pyrosetta.io Namespace Reference

Namespaces
	silent_file_map

Functions
def	pose_from_file (*args, **kwargs)
def	pose_from_pdb (*args, **kwargs)
def	pose_from_pdbstring (*args, **kwargs)
def	pose_from_sequence (seq, res_type="fa_standard", auto_termini=True)
def	poses_from_files (objs, *args, **kwargs)
def	poses_from_sequences (objs, *args, **kwargs)
def	poses_from_silent (silent_filename)
def	poses_from_multimodel_pdb (filename, *args, **kwargs)
def	poses_to_silent (poses, output_filename)
def	to_pdbstring (pose)
def	dump_pdb (pose, output_filename)
def	dump_multimodel_pdb (poses, output_filename)
def	dump_file (pose, output_filename)
def	dump_scored_pdb (pose, output_filename, scorefxn)

Variables
	create_score_function = rosetta.core.scoring.ScoreFunctionFactory.create_score_function

Function Documentation

dump_file()

def pyrosetta.io.dump_file	(		pose,
			output_filename
	)

Referenced by pyrosetta.distributed.io.dump_file(), and pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_file_io().

dump_multimodel_pdb()

def pyrosetta.io.dump_multimodel_pdb	(		poses,
			output_filename
	)

Dump a multimodel PDB file from a `list`, `tuple`, or `set` of `Pose` objects,
and an output filename.

Inputs:
poses: `Pose` or iterable of `Pose` objects. This function automatically detects which one.
output_filename: The desired name of the output PDB file.

Example:
dump_multimodel_pdb(poses, "designs.pdb")

@klimaj

Referenced by pyrosetta.distributed.io.dump_multimodel_pdb(), and pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_multimodel_pdb_io().

dump_pdb()

def pyrosetta.io.dump_pdb	(		pose,
			output_filename
	)

Dump a PDB file from a `Pose` object and output filename.
If the output filename ends with ".pdb.bz2" or ".bz2", then dump a bz2-encoded PDB file.
If the output filename ends with ".pdb.gz" or ".gz", then dump a gzip-encoded PDB file.
If the output filename ends with ".pdb.xz" or ".xz", then dump a xz-encoded PDB file.

@klimaj

References basic::database.open(), and pyrosetta.io.to_pdbstring().

Referenced by pyrosetta.distributed.io.dump_pdb(), pyrosetta.distributed.io.dump_scored_pdb(), and pyrosetta.io.dump_scored_pdb().

dump_scored_pdb()

def pyrosetta.io.dump_scored_pdb	(		pose,
			output_filename,
			scorefxn
	)

Dump a scored PDB file from a `Pose` object, output filename, and score function.
If the output filename ends with ".pdb.bz2" or ".bz2", then dump a bz2-encoded PDB file.
If the output filename ends with ".pdb.gz" or ".gz", then dump a gzip-encoded PDB file.
If the output filename ends with ".pdb.xz" or ".xz", then dump a xz-encoded PDB file.
Otherwise, implement the `Pose.dump_scored_pdb` method.

@klimaj

References pyrosetta.io.dump_pdb(), and oop_conformations.scorefxn.

Referenced by pyrosetta.distributed.io.dump_scored_pdb(), and pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_file_io().

pose_from_file()

def pyrosetta.io.pose_from_file	(	*	args,
		**	kwargs
	)

Uses the input filename from `*args` or `**kwargs` and returns a `Pose` object from it,
deserializing:
    - bz2-encoded files ending with file extensions: (".pdb.bz2", ".bz2")
    - gzip-encoded files ending with file extensions: (".pdb.gz", ".gz")
    - xz-encoded files ending with file extensions: (".pdb.xz", ".xz")
Otherwise, implements `pyrosetta.rosetta.core.import_pose.pose_from_file(*args, **kwargs))`.

@klimaj

References setup.FileNotFoundError, filter, basic::database.open(), and pyrosetta.io.pose_from_pdbstring().

Referenced by pyrosetta.distributed.io.pose_from_file(), pyrosetta.io.pose_from_pdb(), pyrosetta.io.poses_from_files(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_cif_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_file_io(), and pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_mmtf_io().

pose_from_pdb()

def pyrosetta.io.pose_from_pdb	(	*	args,
		**	kwargs
	)

References pyrosetta.io.pose_from_file().

pose_from_pdbstring()

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

Instantiate a `Pose` object from a PDB string. If a `Pose` object is provided,
it is passed to `pyrosetta.rosetta.core.import_pose.pose_from_pdbstring`,
otherwise a new `Pose` object is instantiated.

