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from matchms.importing import load_from_mgf
from matchms.filtering import default_filters
from matchms.filtering import normalize_intensities
from matchms import calculate_scores
from matchms.similarity import CosineGreedy

# Read spectrums from a MGF formatted file, for other formats see https://matchms.readthedocs.io/en/latest/api/matchms.importing.html
file = load_from_mgf("tests/pesticides.mgf")

# Apply filters to clean and enhance each spectrum
spectrums = []
for spectrum in file:
    # Apply default filter to standardize ion mode, correct charge and more.
    # Default filter is fully explained at https://matchms.readthedocs.io/en/latest/api/matchms.filtering.html .
    spectrum = default_filters(spectrum)
    # Scale peak intensities to maximum of 1
    spectrum = normalize_intensities(spectrum)
    spectrums.append(spectrum)

# Calculate Cosine similarity scores between all spectrums
# For other similarity score methods see https://matchms.readthedocs.io/en/latest/api/matchms.similarity.html .
scores = calculate_scores(references=spectrums,
                          queries=spectrums,
                          similarity_function=CosineGreedy())

# Print the calculated scores for each spectrum pair
for score in scores:
    (reference, query, score, n_matching) = score
    # Ignore scores between same spectrum and
    # pairs which have less than 20 peaks in common
    if reference != query and n_matching >= 20:
        print(f"Reference scan id: {reference.metadata['scans']}")
        print(f"Query scan id: {query.metadata['scans']}")
        print(f"Score: {score:.4f}")
        print(f"Number of matching peaks {n_matching}")
        print("----------------------------")