matchms.calculate_scores module

matchms.calculate_scores.calculate_scores(spectra_1: Sequence[Spectrum], spectra_2: Sequence[Spectrum], similarity_function: BaseSimilarity) → Scores

Calculate the similarity between all reference objects versus all query objects.

Example to calculate scores between 2 spectra and iterate over the scores

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'})
spectra = [spectrum_1, spectrum_2]

scores = calculate_scores(spectra, spectra, CosineGreedy())

for (reference, query, score) in scores:
    print(f"Cosine score between {spectrum_1.get('id')} and {spectrum_2.get('id')}" +
          f" is {score[0]:.2f} with {score[1]} matched peaks")

Should output

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:

• spectra_1 – List of reference objects

• spectra_2 – List of query objects

• similarity_function – Function which accepts a reference + query object and returns a score or tuple of scores

Return type:

Scores