matchms.similarity.FingerprintSimilarity module

class matchms.similarity.FingerprintSimilarity.FingerprintSimilarity(similarity_measure: str = 'jaccard', set_empty_scores: float | int | str = 'nan')

Bases: BaseSimilarity

Calculate similarity between molecules based on their fingerprints.

For this similarity measure to work, fingerprints are expected to be derived by running add_fingerprint().

Code example:

import numpy as np
from matchms import calculate_scores
from matchms import Spectrum
from matchms.filtering import add_fingerprint
from matchms.similarity import FingerprintSimilarity

spectrum_1 = Spectrum(
    mz=np.array([], dtype="float"),
    intensities=np.array([], dtype="float"),
    metadata={"smiles": "CCC(C)C(C(=O)O)NC(=O)CCl", "precursor_mz": 200.2}
    )

spectrum_2 = Spectrum(
    mz=np.array([], dtype="float"),
    intensities=np.array([], dtype="float"),
    metadata={"smiles": "CC(C)C(C(=O)O)NC(=O)CCl", "precursor_mz": 200.2}
)

spectrum_3 = Spectrum(
    mz=np.array([], dtype="float"),
    intensities=np.array([], dtype="float"),
    metadata={"smiles": "C(C(=O)O)(NC(=O)O)S", "precursor_mz": 200.2}
)

spectra = [spectrum_1, spectrum_2, spectrum_3]
# Add fingerprints
spectra = [add_fingerprint(x, nbits=256) for x in spectra]

# Specify type and calculate similarities
similarity_measure = FingerprintSimilarity("jaccard")
scores = calculate_scores(spectra, spectra, similarity_measure)
print(np.round(scores.scores.to_array(), 3).tolist())

Should output

[[1.0, 0.878, 0.415], [0.878, 1.0, 0.444], [0.415, 0.444, 1.0]]

__init__(similarity_measure: str = 'jaccard', set_empty_scores: float | int | str = 'nan')

Parameters:

• similarity_measure – Chose similarity measure form “cosine”, “dice”, “jaccard”. The default is “jaccard”.

• set_empty_scores – Define what should be given instead of a similarity score in cases where fingprints are missing. The default is “nan”, which will return np.nan’s in such cases.

keep_score(score)

In the .matrix method scores will be collected in a sparse way. Overwrite this method here if values other than False or 0 should not be stored in the final collection.

matrix(references: List[Spectrum], queries: List[Spectrum], array_type: str = 'numpy', is_symmetric: bool = False) → array

Calculate matrix of fingerprint based similarity scores.

Parameters:

• references – List of reference spectra.

• queries – List of query spectra.

• array_type – Specify the output array type. Can be “numpy” or “sparse”. Default is “numpy” and will return a numpy array. “sparse” will return a COO-sparse array

pair(reference: Spectrum, query: Spectrum) → float

Calculate fingerprint based similarity score between two spectra.

Parameters:

• reference – Single reference spectrum.

• query – Single query spectrum.

score_datatype

alias of float64

sparse_array(references: List[Spectrum], queries: List[Spectrum], idx_row, idx_col, is_symmetric: bool = False, progress_bar: bool = True)

Optional: Provide optimized method to calculate an sparse matrix of similarity scores.

Compute similarity scores for pairs of reference and query spectra as given by the indices idx_row (references) and idx_col (queries). If no method is added here, the following naive implementation (i.e. a for-loop) is used.

Parameters:

• references – List of reference objects

• queries – List of query objects

• idx_row – List/array of row indices

• idx_col – List/array of column indices

• 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.

• progress_bar – When True a progress bar is shown. Default is True.

to_dict() → dict

Return a dictionary representation of a similarity function.