pyrosetta.distributed.cluster.converters Namespace Reference

Functions
List[int]	_parse_decoy_ids (Any objs)
None	_parse_empty_queue (str protocol_name, bool ignore_errors)
str	_parse_environment (Any obj)
List[Union[Callable[..., Any], Iterable[Any]]]	_parse_protocols (Any objs)
str	_parse_pyrosetta_build (Any obj)
str	_parse_scratch_dir (Any obj)
List[str]	_parse_seeds (Any objs)
str	_parse_sha1 (Any obj)
Dict[Any, Any]	_parse_system_info (Any obj)
Optional[int]	_get_decoy_id (Sized protocols, List[int] decoy_ids)
Tuple[List[PackedPose], Dict[Any, Any]]	_get_packed_poses_output_kwargs (Any result, Dict[Any, Any] input_kwargs, str protocol_name)
List[Tuple[bytes, bytes]]	_get_compressed_packed_pose_kwargs_pairs_list (List[PackedPose] packed_poses, Dict[Any, Any] output_kwargs, str protocol_name, str protocols_key, List[int] decoy_ids, S serializer)
List[Tuple[bytes, bytes]]	_parse_protocol_results (Any result, Dict[Any, Any] input_kwargs, str protocol_name, str protocols_key, List[int] decoy_ids, S serializer)
List[Tuple[bytes, bytes]]	_parse_target_results (List[Tuple[bytes, bytes]] objs)
def	_parse_tasks (objs)

Variables
string	__author__ = "Jason C. Klima"
	S = TypeVar("S", bound=Serialization)

Function Documentation

_get_compressed_packed_pose_kwargs_pairs_list()

List[Tuple[bytes, bytes]] pyrosetta.distributed.cluster.converters._get_compressed_packed_pose_kwargs_pairs_list ( List[PackedPose]  packed_poses, Dict[Any, Any]  output_kwargs, str  protocol_name, str  protocols_key, List[int]  decoy_ids, S  serializer  )

private

References pyrosetta.distributed.cluster.converters._get_decoy_id(), basic::options::OptionKeys::stepwise.enumerate, and ObjexxFCL.len().

Referenced by pyrosetta.distributed.cluster.converters._parse_protocol_results().

_get_decoy_id()

Optional[int] pyrosetta.distributed.cluster.converters._get_decoy_id ( Sized  protocols, List[int]  decoy_ids  )

private

Get the decoy number given the user-provided PyRosetta protocols.

References ObjexxFCL.len().

Referenced by pyrosetta.distributed.cluster.converters._get_compressed_packed_pose_kwargs_pairs_list().

_get_packed_poses_output_kwargs()

Tuple[List[PackedPose], Dict[Any, Any]] pyrosetta.distributed.cluster.converters._get_packed_poses_output_kwargs ( Any  result, Dict[Any, Any]  input_kwargs, str  protocol_name  )

private

References pyrosetta.distributed.cluster.converter_tasks.is_dict(), pyrosetta.distributed.cluster.converter_tasks.is_packed(), ObjexxFCL.len(), and pyrosetta.distributed.cluster.converter_tasks.to_iterable().

Referenced by pyrosetta.distributed.cluster.converters._parse_protocol_results().

_parse_decoy_ids()

List[int] pyrosetta.distributed.cluster.converters._parse_decoy_ids ( Any  objs )

private

Normalize user-provided PyRosetta 'decoy_ids' to a `list` object containing `int` objects.

References pyrosetta.distributed.cluster.converter_tasks.to_iterable().

_parse_empty_queue()

None pyrosetta.distributed.cluster.converters._parse_empty_queue ( str  protocol_name, bool  ignore_errors  )

private

Return a `None` object when a protocol results in an error with `ignore_errors=True`.

Referenced by pyrosetta.distributed.cluster.multiprocessing.get_target_results_kwargs().

_parse_environment()

str pyrosetta.distributed.cluster.converters._parse_environment ( Any  obj )

private

Parse the input `environment` attribute of PyRosettaCluster.

References pyrosetta.distributed.cluster.converter_tasks._parse_str(), and pyrosetta.distributed.cluster.converter_tasks.get_yml().

