enumerate_junctions Namespace Reference

Classes
class	Component
class	Design
class	DHR
class	Junction

Functions
def	generate_dhrs_txt_file (dhr_location)
def	get_single_junction (junction_fn)
def	generate_junctions_txt_file (junction_location, options)
def	get_terminal_pdb (options, dhrs_dict)
def	get_all_dhrs (dhr_run_location)
def	get_all_junctions (junction_run_location, dhrs_dict)
def	generate_all_dhr_attach_permutations (design, dhrs_dict, n_term_min, n_term_max, c_term_min, c_term_max, output_wo_extension)
def	generate_all_junction_attach_permutations (design, dhrs_dict, n_term_junc_dict, c_term_junc_dict, options)
def	generate_all_terminal_pdb_permutations (design, terminal_pdb, dhrs_dict, options)
def	generate_starting_round_structures (n_term_junc_dict, dhrs_dict, options)
def	enumerate_tranform_db (dhrs_dict, n_term_junc_dict, c_term_junc_dict, options)
def	generate_structures (design, n_term_junc_dict, c_term_junc_dict, dhrs_dict, options, queue, terminal_pdb, output_wo_extension, recursive)
def	listener (q, options)
def	generate_structures_wrapper (data, q)

Variables
	parser = ArgumentParser( description="" )
	type
	str
	default
	help
	bool
	False
	None
	int
	True
	options = parser.parse_args()
string	current_machine = "jojo"
string	DHR_location_jojo = "/home/brunette/DBs/repeats/DHRs"
string	Junction_location_jojo = "/home/brunette/DBs/building_components/DHR_junctions_all_filters_plus_L1"
string	DHR_location_hyak = "/gscratch/baker/brunette/DBs/repeats/DHRs"
string	Junction_location_hyak = "/gscratch/baker/brunette/DBs/repeats/junctions"
string	DHR_location_digs = "/work/brunette/DBs/repeats/DHRs"
string	Junction_location_digs = "/work/brunette/DBs/repeats/junctions"
string	DHR_location_short = ""
string	Junction_location_short = ""
string	dhr_location = DHR_location_jojo
string	junction_location = Junction_location_jojo
string	dhr_run_location = DHR_location_jojo
string	junction_run_location = Junction_location_jojo
	manager = mp.Manager()
	q = manager.Queue()
	pool = mp.Pool( processes = options.n_core )
	watcher = pool.apply_async(listener, (q,options,) )
def	dhrs_dict = get_all_dhrs(dhr_run_location)
	n_term_junc_dict
	c_term_junc_dict
	terminal_pdb = None
def	designs_rd1 = generate_starting_round_structures(n_term_junc_dict,dhrs_dict,options)
list	designs_rd2 = []
	tmp_data = Pool_data(tmp_design,n_term_junc_dict,c_term_junc_dict,dhrs_dict,options,terminal_pdb,True,True)

Function Documentation

enumerate_tranform_db()

def enumerate_junctions.enumerate_tranform_db	(		dhrs_dict,
			n_term_junc_dict,
			c_term_junc_dict,
			options
	)

References pyrosetta.tests.distributed.test_dask.format, and basic::database.open().

generate_all_dhr_attach_permutations()

def enumerate_junctions.generate_all_dhr_attach_permutations	(		design,
			dhrs_dict,
			n_term_min,
			n_term_max,
			c_term_min,
			c_term_max,
			output_wo_extension
	)

References if(), and range.

Referenced by generate_structures().

generate_all_junction_attach_permutations()

def enumerate_junctions.generate_all_junction_attach_permutations	(		design,
			dhrs_dict,
			n_term_junc_dict,
			c_term_junc_dict,
			options
	)

References if(), and range.

Referenced by generate_structures().

generate_all_terminal_pdb_permutations()

def enumerate_junctions.generate_all_terminal_pdb_permutations	(		design,
			terminal_pdb,
			dhrs_dict,
			options
	)

References if(), and range.

