pyrosetta.distributed.io Namespace Reference

Functions
def	pose_from_pdbstring (*args, **kwargs)
def	to_silent (inp, output_filename)
def	to_pdbstring (inp)
def	to_output_record (inp)

Variables
list	__all__
	pose_from_file
	pose_from_sequence
	poses_from_silent

Detailed Description

IO routines operating on PackedPose representations.

Function Documentation

pose_from_pdbstring()

def pyrosetta.distributed.io.pose_from_pdbstring	(	*	args,
		**	kwargs
	)

Referenced by ui::task.create_viewer_for_file(), main(), ui::widgets::PoseEditor.on_action_open_pose_triggered(), and PDB_IOBenchmark.run().

to_output_record()

def pyrosetta.distributed.io.to_output_record

(

inp

)

Convert to an "archive" output record with scores, pdb string and packed string.

References pyrosetta.distributed.packed_pose.register_container_traversal(), pyrosetta.distributed.packed_pose.core.to_dict(), pyrosetta.distributed.cluster.converter_tasks.to_packed(), pyrosetta.distributed.io.to_pdbstring(), and utility::Version.version().

to_pdbstring()

def pyrosetta.distributed.io.to_pdbstring

(

inp

)

Convert to pdb-formatted string with score and energy data.

References basic::options::OptionKeys::matdes::dock.dump_pdb, pyrosetta.distributed.packed_pose.register_container_traversal(), pyrosetta.distributed.cluster.converter_tasks.to_packed(), and pyrosetta.distributed.packed_pose.core.to_pose().

Referenced by pyrosetta.distributed.viewer.core.init(), and pyrosetta.distributed.io.to_output_record().

to_silent()

def pyrosetta.distributed.io.to_silent	(		inp,
			output_filename
	)

Takes a Pose, PackedPose, or a list and outputs them as a silent file.
This currently only outputs to a binary silent file.

Inputs:
poses: Pose object, PackedPose object or list of either.
output_filename: The desired name of the output silent file.

Example:
pyrosetta.distributed.io.to_silent(poses, "mydesigns.silent")

The decoy name in your silent file is take from pose.pdb_info().name()
To set a different decoy name, change it in your pose before calling this function.
To change the name, you must have a Pose object, not a PackedPose
Example:
pose = pyrosetta.distributed.packed_pose.to_pose(packed_pose)
pose.pdb_info().name("my_tag")

@srgerb

References pyrosetta.io.poses_to_silent(), and pyrosetta.distributed.packed_pose.core.to_pose().

Variable Documentation

__all__

list pyrosetta.distributed.io.__all__

private

Initial value:

=  [
    "pose_from_file",
    "pose_from_sequence",
    "poses_from_silent",
    "pose_from_pdbstring",
    "to_silent",
    "to_pdbstring",
    "to_output_record"
]

pose_from_file

pyrosetta.distributed.io.pose_from_file

Initial value:

=  requires_init(pack_result(
    pyrosetta.io.pose_from_file))

