converter_tasks

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

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’, ‘.pdb.bz2’, ‘.pkl_pose’,

‘.pkl_pose.bz2’, ‘.b64_pose’, ‘.b64_pose.bz2’, ‘.init’, or ‘.init.bz2’ file, or a Pose or PackedPose object, from which to extract PyRosettaCluster instance kwargs. If ‘input_file’ is provided, then ignore the ‘scorefile’ and ‘decoy_name’ keyword argument parameters. Default: None

scorefile: A str object specifying the path to the JSON-formatted scorefile

(or pickled pandas.DataFrame scorefile) from a PyRosettaCluster simulation 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.

pyrosetta.distributed.cluster.converter_tasks.get_scores_dict(obj: Union[str, Pose, PackedPose]) → Union[Dict[str, Dict[str, Any]], NoReturn]

Get the PyRosettaCluster scores dictionary from either a Pose or PackedPose object, or a ‘.pdb’, ‘.pdb.bz2’, ‘.pkl_pose’, ‘.pkl_pose.bz2’, ‘.b64_pose’, ‘.b64_pose.bz2’, ‘.init’, or ‘.init.bz2’ file.

pyrosetta.distributed.cluster.converter_tasks.export_init_file(output_file: str, output_init_file: Optional[str] = None, compressed: Optional[bool] = None) → None

Export a PyRosetta initialization file from a decoy output file. The PyRosettaCluster simulation that produced the decoy output file must have had the ‘output_init_file’ instance attribute enabled, so the ‘init_file’ key value can be detected in the metadata of the decoy output file. This function can be used to prepend the decoy output file to the detected PyRosetta initialization file for more facile simulation reproduction using the reproduce() function.

Args:

output_file: A required str object representing the decoy output file. The file must end in

either: ‘.pdb’, ‘.pdb.bz2’, ‘.pkl_pose’, ‘.pkl_pose.bz2’, ‘.b64_pose’, or ‘.b64_pose.bz2’.

output_init_file: An optional str object specifying the output PyRosetta initialization file

path ending with ‘.init’. If NoneType is provided, then the PyRosetta initialization file path is derived from the ‘output_file’ argument parameter by replacing the file extension with ‘.init’ (or ‘.init.bz2’ when the ‘compressed’ argument parameter is set to True). Default: None

compressed: A bool object specifying whether or not to compress the output PyRosetta initialization

file with bzip2, resulting in a ‘.init.bz2’ output PyRosetta initialization file.

Default: True

Returns:

None

pyrosetta.distributed.cluster.converter_tasks.get_yml() → str

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

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

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

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

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

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

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

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

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

pyrosetta.distributed.cluster.converter_tasks.to_int(obj: int, attribute: str) → int

pyrosetta.distributed.cluster.converter_tasks.to_int(obj: float, attribute: str) → NoReturn

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

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

pyrosetta.distributed.cluster.converter_tasks.to_packed(obj: Pose, protocol_name: str) → PackedPose

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

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

pyrosetta.distributed.cluster.converter_tasks.to_packed(obj: None, protocol_name: str) → PackedPose

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

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

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

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

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

pyrosetta.distributed.cluster.converter_tasks.to_str(obj: int, attribute: str) → str

pyrosetta.distributed.cluster.converter_tasks.to_str(obj: float, attribute: str) → NoReturn

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

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

pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_protocols_str(obj: Any) → NoReturn

pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_protocols_str(obj: str) → List[str]

pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_protocols_str(obj: str) → List[str]

pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_protocols_str(obj: str) → List[str]

pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_instance_kwargs(obj: Any) → NoReturn

pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_instance_kwargs(obj: str) → Dict[str, Any]

pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_instance_kwargs(obj: str) → Dict[str, Any]

pyrosetta.distributed.cluster.converter_tasks.parse_input_file_to_instance_kwargs(obj: str) → Dict[str, Any]

pyrosetta.distributed.cluster.converter_tasks.parse_scorefile(obj: Any) → NoReturn

pyrosetta.distributed.cluster.converter_tasks.parse_scorefile(obj: str) → Union[str, NoReturn]

pyrosetta.distributed.cluster.converter_tasks._parse_str(obj: str) → Union[str, NoReturn]

pyrosetta.distributed.cluster.converter_tasks.parse_decoy_name(obj: Any) → NoReturn

pyrosetta.distributed.cluster.converter_tasks.parse_decoy_name(obj: str) → str

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

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

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

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

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

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

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

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

pyrosetta.distributed.cluster.converter_tasks.parse_client(obj: Any) → NoReturn

pyrosetta.distributed.cluster.converter_tasks.parse_client(obj: Optional[ClientType]) → Optional[ClientType]

pyrosetta.distributed.cluster.converter_tasks.parse_client(obj: Optional[ClientType]) → Optional[ClientType]

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

pyrosetta.distributed.cluster.converter_tasks.parse_input_packed_pose(obj: Any) → NoReturn

pyrosetta.distributed.cluster.converter_tasks.parse_input_packed_pose(obj: Optional[PackedPose]) → Optional[PackedPose]

pyrosetta.distributed.cluster.converter_tasks.parse_input_packed_pose(obj: Optional[PackedPose]) → Optional[PackedPose]

pyrosetta.distributed.cluster.converter_tasks.parse_input_packed_pose(obj: Pose) → PackedPose

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

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

pyrosetta.distributed.cluster.converter_tasks.parse_instance_kwargs(obj: Any) → NoReturn

pyrosetta.distributed.cluster.converter_tasks.parse_instance_kwargs(obj: Dict[Any, Any]) → Dict[Any, Any]

pyrosetta.distributed.cluster.converter_tasks.parse_instance_kwargs(obj: None) → Dict[Any, Any]

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

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

pyrosetta.distributed.cluster.converter_tasks.parse_init_file(input_file: str, input_packed_pose: Optional[PackedPose], skip_corrections: bool, init_from_file_kwargs: Dict[str, Any]) → Union[Tuple[Optional[PackedPose], PackedPose], NoReturn]

Return a tuple object of the input PackedPose object and the output PackedPose object from a ‘.init’ or ‘.init.bz2’ file, verifying PyRosettaCluster metadata in the ‘.init’ or ‘.init.bz2’ file.

pyrosetta.distributed.cluster.converter_tasks.is_empty(obj: Any) → NoReturn

pyrosetta.distributed.cluster.converter_tasks.is_empty(obj: None) → bool

pyrosetta.distributed.cluster.converter_tasks.is_empty(obj: PackedPose) → bool

Test whether a PackedPose object is empty.

pyrosetta.distributed.cluster.converter_tasks._from_none(obj: None) → bool

pyrosetta.distributed.cluster.converter_tasks._from_packed(obj: PackedPose) → bool

pyrosetta.distributed.cluster.converter_tasks.identical_b64_poses(packed_pose_1: Union[Pose, PackedPose], packed_pose_2: Union[Pose, PackedPose]) → bool

Test whether b64-encoded pickled Pose objects are identical.

pyrosetta.distributed.cluster.converter_tasks.is_bytes(obj: Any) → bool

pyrosetta.distributed.cluster.converter_tasks.is_packed(obj: Any) → bool

pyrosetta.distributed.cluster.converter_tasks.is_dict(obj: Any) → bool