Referenced by generate_structures().

generate_dhrs_txt_file()

def enumerate_junctions.generate_dhrs_txt_file

(

dhr_location

)

References if(), int, basic::database.open(), and pyrosetta.distributed.io.pose_from_file.

generate_junctions_txt_file()

def enumerate_junctions.generate_junctions_txt_file	(		junction_location,
			options
	)

References if(), and basic::database.open().

generate_starting_round_structures()

def enumerate_junctions.generate_starting_round_structures	(		n_term_junc_dict,
			dhrs_dict,
			options
	)

References if(), pyrosetta.distributed.io.pose_from_file, and return.

generate_structures()

def enumerate_junctions.generate_structures	(		design,
			n_term_junc_dict,
			c_term_junc_dict,
			dhrs_dict,
			options,
			queue,
			terminal_pdb,
			output_wo_extension,
			recursive
	)

References generate_all_dhr_attach_permutations(), generate_all_junction_attach_permutations(), generate_all_terminal_pdb_permutations(), and if().

Referenced by generate_structures_wrapper().

generate_structures_wrapper()

def enumerate_junctions.generate_structures_wrapper	(		data,
			q
	)

References pyrosetta.tests.distributed.test_dask.format, generate_structures(), and print().

get_all_dhrs()

def enumerate_junctions.get_all_dhrs

(

dhr_run_location

)

References int, basic::database.open(), return, and ObjexxFCL.strip().

get_all_junctions()

def enumerate_junctions.get_all_junctions	(		junction_run_location,
			dhrs_dict
	)

References int, basic::database.open(), return, and ObjexxFCL.strip().

get_single_junction()

def enumerate_junctions.get_single_junction

(

junction_fn

)

References pyrosetta.distributed.io.pose_from_file, return, and binder.split().

get_terminal_pdb()

def enumerate_junctions.get_terminal_pdb	(		options,
			dhrs_dict
	)

References if(), pyrosetta.distributed.io.pose_from_file, and return.

listener()

def enumerate_junctions.listener	(		q,
			options
	)

References pyrosetta.tests.distributed.test_dask.format, if(), basic::database.open(), print(), and set().

Referenced by basic::mpi::MessageListenerFactory.get_listener().

Variable Documentation

bool

enumerate_junctions.bool

Referenced by DB_Builder.add_data(), bind_std_stl_function(), helpers.cache_array(), apps::pilot::frankdt.check_motifs(), utility::pointer::DeepCopyOP< T >.operator bool(), PyMOL-Rosetta-relay-client.PR_PyMOLServer.process_packet(), PyMOL-RosettaServer.PR_PyMOLServer.process_packet(), pyrosetta.PyMOLRosettaServer.PR_PyMOLServer.process_packet(), and numeric::interpolation::spline::PolycubicSpline< N >.train().

c_term_junc_dict

enumerate_junctions.c_term_junc_dict

current_machine

string enumerate_junctions.current_machine = "jojo"

