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Functions | Variables
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)
def pyrosetta.distributed.io.to_pdbstring (   inp)
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:
1 = [
2  "pose_from_file",
3  "pose_from_sequence",
4  "poses_from_silent",
5  "pose_from_pdbstring",
6  "to_silent",
7  "to_pdbstring",
8  "to_output_record"
9 ]
tuple pyrosetta.distributed.io.pose_from_file
Initial value:
2  pyrosetta.io.pose_from_file))
def requires_init
Definition: __init__.py:64
def pack_result
Definition: core.py:73

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(), 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(), LigandDockBenchmark.setUp(), DesignBenchmark.setUp(), SmallMoverBenchmark.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(), and zinc2_homodimer_setup.zinc2_homodimer_setup().

tuple pyrosetta.distributed.io.pose_from_sequence
Initial value:
2  pyrosetta.io.pose_from_sequence))
def requires_init
Definition: __init__.py:64
def pack_result
Definition: core.py:73

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

tuple pyrosetta.distributed.io.poses_from_silent
Initial value:
2  pyrosetta.io.poses_from_silent))
def requires_init
Definition: __init__.py:64
def pack_result
Definition: core.py:73