pyrosetta.distributed.packed_pose.core.PackedPose Class Reference

Public Member Functions
def	__init__ (self, pose_or_pack)
def	pose (self)
def	update_scores (self, *score_dicts, **score_kwargs)
def	clone (self)
def	empty (self)

Public Attributes
	pickled_pose
	scores

Static Private Attributes
tuple	__slots__ = ("scores", "pickled_pose")

Detailed Description

Serializable, read-only access to a serialized pose object.

PackedPose functions as the equivalent of the "Pose" object within the pyrosetta.distributed
namespace. It holds a serialized pose object and a cached dictionary of scores extracted
from the serialized pose. It can be "unpacked" into a working pose or isomorphicly represented
as primitive datatypes or pandas data structures.

The "primitive" datatype represention of PackedPosed is a dict containing, at least, the
key "packed_pose" holding a base64-encoded unicode string of the pickled pose object. This
representation supports transparent interconversion between json and the packed format. In
contrast, PackedPose includes the *bytes* representation of the pose object and is not suitable
for serialization as text.

It should be noted that all pickled representations are *highly* compressible.

Constructor & Destructor Documentation

__init__()

def pyrosetta.distributed.packed_pose.core.PackedPose.__init__	(		self,
			pose_or_pack
	)

Create a packed pose from pose, pack, or pickled bytes.

Referenced by pyrosetta.distributed.tasks.taskbase.TaskBase.__setstate__().

Member Function Documentation

clone()

def pyrosetta.distributed.packed_pose.core.PackedPose.clone

(

self

)

References PDB_IOBenchmark.pose, ScoreBenchmark.pose, ShearMoverBenchmark.pose, SmallMoverBenchmark.pose, SamplingManager.pose, apps::pilot::KicSandbox.pose, PoseAndData.pose, PoseWrap.pose, MatchBase.pose, MatchLig.pose, SlideTask.pose(), HIT.pose, WorkDat.pose, pyrosetta.bindings.pose.PoseResidueAccessor.pose, pyrosetta.bindings.pose.PoseResidueLabelAccessor.pose, pyrosetta.bindings.pose.PoseScoreAccessor.pose, pyrosetta.bindings.scores.base.PoseCacheAccessorBase.pose, ui::ui_core::pose_draw::SimplePoseDrawOpenGLWidget.pose(), pyrosetta.distributed.packed_pose.core.PackedPose.pose(), pyrosetta.tests.bindings.core.test_pose.TestPoseCacheAccessor.pose, test.T010_LoadPDB.LoadPDBTest.pose, test.T300_PyJobDistributor.TestPyJobDistributor.pose, myspace::DataStruct.scores, and pyrosetta.distributed.packed_pose.core.PackedPose.scores.

empty()

def pyrosetta.distributed.packed_pose.core.PackedPose.empty

(

self

)

References PDB_IOBenchmark.pose, ScoreBenchmark.pose, ShearMoverBenchmark.pose, SmallMoverBenchmark.pose, SamplingManager.pose, apps::pilot::KicSandbox.pose, PoseAndData.pose, PoseWrap.pose, MatchBase.pose, MatchLig.pose, SlideTask.pose(), HIT.pose, WorkDat.pose, pyrosetta.bindings.pose.PoseResidueAccessor.pose, pyrosetta.bindings.pose.PoseResidueLabelAccessor.pose, pyrosetta.bindings.pose.PoseScoreAccessor.pose, pyrosetta.bindings.scores.base.PoseCacheAccessorBase.pose, ui::ui_core::pose_draw::SimplePoseDrawOpenGLWidget.pose(), pyrosetta.distributed.packed_pose.core.PackedPose.pose(), pyrosetta.tests.bindings.core.test_pose.TestPoseCacheAccessor.pose, test.T010_LoadPDB.LoadPDBTest.pose, and test.T300_PyJobDistributor.TestPyJobDistributor.pose.

pose()

def pyrosetta.distributed.packed_pose.core.PackedPose.pose

(

self

)

References pyrosetta.distributed.packed_pose.core.PackedPose.pickled_pose.