default

enumerate_junctions.default

Referenced by aa2index(), numeric.access_Real_MathNTensor(), PhProtocol.apply(), utility::sql_database::session.begin_transaction(), apps::pilot::momeara::HBondConformation.build_acceptor_frame(), numeric::xyzMatrix< T >.col(), utility::sql_database::session.commit_transaction(), numeric.const_access_Real_MathNTensor(), utility::CSI_Sequence.CSI_Sequence(), ObjexxFCL.date(), numeric::interpolation::Histogram< X, Y >.derivative(), numeric::interpolation::Histogram< X, Y >.derivative_linear(), fetch_atom_names(), ElecDensMinPackMinReporter.find_flips(), utility::sql_database::session.force_commit_transaction(), ClosabilityScore.gap_upper_boundary(), numeric::RocCurve.generate_roc_curve(), utility.get_current_date(), get_D_name(), utility::sql_database::DatabaseSessionManager.get_db_session(), basic::database.get_db_session(), basic::citation_manager::Citation.get_formatted_citation(), basic::mpi::MessageListenerFactory.get_listener(), utility::xsd_util.get_module_type_as_it_appears_in_xsd(), numeric::interpolation::spline.get_PolycubicSpline_F(), numeric::interpolation::spline.get_PolycubicSpline_gradient(), numeric.get_Real_MathNTensor_dimension_size(), get_rsrpl(), utility::xsd_util.get_specific_module_name_as_it_appears_in_xsd(), numeric::interpolation.get_val(), numeric.hsv_to_rgb(), basic::database.insert_or_ignore(), numeric::RocCurve.insert_point(), numeric::interpolation::Histogram< X, Y >.interpolate(), numeric::interpolation::Histogram< X, Y >.interpolate_linear(), Kernel.k_function(), numeric::fourier.kf_factor(), numeric::fourier.kf_work(), basic::mpi.listener_tag_to_name(), main(), apps::pilot::momeara::HBondConformation.make_conformation(), max_atom_hbonds(), numeric::interpolation::Histogram< X, Y >.maximum(), numeric::interpolation::Histogram< X, Y >.minimum(), utility::sql_database.name_from_database_mode(), utility::sql_database.name_from_transaction_mode(), normalize_residue_sasa(), numeric::xyzMatrix< T >.operator()(), utility::options::OptionCollection.operator()(), utility::options::OptionCollection.operator[](), utility::json_spirit::Generator< Value_type, Ostream_type >.output(), basic::database.parse_database_connection(), pose_from_posedata(), basic::database::schema_generator::Index.print(), basic::database::schema_generator::Column.print(), basic::database::schema_generator::ForeignKey.print(), basic::database::schema_generator::DbText.print(), basic::database::schema_generator::DbTextKey.print(), basic::database::schema_generator::DbBigInt.print(), basic::database::schema_generator::DbDouble.print(), basic::database::schema_generator::DbReal.print(), basic::database::schema_generator::DbUUID.print(), print_energies(), numeric::linear_algebra.qzvec(), numeric::interpolation::Histogram< X, Y >.read_from_db(), EnvToolMover.representative_atom_name(), numeric::xyzMatrix< T >.row(), numeric::interpolation::Histogram< X, Y >.set_params(), InteractionGraphPerformanceBenchmark.setUp(), sicdock_thread_num(), utility.signal_handler(), storeposedata(), basic::database.table_exists(), basic::database::schema_generator::Schema.table_init_statements(), basic::database::schema_generator::Schema.table_schema_statements(), numeric::expression_parser.token_type_name(), write_score_types_to_database(), and basic::database::insert_statement_generator::InsertGenerator.write_to_database().

designs_rd1

def enumerate_junctions.designs_rd1 = generate_starting_round_structures(n_term_junc_dict,dhrs_dict,options)

designs_rd2

list enumerate_junctions.designs_rd2 = []

dhr_location

string enumerate_junctions.dhr_location = DHR_location_jojo

DHR_location_digs

string enumerate_junctions.DHR_location_digs = "/work/brunette/DBs/repeats/DHRs"

DHR_location_hyak

string enumerate_junctions.DHR_location_hyak = "/gscratch/baker/brunette/DBs/repeats/DHRs"

DHR_location_jojo

string enumerate_junctions.DHR_location_jojo = "/home/brunette/DBs/repeats/DHRs"

DHR_location_short

string enumerate_junctions.DHR_location_short = ""

dhr_run_location

string enumerate_junctions.dhr_run_location = DHR_location_jojo

dhrs_dict

def enumerate_junctions.dhrs_dict = get_all_dhrs(dhr_run_location)

False

enumerate_junctions.False

help

enumerate_junctions.help

Referenced by utility::options::OptionCollection.add_built_in_options(), and utility::options::OptionCollection.load().

