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Rosetta
2021.07
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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 |
IO routines operating on PackedPose representations.
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().
list pyrosetta.distributed.io.__all__ |
tuple pyrosetta.distributed.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 |
Referenced by demo.D030_Fold_tree.fold_tree(), and demo.D060_Folding.sample_folding().
tuple pyrosetta.distributed.io.poses_from_silent |