves

string run_backbone.breadth_moves = 'uniform', 'omega', 'rama'

◆ choices

run_backbone.choices

Referenced by ga_main(), Mutate1Randomizer.mutate(), ConstraintConfig.pick_sequence(), Bola.random_move(), sequence_tolerance_main(), and sequence_tolerance_mf_main().

◆ closure_moves

string run_backbone.closure_moves = 'naive', 'balanced',

◆ command

run_backbone.command = 'git', 'rev-parse', '--show-toplevel'

◆ default

run_backbone.default

◆ default_breadth_move

run_backbone.default_breadth_move = 'omega'

◆ default_closure_move

run_backbone.default_closure_move = 'naive'

◆ default_name

string run_backbone.default_name = 'sandbox'

◆ default_pivots

dictionary run_backbone.default_pivots

Initial value:

 =  {
         'structures/linear/4.helix.pdb': (1, 2, 4),
         'structures/linear/5.helix.pdb': (2, 3, 4),
         'structures/linear/6.symmetry.pdb': (2, 3, 5),
         'structures/linear/7.helix.pdb': (2, 4, 6),
         'structures/linear/7.1ubq.pdb': (2, 4, 6),
         'structures/linear/14.1eco.pdb': (2, 7, 12),
         'structures/linear/14.cycle.pdb': (2, 7, 12),
         'structures/kic/1srp.pdb': (308, 319)
 }

◆ default_sampling_move

run_backbone.default_sampling_move = 'uniform'

◆ default_score_function

run_backbone.default_score_function = 'off'

◆ default_structure

string run_backbone.default_structure = 'structures/linear/6.symmetry.pdb'

◆ dest

run_backbone.dest

◆ dry_run

run_backbone.dry_run

◆ float

run_backbone.float

Referenced by PyMOL-Rosetta-relay-client.Matrix.__init__(), PyMOL-RosettaServer.Matrix.__init__(), pyrosetta.distributed.cluster.validators._validate_float(), pyrosetta.bindings.energies.active_total_energies(), DB_Builder.add_data(), Benchmark.apply(), bin_torsions.bin_histograms(), bind_std_forward_list(), bind_std_functional_hash(), bind_std_stl_function(), bind_std_stl_multiset(), bind_std_unordered_map(), bind_std_unordered_set(), bind_T81_custom_trampoline_with_args(), helpers.cache_trajectory(), calculate_percent_hydrophobic_distribution(), calculate_percent_hydrophobic_stats(), clean_pdb_keep_ligand.check_and_print_pdb(), add_xyz_to_pose.collect_xyz(), compare_times.compare_times(), erraser_wrapper.erraser(), erraser_wrapper.erraser_single_res(), erraser_single_res_analysis.extract_info(), DRRAFTER_util.extract_lowscore_decoys(), erraser_util.find_chi_angle(), erraser_analysis.find_chi_angle_std_pdb(), erraser_single_res_analysis.find_chi_angle_std_pdb(), erraser_util.find_error_res(), bin_torsions.find_y_limits(), float_as_aidr(), cal_vdw_radius_pool.get_pair_counts(), get_final_ddG_scores.get_scores(), apps::pilot::AlignChunkMover.get_superposition_transformation(), get_superposition_transformation(), util.get_surrounding_res(), harvest_scores(), pyrosetta.distributed.viewer.core.init(), dbscan_cluster_rotamer.load_centroid(), kmeans_adaptive_kernel_density_bb_dependent_rotlib.load_centroid(), kmeans_bb_dependent_rotlib.load_centroid(), kmeans_common.load_centroid(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.load_centroid(), kmeans_adaptive_kernel_density_bb_dependent_rotlib.load_centroid_xyz(), kmeans_common.load_centroid_xyz(), dbscan_adaptive_kernel_density_bb_dependent_rotlib.load_data(), erraser_util.load_pdb_coord(), erraser_util.load_pdb_coord_old(), bin_torsions.load_torsions_from_dat(), setup_for_complex_scoring_general.main(), dbscan_cluster_rotamer.main(), find_lowest_scoring_relaxed_struct.main(), get_final_ddG_scores.main(), mp_ddG.main(), get_lowest_scoring_relaxed_models.main(), best_ifaceE.main(), prune_atdiff_top5pct.main(), main(), dbscan_cluster_rotamer.main_old_kmeans(), PyMOL-Rosetta-relay-client.make_axis(), PyMOL-RosettaServer.make_axis(), pyrosetta.PyMOLRosettaServer.make_axis(), average_rmsds.mean(), mp_ddG.mutate_residue(), pyrosetta.toolbox.py_jobdistributor.output_scorefile(), percent_subangstrom.parse_job(), score_vs_rmsd.parse_old_source(), dbscan_adaptive_kernel_density_bb_dependent_rotlib.parse_opt(), erraser_util.parse_options(), cal_NBR_radius.parse_res_lines(), erraser_util.pdb2rosetta(), histogram.plot_ideal_torsions(), histogram.plot_rama_kic(), bin_torsions.plot_score_function(), histogram.plot_uniform_kic(), mp_ddG.print_ddG_breakdown(), PyMOL-Rosetta-relay-client.PR_PyMOLServer.process_packet(), PyMOL-RosettaServer.PR_PyMOLServer.process_packet(), pyrosetta.PyMOLRosettaServer.PR_PyMOLServer.process_packet(), DRRAFTER_util.read_pdb(), util.read_pdb(), DRRAFTER_util.read_pdb_with_segid(), erraser_util.regularize_OP1_OP2(), best_beta_backbones.report_proportion_accessible(), best_beta_backbones.report_proportion_accessible_alpha(), numeric::geometry::hashing::xyzStripeHash.sanity_check(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.sanity_check(), demo.D090_Ala_scan.scanning_analysis(), evaluate_beta_mutants.score_ensemble(), sicdock_thread_num(), average_rmsds.subangstrom(), test_k_square(), and CrystFFTDock.writeMRC().

