pyrosetta.distributed.cluster.io.IO Class Reference

Inheritance diagram for pyrosetta.distributed.cluster.io.IO:

Static Public Attributes
	str

Private Member Functions
Tuple[Dict[Any, Any], Dict[Any, Any]]	_get_instance_and_metadata (self, Dict[Any, Any] kwargs)
str	_get_output_dir (self, str decoy_dir)
Union[List[Tuple[str, Dict[Any, Any]]], NoReturn]	_parse_results (self, Union[Iterable[Optional[Union[Pose, PackedPose, bytes]]], Optional[Union[Pose, PackedPose]],] results)
Dict[Any, Any]	_process_kwargs (self, Dict[Any, Any] kwargs)
None	_save_results (self, Any results, Dict[Any, Any] kwargs)
None	_write_environment_file (self, str filename)

Static Private Member Functions
Dict[Any, Any]	_filter_scores_dict (Dict[Any, Any] scores_dict)
Tuple[str, Dict[Any, Any]]	_format_result (Union[Pose, PackedPose] result)

Detailed Description

Input/Output methods for PyRosettaCluster.

Member Function Documentation

_filter_scores_dict()

Dict[Any, Any] pyrosetta.distributed.cluster.io.IO._filter_scores_dict ( Dict[Any, Any]  scores_dict )

staticprivate

References basic::options::OptionKeys::in::file.list.

_format_result()

Tuple[str, Dict[Any, Any]] pyrosetta.distributed.cluster.io.IO._format_result ( Union[Pose, PackedPose]  result )

staticprivate

Given a `Pose` or `PackedPose` object, return a tuple containing
the pdb string and a scores dictionary.

References pyrosetta.distributed.cluster.serialization.update_scores().

_get_instance_and_metadata()

Tuple[Dict[Any, Any], Dict[Any, Any]] pyrosetta.distributed.cluster.io.IO._get_instance_and_metadata (   self, Dict[Any, Any]   kwargs  )

private

Get the current state of the PyRosettaCluster instance, and split the
kwargs into the PyRosettaCluster instance kwargs and ancillary metadata.

References pyrosetta.distributed.tasks.taskbase.TaskBase.__getstate__(), pyrosetta.bindings.pose.ResidueLabelAccessor.__slots__, pyrosetta.bindings.pose.PoseResidueLabelMaskAccessor.__slots__, pyrosetta.bindings.pose.PoseResidueLabelAccessor.__slots__, pyrosetta.bindings.pose.PoseScoreAccessor.__slots__, pyrosetta.bindings.scores.base.PoseCacheAccessorBase.__slots__, pyrosetta.bindings.scores.core.PoseCacheAccessor.__slots__, pyrosetta.bindings.scores.energies.EnergiesAccessor.__slots__, pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase.__slots__, pyrosetta.bindings.scores.extra_scores.ExtraFloatScoresDataAccessor.__slots__, pyrosetta.bindings.scores.extra_scores.ExtraStringScoresDataAccessor.__slots__, pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricStringDataAccessor.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricRealDataAccessor.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeStringDataAccessor.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeRealDataAccessor.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueStringDataAccessor.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueRealDataAccessor.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueProbabilitiesDataAccessor.__slots__, pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor.__slots__, pyrosetta.distributed.packed_pose.core.PackedPose.__slots__, pyrosetta.distributed._normflags(), pyrosetta.distributed.cluster.core.PyRosettaCluster.serializer, and basic::options::OptionKeys::in::file.zip.

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

_get_output_dir()

str pyrosetta.distributed.cluster.io.IO._get_output_dir (   self, str  decoy_dir  )

private

Get the output directory in which to write files to disk.

References enumerate_junctions.int, ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, and pyrosetta.distributed.cluster.io.IO.str.

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

_parse_results()

Union[List[Tuple[str, Dict[Any, Any]]], NoReturn] pyrosetta.distributed.cluster.io.IO._parse_results (   self, Union[ Iterable[Optional[Union[Pose, PackedPose, bytes]]], Optional[Union[Pose, PackedPose]], ]  results  )

private

Format output results on distributed worker. Input argument `results` can be a
`Pose`, `PackedPose`, or `None` object, or a `list` or `tuple` of `Pose` and/or `PackedPose`
objects, or an empty `list` or `tuple`. Returns a list of tuples, each tuple
containing the pdb string and a scores dictionary.

References basic::options::OptionKeys::score.empty, and pyrosetta.distributed.cluster.core.PyRosettaCluster.serializer.

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

_process_kwargs()

Dict[Any, Any] pyrosetta.distributed.cluster.io.IO._process_kwargs (   self, Dict[Any, Any]  kwargs  )

private

Remove seed specification from 'extra_options' or 'options',
and remove protocols_key from kwargs.

References ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, pyrosetta.distributed.cluster.core.PyRosettaCluster.protocols_key, and range.

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

_save_results()

None pyrosetta.distributed.cluster.io.IO._save_results (   self, Any  results, Dict[Any, Any]  kwargs  )

private

Write results and kwargs to disk.

References pyrosetta.distributed.cluster.io.IO._get_instance_and_metadata(), pyrosetta.distributed.cluster.io.IO._get_output_dir(), pyrosetta.distributed.cluster.io.IO._parse_results(), pyrosetta.distributed.cluster.io.IO._process_kwargs(), ObjexxFCL::Cstring.compressed(), ObjexxFCL::Fstring.compressed(), pyrosetta.distributed.cluster.core.PyRosettaCluster.compressed, utility::io::irstream.compressed(), utility::io::orstream.compressed(), utility::io::icstream.compressed(), utility::io::izstream.compressed(), utility::io::ocstream.compressed(), utility::io::ozstream.compressed(), pyrosetta.distributed.cluster.core.PyRosettaCluster.decoy_path, pyrosetta.distributed.cluster.core.PyRosettaCluster.dry_run, pyrosetta.distributed.cluster.core.PyRosettaCluster.environment_file, join(), basic::database.open(), pyrosetta.distributed.cluster.core.PyRosettaCluster.scorefile_path, pyrosetta.distributed.cluster.core.PyRosettaCluster.simulation_name, pyrosetta.distributed.cluster.core.PyRosettaCluster.simulation_records_in_scorefile, pyrosetta.distributed.cluster.io.IO.str, and detail.strftime().

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster._run().

_write_environment_file()

None pyrosetta.distributed.cluster.io.IO._write_environment_file (   self, str  filename  )

private

Write the YML string to the input filename.

References pyrosetta.distributed.cluster.core.PyRosettaCluster.dry_run, pyrosetta.distributed.cluster.core.PyRosettaCluster.environment, basic::database.open(), and pyrosetta.distributed.cluster.core.PyRosettaCluster.simulation_records_in_scorefile.

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.__attrs_post_init__().

Member Data Documentation

str

pyrosetta.distributed.cluster.io.IO.str

static

Referenced by pyrosetta.distributed.cluster.io.IO._get_output_dir(), and pyrosetta.distributed.cluster.io.IO._save_results().

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

• src/python/PyRosetta/src/pyrosetta/distributed/cluster/io.py