class modifinder.engines.annotation.MAGMaAnnotationEngine.MAGMaAnnotationEngine(breaks=2, max_water_losses=2, ionisation_mode=0, mz_tolerance=0.1, ppm_tolerance=40, **kwargs)

Bases: AnnotationEngine

annotate(network: DiGraph, annotate_all: bool = False, **kwargs)

Annotates the network using the MAGMa model

:param : network (Network): the network to be annotated :param : annotate_all (bool): whether to annotate all compounds or only the ones that have not been annotated yet :param : kwargs: additional arguments

annotate_single(compound: Compound, modify_compound: bool = True, **kwargs) → List[Tuple[int, List[str]]]

provides annotation for the peaks in a single compound

:param : compound (Compound): the compound to be annotated :param : modify_compound (bool): whether to modify the passed compound with the annotations :param : kwargs: additional arguments

Returns:

Mapping[int, List[str]]: a dictionary with the indices of the peaks as keys and the list of annotations as values

get_fragment_info(Compound: Compound, fragment)

converts a fragment to a SMILES string

Parameters:

• (Compound) (Compound) –

• fragment (the fragment representation) –

Returns:

tuple(atomlist -> List[int], edge_list -> List[Tuple[int, int]], formula -> str, smiles -> str)

Return type:

a tuple containing the atom list, the edge list, the formula and the SMILES string

refine_annotations_by_formula(compound: Compound, peak_fragments_map, modify_compound: bool = True)

Refines the annotations of a compound by using the formula from msbuddy

See also

MSBuddy

Parameters:

(Compound) (compound) –

refine_annotations_by_helper(main_compound: Compound, helper_compound: Compound, edgeDetail: EdgeDetail, modify_compound: bool = True)

Refines the annotations of a compound by using the helper compound