pyrosetta.distributed.cluster.converter_tasks Namespace Reference

Functions
Union[List[str], NoReturn]	get_protocols_list_of_str (Optional[str] input_file=None, Optional[str] scorefile=None, Optional[str] decoy_name=None)
def	get_scores_dict (obj)
str	get_yml ()
List[Any]	to_iterable (Any obj, Callable[..., Any] func, str attr)
List[Any]	_catch_pose_or_kwargs (Union[Pose, PackedPose, Dict[Any, Any]] obj, Callable[..., Any] func, str attr)
List[Any]	_iterate (Iterable[Any] objs, Callable[..., Any] func, str attr)
Union[int, NoReturn]	to_int (Any obj, str attribute)
int	_is_int (int obj, str attribute)
NoReturn	to_packed (Any obj, str protocol_name)
PackedPose	_to_packed (Pose obj, str protocol_name)
PackedPose	_is_packed_or_kwargs (Union[PackedPose, Dict[Any, Any]] obj, str protocol_name)
PackedPose	_none_to_packed (None obj, str protocol_name)
Union[str, NoReturn]	to_str (Any obj, str attribute)
str	_to_int (int obj, str attribute)
NoReturn	_to_float (float obj, str attribute)
NoReturn	parse_input_file_to_protocols_str (Any obj)
List[str]	_parse_str (str obj)
NoReturn	parse_input_file_to_instance_kwargs (Any obj)
NoReturn	parse_scorefile (Any obj)
NoReturn	parse_decoy_name (Any obj)
str	_from_str (str obj)
NoReturn	reserve_scores_in_results (Any obj, Dict[Any, Any] _scores_dict, str protocol_name)
List[PackedPose]	_parse_packed (Union[Pose, PackedPose] obj, Dict[Any, Any] _scores_dict, str protocol_name)
List[PackedPose]	_parse_iterable (Iterable[Any] objs, Dict[Any, Any] _scores_dict, str protocol_name)
PackedPose	_default_none (None obj, Dict[Any, Any] _scores_dict, str protocol_name)
NoReturn	parse_client (Any obj)
Optional[ClientType]	_default (Optional[ClientType] obj)
NoReturn	parse_input_packed_pose (Any obj)
Optional[PackedPose]	_from_packed_or_none (Optional[PackedPose] obj)
PackedPose	_from_pose (Pose obj)
NoReturn	parse_instance_kwargs (Any obj)
Dict[Any, Any]	_parse_dict (Dict[Any, Any] obj)
Dict[Any, Any]	_default_none (None obj)
bool	is_bytes (Any obj)
bool	is_packed (Any obj)
bool	is_dict (Any obj)

Variables
string	__author__ = "Jason C. Klima"
	ClientType = TypeVar("ClientType", bound=distributed.client.Client)

Function Documentation

_catch_pose_or_kwargs()

List[Any] pyrosetta.distributed.cluster.converter_tasks._catch_pose_or_kwargs ( Union[Pose, PackedPose, Dict[Any, Any]]  obj, Callable[..., Any]  func, str   attr  )

private

_default()

Optional[ClientType] pyrosetta.distributed.cluster.converter_tasks._default ( Optional[ClientType]  obj )

private

_default_none() [1/2]

Dict[Any, Any] pyrosetta.distributed.cluster.converter_tasks._default_none ( None  obj )

private

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

_default_none() [2/2]

PackedPose pyrosetta.distributed.cluster.converter_tasks._default_none ( None  obj, Dict[Any, Any]  _scores_dict, str   protocol_name  )

private

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

Referenced by pyrosetta.distributed.cluster.converter_tasks._default_none(), pyrosetta.distributed.cluster.converters._parse_pyrosetta_build(), pyrosetta.distributed.cluster.converters._parse_scratch_dir(), pyrosetta.distributed.cluster.converters._parse_sha1(), and pyrosetta.distributed.cluster.converters._parse_system_info().

