AlignmentEngine

class modifinder.engines.Abtracts.AlignmentEngine(**kwargs)[source]

Bases: ABC

Base class for alignment engines

It provides the basic structure for alignment engines in ModiFinder.

abstract align(network: DiGraph, mz_tolerance: float = 0.02, ppm_tolerance: float = 100.0, align_all: bool = True, **kwargs)[source]

Aligns the spectra in the network

For each edge in the network, aligns the spectrum of the start node with the spectrum of the end node. If the edge has already been aligned, and align_all is False, the edge will not be realigned.

Parameters:

  • (nx.DiGraph) (network) –

  • (float (ppm_tolerance) –

  • optional) (If True, all edges will be aligned. If False, only the edges that have not been aligned will be aligned. Defaults to False.) –

  • (float –

  • optional) –

  • (bool (align_all) –

  • optional) –

abstract align_single(SpectrumTuple1, SpectrumTuple2, mz_tolerance: float = 0.02, ppm_tolerance: float = 100.0, **kwargs)[source]

Aligns two spectra, returns the alignment details as an EdgeDetail object

Parameters:

  • (SpectrumTuple) (SpectrumTuple2) –

  • (SpectrumTuple) –

  • (float) (ppm_tolerance) –

  • (float) –

  • kwargs (additional arguments) –

Returns:

EdgeDetail

Return type:

the edge detail object

See also

For an example of an AlignmentEngine, see CosineAlignmentEngine

AnnotationEngine

class modifinder.engines.Abtracts.AnnotationEngine(**kwargs)[source]

Bases: ABC

Base class for annotation engines

It provides the basic structure for annotation engines in ModiFinder.

abstract annotate(network, **kwargs)[source]
abstract annotate_single(compound, modify_compound: bool = True, **kwargs) → List[Tuple[int, List[str]]][source]

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

abstract get_fragment_info(Compound: Compound, fragment: int) → Tuple[List[int], List[Tuple[int, int]], str, str][source]

converts a fragment to a SMILES string

:param : Compound (Compound): the compound :param : fragment (int): the fragment

Returns:

tuple(atomlist -> List[int], edge_list -> List[Tuple[int, int]], formula -> str, smiles -> str): a tuple containing the atom list, the edge list, the formula and the SMILES string

See also

For an example of an AnnotationEngine, see MAGMaAnnotationEngine

EvaluationEngine

class modifinder.engines.Abtracts.EvaluationEngine(**kwargs)[source]

Bases: ABC

Base class for evaluation engines

It provides the basic structure for evaluation engines in ModiFinder.

abstract evaluate(network, **kwargs)[source]
Parameters:

network (_type_) – _description_

abstract evaluate_single(known_compound_structure: Mol, unknonwn_compound_structure: Mol, probabilities: List[float], **kwargs)[source]

Evaluates the prediction of a single compound

Parameters:

  • known_compound_structure (rdkit Chem.Mol) – The known compound structure

  • unknonwn_compound_structure (rdkit Chem.Mol) – The unknown compound structure

  • probabilities (List[float]) – The probabilities of each atom being the modification site

  • kwargs (dict) – additional arguments

See also

For an example of an EvaluationEngine, see BasicEvaluationEngine