◆ foreground

run_backbone.foreground

◆ hook

run_backbone.hook

◆ int

run_backbone.int

Referenced by smart_int().

◆ job

run_backbone.job = scripting.Job()

◆ name_abbreviations

dictionary run_backbone.name_abbreviations

Initial value:

 =  {
         'sm':            'jobs/sampling/{0.sampling_move}',
         'sampling':      'jobs/sampling/{0.sampling_move}',
         'free':          'jobs/{0.sampling_move}-{0.score_function}/free/{0.closure_move}',
         'fixed':         'jobs/{0.sampling_move}-{0.score_function}/fixed/{0.closure_move}',
         'fixed-pivots':  'jobs/{0.sampling_move}-{0.score_function}/fixed/{0.closure_move}/{0.pivot_string}',
         'sandbox':       'jobs/sandbox',
 }

◆ names

dictionary run_backbone.names = name_abbreviations.keys()

Referenced by get_base_pucker(), InstantiateModulesBenchmark.instantiate_filters(), InstantiateModulesBenchmark.instantiate_movers(), InstantiateModulesBenchmark.instantiate_packer_palettes(), InstantiateModulesBenchmark.instantiate_res_selectors(), InstantiateModulesBenchmark.instantiate_reslvl_taskops(), InstantiateModulesBenchmark.instantiate_simple_metrics(), InstantiateModulesBenchmark.instantiate_taskops(), main(), and basic::options.start_files().

◆ nargs

run_backbone.nargs

◆ output

run_backbone.output = check_output(command, stderr=devnull)

◆ overwrite

run_backbone.overwrite

◆ parser

run_backbone.parser = argparse.ArgumentParser()

◆ pdb_string

run_backbone.pdb_string

◆ pivot_string

run_backbone.pivot_string

◆ pivots

run_backbone.pivots

Referenced by numeric::kinematic_closure::radians.bridge_objects(), numeric::kinematic_closure.bridgeObjects(), numeric::kinematic_closure.bridgeObjects_nonredundant(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his4(), ik_his_clamp(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), KIC_loop_close(), loop_closure_test(), main(), SamplingManager.SamplingManager(), test_bridgeObjects(), numeric::kinematic_closure.test_bridgeObjects(), test_kc(), and test_kc2().

◆ rosetta_path

run_backbone.rosetta_path = output.strip()

◆ rosetta_subpath

run_backbone.rosetta_subpath = lambda subpath: os.path.join(rosetta_path, subpath)

Referenced by setup_hook().

◆ sampling_moves

string run_backbone.sampling_moves = 'uniform', 'rama', 'walking', 'vicinity'

◆ score_functions

string run_backbone.score_functions = 'rama', 'off'

◆ smart_int

run_backbone.smart_int