pyrosetta.distributed.io Namespace Reference

Functions
def	pose_from_pdbstring
def	to_silent
def	to_pdbstring
def	to_output_record

Variables
list	__all__
tuple	pose_from_file
tuple	pose_from_sequence
tuple	poses_from_silent

Detailed Description

IO routines operating on PackedPose representations.

Function Documentation

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

Referenced by main(), and PDB_IOBenchmark.run().

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(), and pyrosetta.distributed.io.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().

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

list pyrosetta.distributed.io.__all__

Initial value:

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

tuple 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(), APDBCMover.APDBCMover(), zinc1_homodimer_setup.apply(), ExposedStrandMover.apply(), HDdesignMover.apply(), MPDomainAssembly.apply(), calc_rms_test(), calc_rmsf_and_avrg(), calculate_sasa(), CaToAllAtom.CaToAllAtom(), pyrosetta.toolbox.cleaning.cleanCRYS(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), create_theozyme_pdb(), cs_rosetta_rna_pdb(), densityTools(), find_close_motifs(), pyrosetta.toolbox.generate_resfile.generate_resfile_from_pdb(), demo.D050_Packer_task.generate_resfile_from_pdb(), get_pose_and_numbering(), import_and_dump_pdb(), UBQ_GTPase_disulfide_Mover.init_on_new_input(), UBQ_E2Mover.init_on_new_input(), initialize_native_pose(), mp_ddG.main(), main(), apps::pilot::frankdt.main(), match_main(), mg_modeler_test(), minimize_test(), mutate_residues_wrapper(), my_main(), nucleobase_probe_score_test(), o2prime_packer(), pdb_to_silent_file(), pep_phipsi_analysis(), pep_rmsd_analysis(), 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(), pyrosetta.io.poses_from_files(), predict_chem_map_test(), Prepare(), quick_score_test(), read_native_sequence_for_entity_elements(), read_pose(), repack_test(), rhiju_pdbstats(), rna_thread_test(), run(), DockFragmentsMover.run(), run_pep_prep(), RunPepSpec(), demo.D110_DNA_interface.sample_dna_interface(), demo.D100_Docking.sample_docking(), demo.D120_Ligand_interface.sample_ligand_interface(), demo.D070_Refinement.sample_refinement(), demo.D080_Loop_modeling.sample_single_loop_modeling(), demo.D090_Ala_scan.scanning(), sequence_tolerance_main(), DockGlycansProtocol.set_ref_pose_from_filename(), ScoreBenchmark.setUp(), SmallMoverBenchmark.setUp(), DesignBenchmark.setUp(), LigandDockBenchmark.setUp(), ShearMoverBenchmark.setUp(), DockingBenchmark< dock, TScale >.setUp(), MinimizerBenchmark< sft, TScale >.setUp(), FastRelaxPerformanceBenchmark.setUp(), ScoreEachBenchmark.setUp(), InteractionGraphPerformanceBenchmark.setUp(), LigandDockScriptBenchmark.setUp(), setup_segment_insert(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), ss_ds_ts_assign_test(), test_cofactor(), and zinc2_homodimer_setup.zinc2_homodimer_setup().

tuple 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().

tuple pyrosetta.distributed.io.poses_from_silent

Initial value:

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