_from_packed_or_none()

Optional[PackedPose] pyrosetta.distributed.cluster.converter_tasks._from_packed_or_none ( Optional[PackedPose]  obj )

private

_from_pose()

PackedPose pyrosetta.distributed.cluster.converter_tasks._from_pose ( Pose  obj )

private

_from_str()

str pyrosetta.distributed.cluster.converter_tasks._from_str ( str  obj )

private

_is_int()

int pyrosetta.distributed.cluster.converter_tasks._is_int ( int  obj, str  attribute  )

private

_is_packed_or_kwargs()

PackedPose pyrosetta.distributed.cluster.converter_tasks._is_packed_or_kwargs ( Union[PackedPose, Dict[Any, Any]]  obj, str  protocol_name  )

private

_iterate()

List[Any] pyrosetta.distributed.cluster.converter_tasks._iterate ( Iterable[Any]  objs, Callable[..., Any]  func, str  attr  )

private

_none_to_packed()

PackedPose pyrosetta.distributed.cluster.converter_tasks._none_to_packed ( None  obj, str  protocol_name  )

private

_parse_dict()

Dict[Any, Any] pyrosetta.distributed.cluster.converter_tasks._parse_dict ( Dict[Any, Any]  obj )

private

_parse_iterable()

List[PackedPose] pyrosetta.distributed.cluster.converter_tasks._parse_iterable ( Iterable[Any]  objs, Dict[Any, Any]  _scores_dict, str   protocol_name  )

private

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

_parse_packed()

List[PackedPose] pyrosetta.distributed.cluster.converter_tasks._parse_packed ( Union[Pose, PackedPose]  obj, Dict[Any, Any]  _scores_dict, str   protocol_name  )

private

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

_parse_str()

List[str] pyrosetta.distributed.cluster.converter_tasks._parse_str ( str  obj )

private

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

Referenced by pyrosetta.distributed.cluster.converters._parse_environment(), pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_instance_kwargs(), and pyrosetta.distributed.cluster.converter_tasks.parse_scorefile().

_to_float()

NoReturn pyrosetta.distributed.cluster.converter_tasks._to_float ( float  obj, str  attribute  )

private

_to_int()

str pyrosetta.distributed.cluster.converter_tasks._to_int ( int  obj, str  attribute  )

private

References pyrosetta.distributed.cluster.str.

_to_packed()

PackedPose pyrosetta.distributed.cluster.converter_tasks._to_packed ( Pose  obj, str  protocol_name  )

private

get_protocols_list_of_str()

Union[List[str], NoReturn] pyrosetta.distributed.cluster.converter_tasks.get_protocols_list_of_str	(	Optional[str]	input_file = None,
		Optional[str]	scorefile = None,
		Optional[str]	decoy_name = None
	)

Get the user-defined PyRosetta protocols as a `list` object of `str` objects.

Args:
    input_file: A `str` object specifying the path to the '.pdb' or '.pdb.bz2'
        file from which to extract PyRosettaCluster instance kwargs. If input_file
        is provided, then ignore the scorefile and decoy_name argument parameters.
        Default: None
    scorefile: A `str` object specifying the path to the JSON-formatted scorefile
        from which to extract PyRosettaCluster instance kwargs. If 'scorefile'
        is provided, 'decoy_name' must also be provided. In order to use a scorefile,
        it must contain full simulation records from the original production
        run; i.e., the attribute 'simulation_records_in_scorefile' was set to True.
        Default: None
    decoy_name: A `str` object specifying the decoy name for which to extract
        PyRosettaCluster instance kwargs. If decoy_name is provided, scorefile
        must also be provided.
        Default: None

Returns:
    A `list` object of `str` objects specifying user-defined PyRosetta protocol names.

References basic::database.open(), pyrosetta.distributed.cluster.converter_tasks.parse_decoy_name(), pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_protocols_str(), and pyrosetta.distributed.cluster.converter_tasks.parse_scorefile().

Referenced by pyrosetta.distributed.cluster.tools.get_protocols().

get_scores_dict()

def pyrosetta.distributed.cluster.converter_tasks.get_scores_dict

(

obj

)

Get the PyRosettaCluster scores dictionary from a .pdb or .pdb.bz2 file.

References all, pyrosetta.tests.distributed.test_dask.format, and basic::database.open().

Referenced by pyrosetta.distributed.cluster.converter_tasks._parse_str(), pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_instance_kwargs(), pyrosetta.tests.distributed.cluster.test_smoke.ResourcesTest.test_resources(), and pyrosetta.tests.distributed.cluster.test_smoke.ResourcesTest.test_resources_clients().

get_yml()

str pyrosetta.distributed.cluster.converter_tasks.get_yml

(

)

Use `conda env export` to return a YML file string with the current conda
enviroment, excluding certain source domains.

References all.

Referenced by pyrosetta.distributed.cluster.converters._parse_environment(), and pyrosetta.distributed.cluster.tools._print_conda_warnings().

is_bytes()

bool pyrosetta.distributed.cluster.converter_tasks.is_bytes

(

Any

obj

)

is_dict()

bool pyrosetta.distributed.cluster.converter_tasks.is_dict

(

Any

obj

)

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

is_packed()

bool pyrosetta.distributed.cluster.converter_tasks.is_packed

(

Any

obj

)

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

parse_client()

NoReturn pyrosetta.distributed.cluster.converter_tasks.parse_client

(

Any

obj

)

References pyrosetta.tests.distributed.test_dask.format.

Referenced by pyrosetta.distributed.cluster.tools.reproduce().

parse_decoy_name()

NoReturn pyrosetta.distributed.cluster.converter_tasks.parse_decoy_name

(

Any

obj

)

References pyrosetta.tests.distributed.test_dask.format.

Referenced by pyrosetta.distributed.cluster.tools.get_instance_kwargs(), and pyrosetta.distributed.cluster.converter_tasks.get_protocols_list_of_str().

parse_input_file_to_instance_kwargs()

NoReturn pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_instance_kwargs

(

Any

obj

)

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

Referenced by pyrosetta.distributed.cluster.tools.get_instance_kwargs().

parse_input_file_to_protocols_str()

NoReturn pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_protocols_str

(

Any

obj

)

Referenced by pyrosetta.distributed.cluster.converter_tasks.get_protocols_list_of_str().

parse_input_packed_pose()

NoReturn pyrosetta.distributed.cluster.converter_tasks.parse_input_packed_pose

(

Any

obj

)

References pyrosetta.tests.distributed.test_dask.format.

parse_instance_kwargs()

NoReturn pyrosetta.distributed.cluster.converter_tasks.parse_instance_kwargs

(

Any

obj

)

References pyrosetta.tests.distributed.test_dask.format.

Referenced by pyrosetta.distributed.cluster.tools.reproduce().

parse_scorefile()

NoReturn pyrosetta.distributed.cluster.converter_tasks.parse_scorefile

(

Any

obj

)

References pyrosetta.distributed.cluster.converter_tasks._parse_str(), and pyrosetta.tests.distributed.test_dask.format.

Referenced by pyrosetta.distributed.cluster.tools.get_instance_kwargs(), and pyrosetta.distributed.cluster.converter_tasks.get_protocols_list_of_str().

reserve_scores_in_results()

NoReturn pyrosetta.distributed.cluster.converter_tasks.reserve_scores_in_results	(	Any	obj,
		Dict[Any, Any]	_scores_dict,
		str	protocol_name
	)

Referenced by pyrosetta.distributed.cluster.tools.reserve_scores().

to_int()

Union[int, NoReturn] pyrosetta.distributed.cluster.converter_tasks.to_int	(	Any	obj,
		str	attribute
	)

References enumerate_junctions.int.

to_iterable()

List[Any] pyrosetta.distributed.cluster.converter_tasks.to_iterable	(	Any	obj,
		Callable[..., Any]	func,
		str	attr
	)

Referenced by pyrosetta.distributed.cluster.converters._get_packed_poses_output_kwargs(), pyrosetta.distributed.cluster.converters._parse_decoy_ids(), and pyrosetta.distributed.cluster.converters._parse_seeds().

to_packed()

NoReturn pyrosetta.distributed.cluster.converter_tasks.to_packed	(	Any	obj,
		str	protocol_name
	)

Parse a single result from the user-provided PyRosetta protocol.

Referenced by pyrosetta.distributed.cluster.converter_tasks._default_none(), pyrosetta.distributed.cluster.converter_tasks._parse_iterable(), pyrosetta.distributed.cluster.converter_tasks._parse_packed(), pyrosetta.distributed.io.to_output_record(), and pyrosetta.distributed.io.to_pdbstring().

to_str()

Union[str, NoReturn] pyrosetta.distributed.cluster.converter_tasks.to_str	(	Any	obj,
		str	attribute
	)

References enumerate_junctions.int, and pyrosetta.distributed.cluster.str.

Variable Documentation

__author__

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

private

ClientType

pyrosetta.distributed.cluster.converter_tasks.ClientType = TypeVar("ClientType", bound=distributed.client.Client)