int

enumerate_junctions.int

Referenced by pyrosetta.EnergyMethod.__call__(), TCDock.__dock_base__(), pyrosetta.distributed.cluster.io.IO._get_output_dir(), DB_Builder.add_data(), pseudoTrace.add_to_C(), ClusterCycDisulf.align_clusters(), align_poses(), alignhelix(), basic.angle_in_range(), annealTemperature(), FaSolReporter.apply(), CrystFFTDock.apply(), apply_transform(), numeric::AxisRotationSampler.AxisRotationSampler(), bind_std_functional_hash(), bind_std_stl_deque(), bind_std_stl_multiset(), bind_std_unordered_map(), bind_T07_class(), bind_T12_operator(), bind_T20_template_variadic(), bind_T32_call_guard(), bind_T70_options(), bind_T81_custom_trampoline_with_args(), utility::graph::Array0< T >.bounds_check(), helpers.cache_trajectory(), calc_rama_scores(), calc_scores(), calculate_hASA_by_type_and_attractiveE(), calculate_helical_tail_variance(), CAtrace.CAtrace(), center_pose_at_origin(), check_coords_match(), zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >.check_header(), numeric::geometry::hashing::xyzStripeHash.clash_not_resid(), ScoreFragmentSetMover.clash_score(), pyrosetta.toolbox.cleaning.cleanCRYS(), compare_gpu_result_against_cpu(), pointGroupHit.contains_symmop(), correct_dunbrack(), correct_rama(), DockFragmentsMover.cut_from_map(), ddg(), dedup(), densityTools(), HubDenovo.design(), CrystDesign.design_cycle(), numeric::interpolation::spline::PolycubicSpline< N >.dFdxi(), CrystFFTDock.do_convolution(), CrystDesign.do_reversion(), dock(), doit(), OutputManager.dump_pose(), TCDock.dump_top_hits(), utility::recent_history_queue.dynamic_memory_usage(), erraser_wrapper.erraser(), erraser_wrapper.erraser_single_res(), CL.errstr(), pointGroupHit.expand(), expand_all_and_check_if_forms_lattice(), numeric::interpolation::spline::PolycubicSpline< N >.F(), numeric.FArray_to_vector_of_xyzvectors(), fastpow2(), erraser_util.find_error_res(), bin_torsions.find_pivots(), demo.D030_Fold_tree.fold_tree(), detail.format_float(), TCDock.gather_hits(), generate_dhrs_txt_file(), generate_disulfide_conformations(), generate_from_fiber(), generate_from_point(), numeric::UniformRotationSampler.generateIcosahedralSamples(), get_all_dhrs(), get_all_junctions(), get_ang_samp(), kmeans_adaptive_kernel_density_bb_dependent_rotlib.get_bb_bin_index(), kmeans_bb_dependent_rotlib.get_bb_bin_index(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.get_bb_bin_index(), get_bps_seq(), get_bps_sub_dir(), get_change_in_distance(), CrystFFTDock.get_clash_score_exact(), get_distance_measure(), pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider.get_fragment_store(), get_hb_info(), mutant_modeler.MutantModeler.get_high_res_command_lines(), get_inflection_points(), get_interface_energies(), get_interface_score(), CrystFFTDock.get_interfaces_allatom(), DRRAFTER_util.get_ints(), get_max_interface(), get_nearest_loop_to_helix(), Spacegroup.get_nsubdivisions(), cal_vdw_radius_pool.get_pair_counts(), numeric::interpolation.get_patch(), get_point_groups(), get_pose_chains(), arls_impl.get_procs_per_case(), get_radius(), CrystFFTDock.get_radius_of_pose(), DRRAFTER_util.get_resnum_chain(), DRRAFTER_util.get_sequences(), apps::pilot::AlignChunkMover.get_superposition_transformation(), get_superposition_transformation(), Spacegroup.get_symmops(), get_tenA_neighbor_residues(), CrystDesign.greedy_revert_unsats(), harvest_motifs(), harvest_scores(), ConstraintConfig.hub_seq_sep(), numeric::geometry::hashing::MinimalClashHash.init(), numeric::geometry::hashing::xyzStripeHash.init(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.init(), interp_linear(), IsctFast.IsctFast(), isctfast(), TCDock.justone(), Kernel.k_function(), Kernel.kernel_precomputed(), erraser_util.load_pdb_coord_old(), bin_torsions.load_torsions_from_dat(), progress_bar.main(), dbscan_cluster_rotamer.main(), mp_ddG.main(), combine_ContactMaps.main(), DB_Builder.main(), best_ifaceE.main(), prune_atdiff_top5pct.main(), main(), dbscan_cluster_rotamer.main_old_kmeans(), make_fragments(), HubDenovo.make_start_pose(), demo.D040_Movemap.movemap(), pyrosetta.toolbox.mutants.mutate_residue(), demo.D090_Ala_scan.mutate_residue(), mutate_to_ala(), my_main(), utility.nmers_worker(), nucleobase_probe_score_test(), utility::options::OptionCollection.operator()(), utility::options::OptionCollection.operator[](), output_packstat(), output_packstat_pdb(), pyrosetta.toolbox.py_jobdistributor.output_scorefile(), ScoreFragmentSetMover.overlap_score(), dbscan_adaptive_kernel_density_bb_dependent_rotlib.parse_opt(), erraser_util.parse_option_chain_res_list(), erraser_util.parse_option_int_list(), erraser_util.parse_options(), DRRAFTER_util.parse_tag(), util.parse_tag(), kmeans_adaptive_kernel_density_bb_dependent_rotlib.pbc(), kmeans_bb_dependent_rotlib.pbc(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.pbc(), erraser_util.pdb_slice(), erraser_util.pdb_slice_into_chunks(), DRRAFTER_util.pdbslice(), erraser_util.phenix_release_tag(), erraser_util.phenix_rna_validate(), pick_normal_sampling(), subloop_histogram.pivots_from_line(), bin_torsions.plot_score_function(), job_manager.CommandRunner.poll(), pose2bin(), demo.D020_Pose_scoring.pose_scoring(), utility::libsvm::Svm_rosetta.predict(), utility::libsvm::Svm_rosetta.predict_probability(), Prepare(), 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(), readline(), refine_pose(), remove_drift(), numeric::UniformRotationSampler.remove_redundant(), removeConstraintsNearGap(), CrystFFTDock.resample_maps_and_get_self(), run(), TCDock.run(), DockFragmentsMover.run(), FragmentAssemblyMover.run(), ConsensusFragmentMover.run(), HubDenovo.run(), scan_energy(), scoreall(), set_chival(), setup_CA_constraints(), protocols::abinitio::JumpSpecificAbrelax.setup_jumps(), CrystFFTDock.setup_maps(), setup_mask(), numeric::VoxelGrid< T >.SetupGrid(), pointGroupHit.show(), kmeans_adaptive_kernel_density_bb_dependent_rotlib.show_bb_table(), kmeans_bb_dependent_rotlib.show_bb_table(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.show_bb_table(), sic_fast_x(), sicdock_thread_num(), sicfast(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), erraser_util.sliced2orig_merge_back(), slow_nbcount(), slow_nbget(), kic_runner.ParseIterations.smart_int(), detail.snprintf_float(), solve_one_class(), strip_termini(), HubDenovo.stupid_ddg(), svm_check_parameter(), svm_group_classes(), svm_load_model(), erraser_wrapper.SWA_rebuild_erraser(), utility.sys_sleep(), IsctFast.test(), test_deriv_pose(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti.test_smoke_multi_from_instance(), pyrosetta.distributed.cluster.converter_tasks.to_int(), pyrosetta.distributed.cluster.converter_tasks.to_str(), pointGroupHit.transform(), numeric::UniformRotationSampler.UniformRotationSampler(), up_jump_tree(), numeric.vector_of_xyzvectors_to_FArray(), numeric::statistics.w(), and CrystFFTDock.writeMRC().