Referenced by pyrosetta.bindings.pose.PoseScoreAccessor.__delitem__(), pyrosetta.bindings.scores.core.PoseCacheAccessor.__delitem__(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase.__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase.__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricStringDataAccessor.__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricRealDataAccessor.__delitem__(), pyrosetta.bindings.pose.PoseResidueAccessor.__getitem__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor.__getitem__(), pyrosetta.bindings.pose.PoseResidueAccessor.__iadd__(), pyrosetta.bindings.pose.PoseResidueAccessor.__imul__(), pyrosetta.bindings.pose.PoseResidueAccessor.__iter__(), pyrosetta.bindings.pose.PoseResidueAccessor.__len__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor.__len__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor.__repr__(), pyrosetta.bindings.pose.PoseResidueAccessor.__reversed__(), pyrosetta.bindings.pose.PoseScoreAccessor.__setitem__(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase.__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase._get_sm_data_dict(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase._has_reserved_custom_metric_keys(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase._maybe_delete_keys_from_sm_data(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase._maybe_delete_reserved_keys_from_sm_data(), pyrosetta.bindings.pose.PoseScoreAccessor.all(), pyrosetta.bindings.scores.energies.EnergiesAccessor.all(), pyrosetta.bindings.scores.extra_scores.ExtraFloatScoresDataAccessor.all(), pyrosetta.bindings.scores.extra_scores.ExtraStringScoresDataAccessor.all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricStringDataAccessor.all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricRealDataAccessor.all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeStringDataAccessor.all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeRealDataAccessor.all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueStringDataAccessor.all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueRealDataAccessor.all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueProbabilitiesDataAccessor.all(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase.apply(), pyrosetta.bindings.pose.PoseScoreAccessor.clear(), pyrosetta.bindings.scores.core.PoseCacheAccessor.clear(), pyrosetta.bindings.scores.energies.EnergiesAccessor.clear(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase.clear(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor.clear(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.clear(), pyrosetta.distributed.packed_pose.core.PackedPose.clone(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.composite_real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.composite_string(), pyrosetta.distributed.packed_pose.core.PackedPose.empty(), pyrosetta.bindings.pose.PoseScoreAccessor.energies(), pyrosetta.bindings.scores.core.PoseCacheAccessor.energies(), pyrosetta.bindings.pose.PoseScoreAccessor.extra(), pyrosetta.bindings.scores.core.PoseCacheAccessor.extra(), pyrosetta.bindings.scores.core.PoseCacheAccessor.metrics(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.per_residue_probabilities(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.per_residue_real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.per_residue_string(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor.real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.real(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor.string(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.string(), test.T300_PyJobDistributor.TestPyJobDistributor.test_jd(), test.T300_PyJobDistributor.TestPyJobDistributor.test_jd_at(), test.T300_PyJobDistributor.TestPyJobDistributor.test_jd_serializable_scores(), test.T300_PyJobDistributor.TestPyJobDistributor.test_jd_unserializable_scores(), test.T010_LoadPDB.LoadPDBTest.test_pdbstring_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseCacheAccessor.test_pose_cache(), test.T010_LoadPDB.LoadPDBTest.test_roundtrip_file(), test.T010_LoadPDB.LoadPDBTest.test_roundtrip_pdb(), test.T010_LoadPDB.LoadPDBTest.test_roundtrip_scored_pdb(), and pyrosetta.distributed.packed_pose.core.PackedPose.update_scores().

update_scores()

def pyrosetta.distributed.packed_pose.core.PackedPose.update_scores	(		self,
		*	score_dicts,
		**	score_kwargs
	)

References PDB_IOBenchmark.pose, ScoreBenchmark.pose, ShearMoverBenchmark.pose, SmallMoverBenchmark.pose, SamplingManager.pose, apps::pilot::KicSandbox.pose, PoseAndData.pose, PoseWrap.pose, MatchBase.pose, MatchLig.pose, SlideTask.pose(), HIT.pose, WorkDat.pose, pyrosetta.bindings.pose.PoseResidueAccessor.pose, pyrosetta.bindings.pose.PoseResidueLabelAccessor.pose, pyrosetta.bindings.pose.PoseScoreAccessor.pose, pyrosetta.bindings.scores.base.PoseCacheAccessorBase.pose, ui::ui_core::pose_draw::SimplePoseDrawOpenGLWidget.pose(), pyrosetta.distributed.packed_pose.core.PackedPose.pose(), pyrosetta.tests.bindings.core.test_pose.TestPoseCacheAccessor.pose, test.T010_LoadPDB.LoadPDBTest.pose, and test.T300_PyJobDistributor.TestPyJobDistributor.pose.

Member Data Documentation

__slots__

tuple pyrosetta.distributed.packed_pose.core.PackedPose.__slots__ = ("scores", "pickled_pose")

staticprivate

Referenced by pyrosetta.distributed.cluster.io.IO._get_instance_and_metadata().

pickled_pose

pyrosetta.distributed.packed_pose.core.PackedPose.pickled_pose

Referenced by pyrosetta.distributed.packed_pose.core.PackedPose.pose().

scores

pyrosetta.distributed.packed_pose.core.PackedPose.scores

Referenced by pyrosetta.distributed.packed_pose.core.PackedPose.clone().

---

The documentation for this class was generated from the following file:

• src/python/PyRosetta/src/pyrosetta/distributed/packed_pose/core.py