_parse_protocol_results()

List[Tuple[bytes, bytes]] pyrosetta.distributed.cluster.converters._parse_protocol_results ( Any  result, Dict[Any, Any]  input_kwargs, str  protocol_name, str  protocols_key, List[int]  decoy_ids, S  serializer  )

private

Parse results from the user-provided PyRosetta protocol.

References pyrosetta.distributed.cluster.converters._get_compressed_packed_pose_kwargs_pairs_list(), and pyrosetta.distributed.cluster.converters._get_packed_poses_output_kwargs().

Referenced by pyrosetta.distributed.cluster.multiprocessing.run_protocol().

_parse_protocols()

List[Union[Callable[..., Any], Iterable[Any]]] pyrosetta.distributed.cluster.converters._parse_protocols ( Any  objs )

private

Parse the `protocols` argument parameters from the PyRosettaCluster().distribute() method.

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

Referenced by pyrosetta.distributed.cluster.base.TaskBase._setup_protocols_protocol_seed(), and pyrosetta.distributed.cluster.tools.get_protocols().

_parse_pyrosetta_build()

str pyrosetta.distributed.cluster.converters._parse_pyrosetta_build ( Any  obj )

private

Parse the PyRosetta build string.

References pyrosetta.distributed.cluster.converter_tasks._default_none(), and pyrosetta._version_string().

_parse_scratch_dir()

str pyrosetta.distributed.cluster.converters._parse_scratch_dir ( Any  obj )

private

Parse the input `scratch_dir` attribute of PyRosettaCluster.

References pyrosetta.distributed.cluster.converter_tasks._default_none().

_parse_seeds()

List[str] pyrosetta.distributed.cluster.converters._parse_seeds ( Any  objs )

private

Normalize user-provided PyRosetta 'seeds' to a `list` object containing `str` objects.

References pyrosetta.distributed.cluster.converter_tasks.to_iterable().

_parse_sha1()

str pyrosetta.distributed.cluster.converters._parse_sha1 ( Any  obj )

private

Parse the input `sha1` attribute of PyRosettaCluster.

References pyrosetta.distributed.cluster.converter_tasks._default_none(), and ObjexxFCL.len().

_parse_system_info()

Dict[Any, Any] pyrosetta.distributed.cluster.converters._parse_system_info ( Any  obj )

private

Parse the input `system_info` attribute of PyRosettaCluster.

References pyrosetta.distributed.cluster.converter_tasks._default_none().

_parse_target_results()

List[Tuple[bytes, bytes]] pyrosetta.distributed.cluster.converters._parse_target_results ( List[Tuple[bytes, bytes]]  objs )

private

Parse results returned from the spawned thread.

References ObjexxFCL.len(), and set().

Referenced by pyrosetta.distributed.cluster.multiprocessing.get_target_results_kwargs().

_parse_tasks()

def pyrosetta.distributed.cluster.converters._parse_tasks (   objs )

private

Parse the input `tasks` attribute of PyRosettaCluster.

Variable Documentation

__author__

string pyrosetta.distributed.cluster.converters.__author__ = "Jason C. Klima"

private

S

pyrosetta.distributed.cluster.converters.S = TypeVar("S", bound=Serialization)

Referenced by bind_T17_anonymous(), detail.compile(), rosetta_binders.fixedsizearray0_add_on_binder(), rosetta_binders.fixedsizearray1_add_on_binder(), rosetta_binders.fixedsizearray_add_on_binder(), utility::FixedSizeLexicographicalIterator< S >.FixedSizeLexicographicalIterator(), format(), format_to(), format_to_n(), interp_linear(), utility::FixedSizeLexicographicalIterator< S >.operator++(), utility.operator<<(), detail::compiled_format_base< S, enable_if_t< is_compile_string< S >::value > >.parts(), numeric.R2quat(), utility::fixedsizearray1< T, S >.range(), numeric.remainder_conversion(), ObjexxFCL.remainder_conversion(), utility::FixedSizeLexicographicalIterator< S >.set_dimension_sizes(), utility::FixedSizeLexicographicalIterator< S >.set_position_from_index(), numeric.sign_transfered(), utility::fixedsizearray0< T, S >.size(), utility::fixedsizearray1< T, S >.size(), numeric::urs_Quat.urs_Quat(), and writeYamlValue().