junction_location

string enumerate_junctions.junction_location = Junction_location_jojo

Junction_location_digs

string enumerate_junctions.Junction_location_digs = "/work/brunette/DBs/repeats/junctions"

Junction_location_hyak

string enumerate_junctions.Junction_location_hyak = "/gscratch/baker/brunette/DBs/repeats/junctions"

Junction_location_jojo

string enumerate_junctions.Junction_location_jojo = "/home/brunette/DBs/building_components/DHR_junctions_all_filters_plus_L1"

Junction_location_short

string enumerate_junctions.Junction_location_short = ""

junction_run_location

string enumerate_junctions.junction_run_location = Junction_location_jojo

manager

enumerate_junctions.manager = mp.Manager()

Referenced by connect_test(), ligand_test(), main(), ui::task.network_access_manager(), and vlb_test().

n_term_junc_dict

enumerate_junctions.n_term_junc_dict

None

enumerate_junctions.None

options

enumerate_junctions.options = parser.parse_args()

parser

enumerate_junctions.parser = ArgumentParser( description="" )

Referenced by FixbbJobQueen.append_common_tag_subelements(), FixbbJobQueen.append_job_tag_subelements(), protocols::jd2::RECONMPIJobDistributor.go(), main(), and FixbbJobQueen.parse_sfxns_and_taskops().

pool

enumerate_junctions.pool = mp.Pool( processes = options.n_core )

Referenced by main().

q

enumerate_junctions.q = manager.Queue()

Referenced by basic::sampling::orientations::QuatSet.Add(), ComputeSAXSSpectrum.apply(), numeric::Quaternion< T >.apply(), apply_all_frags(), assign_tag(), clockwise(), distance_from_line2D(), dock(), numeric::Quaternion< T >.dot(), numeric::Quaternion< T >.dot_product(), enclosing_angles(), numeric::coordinate_fitting::CoordinateArray_RMSD_FlatLookup< Real >.entry_distance(), basic::sampling::orientations::Quaternion.euler(), files_for_openMM_test(), generate_from_point(), get_angles(), get_distances(), get_hbond_rotation_samples(), graft_in_positions(), numeric.hsv_to_rgb(), inside_polygon(), intersect(), numeric::fourier.kf_bfly_generic(), numeric::statistics.kl_divergence(), kono_sarai_stats(), kono_sarai_zscore(), numeric::Quaternion< T >.left_multiply_by(), numeric::Quaternion< T >.left_multiply_by_inverse_of(), main(), mg_hires_pdbstats_from_pose(), mg_modeler_test(), on_segment(), numeric.operator<<(), numeric::Quaternion< T >.operator=(), numeric.operator>>(), output_general_base_pair_steps(), BruteFunGroupTK.place_c(), KinFunGroupTK.place_c(), points_in_triangle(), pose2frags(), numeric::coordinate_fitting::CoordinateArray_RMSD_FlatLookup< Real >.prepare_for_query(), basic::sampling::orientations::QuaternionGrid.QuaternionGrid(), numeric::linear_algebra.qzvec(), numeric::random.random_rotation(), numeric::Quaternion< T >.right_multiply_by(), numeric::Quaternion< T >.right_multiply_by_inverse_of(), run(), run_hd(), run_hh(), sigmoid_train(), svm_train(), numeric::Quaternion< T >.swap(), ui::task::Task.task_data(), TEST(), basic::sampling::orientations::Quaternion.Times(), and to_left().

str

enumerate_junctions.str

terminal_pdb

def enumerate_junctions.terminal_pdb = None

tmp_data

enumerate_junctions.tmp_data = Pool_data(tmp_design,n_term_junc_dict,c_term_junc_dict,dhrs_dict,options,terminal_pdb,True,True)

True

enumerate_junctions.True

type

enumerate_junctions.type

watcher

enumerate_junctions.watcher = pool.apply_async(listener, (q,options,) )