matchms.similarity.FingerprintSimilarity module¶
- class matchms.similarity.FingerprintSimilarity.FingerprintSimilarity(similarity_measure: str = 'jaccard', set_empty_scores: float | int | str = 'nan')[source]¶
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"}) spectrum_2 = Spectrum(mz=np.array([], dtype="float"), intensities=np.array([], dtype="float"), metadata={"smiles": "CC(C)C(C(=O)O)NC(=O)CCl"}) spectrum_3 = Spectrum(mz=np.array([], dtype="float"), intensities=np.array([], dtype="float"), metadata={"smiles": "C(C(=O)O)(NC(=O)O)S"}) spectrums = [spectrum_1, spectrum_2, spectrum_3] # Add fingerprints spectrums = [add_fingerprint(x, nbits=256) for x in spectrums] # Specify type and calculate similarities similarity_measure = FingerprintSimilarity("jaccard") scores = calculate_scores(spectrums, spectrums, similarity_measure) print(np.round(scores.scores.to_array(), 3))
Should output
[[1. 0.878 0.415] [0.878 1. 0.444] [0.415 0.444 1. ]]
- __init__(similarity_measure: str = 'jaccard', set_empty_scores: float | int | str = 'nan')[source]¶
- 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 [source]¶
Calculate matrix of fingerprint based similarity scores.
- Parameters:
references – List of reference spectrums.
queries – List of query spectrums.
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 [source]¶
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)¶
Optional: Provide optimized method to calculate an sparse matrix of similarity scores.
Compute similarity scores for pairs of reference and query spectrums 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.