Referenced by align_pdbs(), analyze_base_pair_test(), analyze_interface_test(), anglestats_local(), APDBCMover.APDBCMover(), protocols::abinitio::ApplicationContext.ApplicationContext(), zinc1_homodimer_setup.apply(), ConstraintMinimizer.apply(), InverseRotlibDumpMover.apply(), abbinding.apply(), LoopHash_Analyze.apply(), InterfaceStrandFinderMover.apply(), HolesTrainingDataMover.apply(), CovalentPeptidomimeticCreator.apply(), MinTestMover.apply(), HotspotPlacementMover.apply(), LoopHashRelax_Sampler.apply(), MinPackMinMover.apply(), RosettaHolesMover.apply(), ExposedStrandMover.apply(), HDdesignMover.apply(), ZincSiteEvaluator.apply(), MPFindInterfaceTestMover.apply(), CrystDesign.apply(), MPDomainAssembly.apply(), compute_Irmsd.apply(), atom_tree_torsion_test(), backrub_min_test(), benzene_pair_score_test(), bk_test(), bk_test2(), block_stack_test(), build_asn_motifs(), build_next_nucleotide_test(), build_template(), buns_stats(), byres_analysis(), bzip_test(), calc_B_values(), calc_rms_test(), calc_rmsd_test(), calc_rmsf_and_avrg(), PhDocking.calc_unbound_score(), CalcCdrRms.CalcCdrRms(), calculate_distances(), calculate_hASA_by_type_and_attractiveE(), calculate_hASA_by_type_and_exposure(), calculate_hASA_by_type_and_nbcount(), calculate_hydrophobic_accessible_surface_area(), calculate_percent_hydrophobic_distribution(), calculate_percent_hydrophobic_stats(), calculate_sasa(), calculate_total_hASA_within_distance_avg_values(), calculate_total_hASA_within_distance_avgresiduevalues_allnbs_conditionalonnumnbs(), calculate_total_hASA_within_distance_exact_hASA_values(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs_exposedornot_conditionalonnumnbs(), calculate_total_hASA_within_distance_miniSASAvalues_allnbs_exposedornot_conditionalonnumnbs(), capri_t033_centroid_trim_dock_test(), capri_t033_loop_test(), capri_t033_trim_dock_test(), CaToAllAtom.CaToAllAtom(), ccd_test(), cendnapose_from_file(), cenpose_from_file(), centroid_rescore_test(), check_structures(), chi_stats_test(), pyrosetta.toolbox.cleaning.cleanCRYS(), coarse_close_loop_test(), coarse_frag_test(), coarse_rna_denovo_test(), coarse_to_full_test(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), combine_search(), compare_dna_energies(), compare_energies(), RelaxJobQueen.complete_larval_job_maturation(), connect_test(), convert_to_coarse_test(), convert_to_native_test(), create_and_score_fragments(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_rna_benchmark_test(), create_rna_vall_torsions_test(), create_starting_template(), create_theozyme_pdb(), cs_rosetta_rna_pdb(), cst_relax_test(), cst_test(), delete_test(), DeleteSegments.DeleteSegments(), densityTools(), design_test(), devel_main(), distribute_jobs(), diversify_sam_loop_test(), dna_chain_check(), dna_coupled_rotamer_design_test(), dna_deriv_test(), dna_deriv_test_old(), dna_design_test(), dna_dr_test(), dna_geometry(), dna_io_test(), dna_motif_matcher(), dna_nbr_radii_test(), dna_specificity_test(), dna_stats(), do_refinement(), do_search(), doit(), doit_refine(), DomainAssemblerNDocker.DomainAssemblerNDocker(), dostuff(), dump_dna_kinemage(), dump_hbonds(), easy_loop_model_test(), easy_target_test(), endo_test(), env_sugar_test(), erraser_monte_carlo(), fa_scorefxn_test(), fere_torsions(), figure_out_icoord_test(), files_for_openMM_test(), fillPoseAndDataList(), find_close_motifs(), find_dna_rotamers(), find_hppatches_distance(), find_hppatches_nb_graph(), Foldptn.Foldptn(), ga_main(), gather_ss_pct(), general_initialize(), enumerate_junctions.generate_dhrs_txt_file(), demo.D050_Packer_task.generate_resfile_from_pdb(), pyrosetta.toolbox.generate_resfile.generate_resfile_from_pdb(), enumerate_junctions.generate_starting_round_structures(), get_centered_pose(), get_info_test(), get_pose_and_numbering(), get_pose_by_id(), get_pose_energy_breakdown(), get_pts(), enumerate_junctions.get_single_junction(), enumerate_junctions.get_terminal_pdb(), go(), gpu_refold_test(), gpu_score_test(), HbondZinc.graft_match(), HbondZincBackbone.graft_match(), graphics_main(), GunnTest.GunnTest(), hbond_stats(), HECTMover.HECTMover(), hermann_phase_two(), hermann_phase_two_minimize(), HubDenovo.HubDenovo(), import_and_dump_pdb(), TestQuickRelaxMover.init_from_cmd(), UBQ_E2Mover.init_on_new_input(), UBQ_GTPase_disulfide_Mover.init_on_new_input(), initialize_from_pdb(), initialize_native_pose(), interface_repack_test(), intra_dna_stats(), juke_sam_test(), apps::pilot::KicSandbox.KicSandbox(), kono_sarai_stats(), kono_sarai_zscore(), lariat_modeling(), ligand_dock_main_jd1(), ligand_test(), ligrot_test(), lk_ball_wtd_deriv_test(), load_pose(), LocalRmsd.LocalRmsd(), loop_closure_test(), LoopBuild_main(), luxr_setup(), luxr_test(), mp_ddG.main(), main(), apps::pilot::frankdt.main(), make_helix(), make_pose(), manual_refine(), match_main(), measure_sequence_recovery(), methane_pair_score_test(), mg_modeler_test(), mg_pdbstats_test(), minimize_pdb(), minimize_test(), minimizer_test(), mismatch_test(), mm_pack_test(), protocols::antibody.model_cdrs(), modeler_closure_test(), morph_pdbs_test(), motif_dna_packer_design(), motif_scan(), MSA_design