Source code for matchms.similarity.FingerprintSimilarity

from typing import List, Union
import numpy
from matchms.typing import SpectrumType
from .BaseSimilarity import BaseSimilarity
from .vector_similarity_functions import (cosine_similarity,
                                          cosine_similarity_matrix,
                                          dice_similarity,
                                          dice_similarity_matrix,
                                          jaccard_index,
                                          jaccard_similarity_matrix)


[docs]class FingerprintSimilarity(BaseSimilarity): """Calculate similarity between molecules based on their fingerprints. For this similarity measure to work, fingerprints are expected to be derived by running :meth:`~matchms.filtering.add_fingerprint`. Code example: .. testcode:: 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, 3)) Should output .. testoutput:: [[1. 0.878 0.415] [0.878 1. 0.444] [0.415 0.444 1. ]] """ # Set key characteristics as class attributes is_commutative = True # Set output data type, e.g. "float" or [("score", "float"), ("matches", "int")] score_datatype = numpy.float64
[docs] def __init__(self, similarity_measure: str = "jaccard", set_empty_scores: Union[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 numpy.nan's in such cases. """ self.set_empty_scores = set_empty_scores assert similarity_measure in ["cosine", "dice", "jaccard"], "Unknown similarity measure." self.similarity_measure = similarity_measure
[docs] def pair(self, reference: SpectrumType, query: SpectrumType) -> float: """Calculate fingerprint based similarity score between two spectra. Parameters ---------- reference Single reference spectrum. query Single query spectrum. """ fingerprint_ref = reference.get("fingerprint") fingerprint_query = query.get("fingerprint") if self.similarity_measure == "jaccard": return jaccard_index(fingerprint_ref, fingerprint_query) if self.similarity_measure == "dice": return dice_similarity(fingerprint_ref, fingerprint_query) if self.similarity_measure == "cosine": score = cosine_similarity(fingerprint_ref, fingerprint_query) return numpy.asarray(score, dtype=self.score_datatype) raise NotImplementedError
[docs] def matrix(self, references: List[SpectrumType], queries: List[SpectrumType], is_symmetric: bool = False) -> numpy.array: """Calculate matrix of fingerprint based similarity scores. Parameters ---------- references: List of reference spectrums. queries: List of query spectrums. """ def get_fingerprints(spectrums): for index, spectrum in enumerate(spectrums): yield index, spectrum.get("fingerprint") def collect_fingerprints(spectrums): """Collect fingerprints and indices of spectrum with finterprints.""" idx_fingerprints = [] fingerprints = [] for index, fp in get_fingerprints(spectrums): if fp is not None: idx_fingerprints.append(index) fingerprints.append(fp) return numpy.asarray(fingerprints), numpy.asarray(idx_fingerprints) def create_full_matrix(): """Create matrix for all similarities.""" similarity_matrix = numpy.zeros((len(references), len(queries))) if self.set_empty_scores == "nan": similarity_matrix[:] = numpy.nan elif isinstance(self.set_empty_scores, (float, int)): similarity_matrix[:] = self.set_empty_scores return similarity_matrix fingerprints1, idx_fingerprints1 = collect_fingerprints(references) fingerprints2, idx_fingerprints2 = collect_fingerprints(queries) assert idx_fingerprints1.size > 0 and idx_fingerprints2.size > 0, ("Not enouth molecular fingerprints.", "Apply 'add_fingerprint'filter first.") # Calculate similarity score matrix following specified method similarity_matrix = create_full_matrix() if self.similarity_measure == "jaccard": similarity_matrix[numpy.ix_(idx_fingerprints1, idx_fingerprints2)] = jaccard_similarity_matrix(fingerprints1, fingerprints2) elif self.similarity_measure == "dice": similarity_matrix[numpy.ix_(idx_fingerprints1, idx_fingerprints2)] = dice_similarity_matrix(fingerprints1, fingerprints2) elif self.similarity_measure == "cosine": similarity_matrix[numpy.ix_(idx_fingerprints1, idx_fingerprints2)] = cosine_similarity_matrix(fingerprints1, fingerprints2) return similarity_matrix.astype(self.score_datatype)