@klimaj

References ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, and range.

Referenced by pyrosetta.io.pose_from_file(), pyrosetta.distributed.io.pose_from_pdbstring(), pyrosetta.io.poses_from_multimodel_pdb(), and test.T010_LoadPDB.LoadPDBTest.test_pdbstring_io().

pose_from_sequence()

def pyrosetta.io.pose_from_sequence	(		seq,
			res_type = "fa_standard",
			auto_termini = True
	)

Returns a Pose object generated from a single-letter sequence of amino acid
residues in <seq> using the <res_type> ResidueType and creates N- and C-
termini if <auto_termini> is set to True.

Unlike make_pose_from_sequence(), this method generates a default PDBInfo
and sets all torsion angles to 180 degrees.

Example:
    pose = pose_from_sequence("THANKSEVAN")
See also:
    Pose
    make_pose_from_sequence()
    pose_from_file()
    pose_from_rcsb()

References range.

Referenced by pyrosetta.io.poses_from_sequences(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_cif_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_file_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_mmtf_io(), pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent.test_poses_to_silent(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTest.test_smoke(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti.test_smoke_multi(), and pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti.test_smoke_multi_from_instance().

poses_from_files()

def pyrosetta.io.poses_from_files	(		objs,
		*	args,
		**	kwargs
	)

Returns an iterator object which is composed of Pose objects from input files.

Example:
import glob
poses = pyrosetta.io.poses_from_files(glob.glob("path/to/pdbs/*.pdb"))

References pyrosetta.io.pose_from_file().

poses_from_multimodel_pdb()

def pyrosetta.io.poses_from_multimodel_pdb	(		filename,
		*	args,
		**	kwargs
	)

Returns an Iterator object which is composed of Pose objects from an input
multimodel PDB file. Poses are generated in the order in which they appear in
the input multimodel PDB file. Any models without lines are skipped with a warning.
Additional input `*args` and `**kwargs` are passed to `pose_from_pdbstring`.

Example:
poses = pyrosetta.io.poses_from_multimodel_pdb(filename)
for pose in poses:
    name = pose.pdb_info().name()

@klimaj

References join(), basic::database.open(), and pyrosetta.io.pose_from_pdbstring().

Referenced by pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_multimodel_pdb_io().

poses_from_sequences()

def pyrosetta.io.poses_from_sequences	(		objs,
		*	args,
		**	kwargs
	)

Returns an iterator object which is composed of Pose objects with input sequences.

Example:
poses = pyrosetta.io.poses_from_sequences(["TEST", "TESTING [ATP]", "ACDEFGHIKLMNPQRSTVWY"])

References pyrosetta.io.pose_from_sequence().

Referenced by pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_multimodel_pdb_io(), and pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_pose_io().

poses_from_silent()

def pyrosetta.io.poses_from_silent

(

silent_filename

)

Returns an Iterator object which is composed of Pose objects from a silent file.

@atom-moyer

Referenced by pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent.test_poses_to_silent().

poses_to_silent()

def pyrosetta.io.poses_to_silent	(		poses,
			output_filename
	)

Takes a Pose or list of poses and outputs them as a binary silent file.
This method requires a Pose object.
If you are using a PackedPose, use pyrosetta.distributed.io.to_silent()

Inputs:
poses: Pose or list of poses. This function automatically detects which one.
output_filename: The desired name of the output silent file.

Example:
poses_to_silent(poses, "mydesigns.silent")

The decoy name written to 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.
Example:
pose.pdb_info().name("my_tag.pdb")

@srgerb

References basic::options::OptionKeys::ddg.output_silent.

Referenced by pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent.test_poses_to_silent(), and pyrosetta.distributed.io.to_silent().

to_pdbstring()

def pyrosetta.io.to_pdbstring

(

pose

)

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

Referenced by pyrosetta.io.dump_pdb(), test.T010_LoadPDB.LoadPDBTest.test_pdbstring_io(), and pyrosetta.distributed.io.to_pdbstring().

