Source code for matchms.calculate_scores

from .Scores import Scores
from .similarity.BaseSimilarity import BaseSimilarity
from .typing import QueriesType, ReferencesType


[docs]def calculate_scores(references: ReferencesType, queries: QueriesType, similarity_function: BaseSimilarity, is_symmetric: bool = False) -> Scores: """Calculate the similarity between all reference objects versus all query objects. Example to calculate scores between 2 spectrums and iterate over the scores .. testcode:: import numpy as np from matchms import calculate_scores, Spectrum from matchms.similarity import CosineGreedy spectrum_1 = Spectrum(mz=np.array([100, 150, 200.]), intensities=np.array([0.7, 0.2, 0.1]), metadata={'id': 'spectrum1'}) spectrum_2 = Spectrum(mz=np.array([100, 140, 190.]), intensities=np.array([0.4, 0.2, 0.1]), metadata={'id': 'spectrum2'}) spectrums = [spectrum_1, spectrum_2] scores = calculate_scores(spectrums, spectrums, CosineGreedy()) for (reference, query, score) in scores: print(f"Cosine score between {reference.get('id')} and {query.get('id')}" + f" is {score['score']:.2f} with {score['matches']} matched peaks") Should output .. testoutput:: Cosine score between spectrum1 and spectrum1 is 1.00 with 3 matched peaks Cosine score between spectrum1 and spectrum2 is 0.83 with 1 matched peaks Cosine score between spectrum2 and spectrum1 is 0.83 with 1 matched peaks Cosine score between spectrum2 and spectrum2 is 1.00 with 3 matched peaks Parameters ---------- references List of reference objects queries List of query objects similarity_function Function which accepts a reference + query object and returns a score or tuple of scores is_symmetric Set to True when *references* and *queries* are identical (as for instance for an all-vs-all comparison). By using the fact that score[i,j] = score[j,i] the calculation will be about 2x faster. Default is False. Returns ------- ~matchms.Scores.Scores """ return Scores(references=references, queries=queries, similarity_function=similarity_function, is_symmetric=is_symmetric).calculate()