enerzyme.tasks.extractor.Extractor

class enerzyme.tasks.extractor.Extractor(reference_mol_path: str, fragment_per_frame: int = 1, local_uncertainty_radius: float = 5, fragment_radius: float = 5, n_centers: int = 1, must_include_indices: List[int] = [])

Bases: object

__init__(reference_mol_path: str, fragment_per_frame: int = 1, local_uncertainty_radius: float = 5, fragment_radius: float = 5, n_centers: int = 1, must_include_indices: List[int] = []) → None

Extractor class for extracting fragments from molecules.

Params:

reference_mol_path: str

The path to the reference molecule.

fragment_per_frame: int

The number of fragments to be extracted per frame.

local_uncertainty_radius: float

The radius of the local uncertainty quantification.

fragment_radius: float

The radius of the fragmentation.

n_centers: int

The number of centers to be used for extracting only one fragment.

build_fragment(y_pred: dict, xyzblocks: List[str] | None = None, prefix: str = '') → None

Build fragments from the prediction results.

Params:

y_pred: dict

The prediction results with uncertainty quantification.

xyzblocks: Optional[List[str]]

The xyz blocks of the molecules.

prefix: str

The prefix of the output sdf file.