Variable Documentation

create_score_function

pyrosetta.io.create_score_function = rosetta.core.scoring.ScoreFunctionFactory.create_score_function

Referenced by zinc_helix_cap.apply(), DougsDockDesignMinimizeMagicMover.apply(), PeptiodMovieMover.apply(), PeptoidRotamerRecoverer.apply(), CartRefineWrapperMover.apply(), CenRelaxMover.apply(), abbinding.apply(), PhDocking.apply(), B3AADihedralGrabber.apply(), LDConverterMover.apply(), SampleTiltProtocol.apply(), FindOptimalHydrophobicThk.apply(), MinCenrotMover.apply(), PeptoidDesignMover.apply(), HDdesignMover.apply(), MotifDock.apply(), MPFindInterfaceTestMover.apply(), MembraneMinMover.apply(), MembraneViewMover.apply(), MembraneDockingxMover.apply(), MembraneRelaxMover.apply(), MembraneSampleMover.apply(), MPInterfaceStatistics.apply(), MPDomainAssembly.apply(), complex_interface_optimize.apply(), run_score_patchdock_hotspot.apply(), run_score_hotspot.apply(), MinPackMin.backbone_minimization(), base_pair_to_base_pair_test(), benzene_pair_score_test(), block_stack_test(), bp_score_calibrate(), build_asn_motifs(), build_full_model_test(), build_next_nucleotide_test(), bzip_test(), calc_B_values(), calc_rmsf_and_avrg(), calculate_sasa(), capri_t033_trim_dock_test(), CaToAllAtom.CaToAllAtom(), cen_fold(), CenRotRBRelaxMover.CenRotRBRelaxMover(), CenRotRelaxMover.CenRotRelaxMover(), centroid_scores_destroys_pose(), check_interface_symmetry(), check_structures(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), compare_dna_energies(), compute_chem_shift_RMSD(), count_contacts(), create_bp_jump_database_test(), create_cs_rosetta_rna_scorefxn(), create_score_function_from_weights_and_refEs(), create_scorefxn(), delta_chi_correction_test(), derive(), design_test(), dinucleotide_test(), dna_dr_loop_test(), dna_specificity_test(), doit(), double_helix_test(), endo_test(), find_close_motifs(), Foldptn.Foldptn(), ga_main(), generate_combined_model(), protocols::abinitio::JumpSpecificAbrelax.generate_scorefxn(), get_rmsd(), get_stepwise_score_function(), graphics_main(), HbondZincBackbone.has_backbone_hbond(), helix_ST(), hessian_estimate(), HubDenovo.HubDenovo(), juke_sam_pos(), juke_sam_test(), lariat_modeling(), mp_ddG.main(), main(), make_sf(), MC_run(), methane_pair_score_test(), minimize_and_score(), minimize_test(), minimize_to_close(), minimize_with_constraints(), my_main(), nucleobase_probe_score_test(), one_chain_MC_sampling(), one_chain_ST_MC(), OPT_KEY(), pack_phosphates(), MinPackMin.pack_sidechains(), pdb_scoring(), pep_rmsd_analysis(), demo.D020_Pose_scoring.pose_scoring(), predict_AE(), process_for_motifs(), process_the_pose(), quick_score_test(), read_silent_input_as_library(), rebuild_centroid_test(), rebuild_test(), relax_cenrot_pose(), HbondZinc.repack(), HbondZincBackbone.repack(), repack_cluster(), repack_step(), repack_test(), resample_full_model_test(), rescore_test(), rna_build_helix_test(), rna_close_chainbreaks_test(), rna_fullatom_minimize_silent_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_motif_test(), rna_protein_rb_test(), rna_torsion_check_test(), rotamerize(), rotamerize_rna_test(), run(), run_hh(), run_mc(), myspace::Scheduler.run_md(), run_parallel_docking(), run_pep_prep(), RunPepSpec(), demo.D110_DNA_interface.sample_dna_interface(), demo.D100_Docking.sample_docking(), demo.D120_Ligand_interface.sample_ligand_interface(), sample_rama_test(), demo.D080_Loop_modeling.sample_single_loop_modeling(), sample_state_to_state(), sample_trp_test(), myspace::Scheduler.Scheduler(), score_and_minimize(), score_rnp(), screen_phosphates(), TestQuickRelaxMover.set_defaults(), ZincMinimize.set_scorefunction(), abbinding.setup_RepulsiveRampMover(), setup_score_function(), zinc1_homodimer_design.setup_scorefunctions(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_scorefxns(), abbinding.setup_task_and_repack(), PhDocking.setup_task_and_repack(), soft_pack(), stepwise_lores_test(), stepwise_template_test(), superimpose_A_to_all(), swa_rna_sample(), SymmAbRelaxTest(), SymmDataTest(), SymmSilentFileTest(), test_membrane_scoring_highres(), test_membrane_scoring_lowres(), test_NMmin(), test_NMrelaxer(), test_scorefxn_io(), test_talaris(), tf_specificity_test(), thermal_sampler(), two_base_pairs_test(), viewer_main(), zf_test(), and zif268_test().