_main(), multiple_variant_type_test(), mutate_residues_wrapper(), my_main(), MyScoreMover.MyScoreMover(), not1_loop_test(), not1_test(), not_main(), nucleobase_probe_score_test(), o2prime_packer(), old_simple_conformation_test(), output_minipose_coords_test(), pack_rotamers_test(), ConstraintConfig.parse_config_file(), parse_pathway_test(), pdb_little_motif_test(), pdb_scoring(), pdb_to_silent_file(), pdb_to_silent_file_simple(), pdbstats_test(), pep_phipsi_analysis(), pep_rmsd_analysis(), phosphate_stats(), picking_test(), polar_pdbstats_test(), InterfaceDDGBindJobInputter.pose_from_job(), pyrosetta.toolbox.load_ligand.pose_from_params(), pyrosetta.io.pose_from_pdb(), pyrosetta.toolbox.load_ligand.pose_from_pubchem(), pyrosetta.toolbox.rcsb.pose_from_rcsb(), poses_from_cmd_line(), poses_from_cmd_line_noPDBtag(), pyrosetta.io.poses_from_files(), posewrap_from_command_line(), predict_chem_map_test(), Prepare(), print_all_torsions_test(), print_hbonds_test(), print_internal_coord_test(), print_secstruct_test(), process_file_list(), processChildren(), processChildrenIntensification(), proclose_test(), protocols_main(), pymol_struct_type_test(), quick_score_test(), rb_entropy_test(), rb_test(), RBSegmentRelax_test(), read_ddg_file(), read_native_pose(), read_native_sequence_for_entity_elements(), read_pdbs(), read_pose(), read_template_structures(), apps::pilot::SampleSecondaryStructureAlignmentMover.read_template_structures(), read_write(), readPoseAndData_PDB(), real_test_GA(), rebuild_centroid_test(), rebuild_test(), relax_test(), repack_minimize_test(), repack_test(), rescore_test(), results_to_pdb(), rhiju_pdbstats(), rna_assemble_all_combinations_test(), rna_backbone_rebuild_test(), rna_chain_closure_test(), rna_close_chainbreaks_test(), rna_design_gap_test(), rna_design_test(), rna_fullatom_minimize_silent_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_idealize_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_o2prime_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), rna_stats_test(), rna_thread_test(), rotamer_trials_test(), RotamerAnalysis(), rotamerize_rna_test(), MPI_Refinement_Launcher.run(), MPI_LoopHash_Launcher.run(), run(), DockFragmentsMover.run(), run_3bpy(), run_aio(), run_diiron_glu(), run_hd(), run_hh(), run_m8(), run_parallel_docking(), run_pep_prep(), run_sandbox(), run_sf4h(), run_test(), run_tests(), run_tyr_his(), run_zn2his(), RunPepSpec(), demo.D110_DNA_interface.sample_dna_interface(), demo.D100_Docking.sample_docking(), demo.D120_Ligand_interface.sample_ligand_interface(), sample_rama_test(), demo.D070_Refinement.sample_refinement(), demo.D080_Loop_modeling.sample_single_loop_modeling(), sample_state_to_state(), sample_trp_test(), sample_trp_tyr_test(), SamplingManager.SamplingManager(), sasa_separation(), sasa_test(), demo.D090_Ala_scan.scanning(), scheme_score(), score_folded_residues(), score_pdb(), separation(), sequence_tolerance_main(), set_basic_dock_options(), set_fullatom_flag_test(), set_ideal_geometry(), DockGlycansProtocol.set_ref_pose_from_filename(), set_stub_transform_test(), set_up_pose(), protocols::abinitio::JumpSpecificAbrelax.setup(), SamplingManager.setup(), protocols::abinitio::Application.setup(), ThisApplication.setup(), DesignBenchmark.setUp(), DockingBenchmark< dock, TScale >.setUp(), FastRelaxPerformanceBenchmark.setUp(), InteractionGraphPerformanceBenchmark.setUp(), LigandDockBenchmark.setUp(), MinimizerBenchmark< sft, TScale >.setUp(), ScoreBenchmark.setUp(), ScoreEachBenchmark.setUp(), ShearMoverBenchmark.setUp(), SmallMoverBenchmark.setUp(), DomainAssemblerNDocker.setup_cen_domains(), setup_coord_csts(), protocols::abinitio::JumpSpecificAbrelax.setup_fold(), CalcIrms.setup_native(), TryScoreFilter.setup_pose(), setup_pose_setup_class(), setup_sam_constraints_for_t033(), setup_segment_insert(), sicdock_thread_num(), simple_centroid_test(), simple_copy_test(), simple_dna_test(), simple_frag_test(), simple_hbond_test(), simple_opte_test(), simple_relax(), simple_rotamer_recovery(), simple_rotamer_test(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), small_min_test(), spinner_test(), ss_ds_ts_assign_test(), ss_test(), stepwise_template_test(), sugar_geometry_RNA_test(), SymmAbRelaxTest(), SymmDataTest(), SymmSilentFileTest(), T400_Refinement(), tar_motif_test(), test(), test_cofactor(), test_dunbrack_io(), test_function(), test_gb(), test_gradient(), test_kc(), test_kc2(), test_rama(), test_replicate_xform(), test_scorefxn_io(), test_suck_res(), tf_specificity_test(), thread_fxn(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), viewer_main(), vlb_test(), water_test(), water_test_fixed_O(), zf_relax_test(), zf_test(), zif268_test(), and zinc2_homodimer_setup.zinc2_homodimer_setup().

pose_from_sequence

pyrosetta.distributed.io.pose_from_sequence

Initial value:

=  requires_init(pack_result(
    pyrosetta.io.pose_from_sequence))

Referenced by demo.D030_Fold_tree.fold_tree(), and demo.D060_Folding.sample_folding().

poses_from_silent

pyrosetta.distributed.io.poses_from_silent

Initial value:

=  requires_init(pack_result(
    pyrosetta.io.poses_from_silent))