def test_cosine_greedy_with_arrays_symmetric():
"""Test if matrix with is_symmetric=True works properly."""
spectrum_1 = Spectrum(mz=numpy.array([100, 200, 300], dtype="float"),
intensities=numpy.array([0.1, 0.2, 1.0], dtype="float"))
spectrum_2 = Spectrum(mz=numpy.array([110, 190, 290], dtype="float"),
intensities=numpy.array([0.5, 0.2, 1.0], dtype="float"))
spectrums = [spectrum_1, spectrum_2]
cosine_greedy = CosineGreedy()
scores = cosine_greedy.matrix(spectrums, spectrums, is_symmetric=True)
assert scores[0][0][0] == pytest.approx(scores[1][1][0], 0.000001), "Expected different cosine score."
assert scores[0][1][0] == pytest.approx(scores[1][0][0], 0.000001), "Expected different cosine score."
def test_cosine_greedy_matrix(symmetric):
builder = SpectrumBuilder()
spectrum_1 = builder.with_mz(numpy.array(
[100, 200, 300], dtype="float")).with_intensities(
numpy.array([0.1, 0.2, 1.0], dtype="float")).build()
spectrum_2 = builder.with_mz(numpy.array(
[110, 190, 290], dtype="float")).with_intensities(
numpy.array([0.5, 0.2, 1.0], dtype="float")).build()
spectrums = [spectrum_1, spectrum_2]
cosine_greedy = CosineGreedy()
scores = cosine_greedy.matrix(spectrums, spectrums, is_symmetric=symmetric)
assert scores[0][0][0] == pytest.approx(
scores[1][1][0], 0.000001), "Expected different cosine score."
assert scores[0][0]["score"] == pytest.approx(scores[1][1]["score"], 0.000001), \
"Expected different cosine score."
assert scores[0][1][0] == pytest.approx(
scores[1][0][0], 0.000001), "Expected different cosine score."
assert scores[0][1]["score"] == pytest.approx(scores[1][0]["score"], 0.000001), \
"Expected different cosine score."
def library_matching(documents_query: List[SpectrumDocument],
documents_library: List[SpectrumDocument],
model,
presearch_based_on=["parentmass", "spec2vec-top10"],
ignore_non_annotated: bool = True,
include_scores=["spec2vec", "cosine", "modcosine"],
intensity_weighting_power: float = 0.5,
allowed_missing_percentage: float = 0,
cosine_tol: float = 0.005,
mass_tolerance: float = 1.0):
"""Selecting potential spectra matches with spectra library.
Suitable candidates will be selected by 1) top_n Spec2Vec similarity, and 2)
same precursor mass (within given mz_ppm tolerance(s)).
For later matching routines, additional scores (cosine, modified cosine)
are added as well.
Args:
--------
documents_query:
List containing all spectrum documents that should be queried against the library.
documents_library:
List containing all library spectrum documents.
model:
Pretrained word2Vec model.
top_n: int, optional
Number of entries witht the top_n highest Spec2Vec scores to keep as
found matches. Default = 10.
ignore_non_annotated: bool, optional
If True, only annotated spectra will be considered for matching.
Default = True.
cosine_tol: float, optional
Set tolerance for the cosine and modified cosine score. Default = 0.005
mass_tolerance
Specify tolerance for a parentmass match.
"""
# Initializations
found_matches = []
m_mass_matches = None
m_spec2vec_similarities = None
def get_metadata(documents):
metadata = []
for doc in documents:
metadata.append(doc._obj.get("smiles"))
return metadata
library_spectra_metadata = get_metadata(documents_library)
if ignore_non_annotated:
# Get array of all ids for spectra with smiles
library_ids = np.asarray(
[i for i, x in enumerate(library_spectra_metadata) if x])
else:
library_ids = np.arange(len(documents_library))
msg = "Presearch must be done either by 'parentmass' and/or 'spec2vec-topX'"
assert "parentmass" in presearch_based_on or np.any(
["spec2vec" in x for x in presearch_based_on]), msg
# 1. Search for top-n Spec2Vec matches ------------------------------------
if np.any(["spec2vec" in x for x in presearch_based_on]):
top_n = int([
x.split("top")[1] for x in presearch_based_on if "spec2vec" in x
][0])
print("Pre-selection includes spec2vec top {}.".format(top_n))
spec2vec = Spec2Vec(
model=model,
intensity_weighting_power=intensity_weighting_power,
allowed_missing_percentage=allowed_missing_percentage)
m_spec2vec_similarities = spec2vec.matrix(
[documents_library[i] for i in library_ids], documents_query)
# Select top_n similarity values:
selection_spec2vec = np.argpartition(m_spec2vec_similarities,
-top_n,
axis=0)[-top_n:, :]
else:
selection_spec2vec = np.empty((0, len(documents_query)), dtype="int")
# 2. Search for parent mass based matches ---------------------------------
if "parentmass" in presearch_based_on:
mass_matching = ParentmassMatch(mass_tolerance)
m_mass_matches = mass_matching.matrix(
[documents_library[i]._obj for i in library_ids],
[x._obj for x in documents_query])
selection_massmatch = []
for i in range(len(documents_query)):
selection_massmatch.append(np.where(m_mass_matches[:, i] == 1)[0])
else:
selection_massmatch = np.empty((len(documents_query), 0), dtype="int")
# 3. Combine found matches ------------------------------------------------
for i in range(len(documents_query)):
s2v_top_ids = selection_spec2vec[:, i]
mass_match_ids = selection_massmatch[i]
all_match_ids = np.unique(np.concatenate(
(s2v_top_ids, mass_match_ids)))
if len(all_match_ids) > 0:
if "modcosine" in include_scores:
# Get cosine score for found matches
cosine_similarity = CosineGreedy(tolerance=cosine_tol)
cosine_scores = []
for match_id in library_ids[all_match_ids]:
cosine_scores.append(
cosine_similarity.matrix(
documents_library[match_id]._obj,
documents_query[i]._obj))
else:
cosine_scores = len(all_match_ids) * ["not calculated"]
if "cosine" in include_scores:
# Get modified cosine score for found matches
mod_cosine_similarity = ModifiedCosine(tolerance=cosine_tol)
mod_cosine_scores = []
for match_id in library_ids[all_match_ids]:
mod_cosine_scores.append(
mod_cosine_similarity.matrix(
documents_library[match_id]._obj,
documents_query[i]._obj))
else:
mod_cosine_scores = len(all_match_ids) * ["not calculated"]
matches_df = pd.DataFrame(
{
"cosine_score": [x[0] for x in cosine_scores],
"cosine_matches": [x[1] for x in cosine_scores],
"mod_cosine_score": [x[0] for x in mod_cosine_scores],
"mod_cosine_matches": [x[1] for x in mod_cosine_scores]
},
index=library_ids[all_match_ids])
if m_mass_matches is not None:
matches_df["mass_match"] = m_mass_matches[all_match_ids, i]
if m_spec2vec_similarities is not None:
matches_df["s2v_score"] = m_spec2vec_similarities[
all_match_ids, i]
elif "spec2vec" in include_scores:
spec2vec_similarity = Spec2Vec(
model=model,
intensity_weighting_power=intensity_weighting_power,
allowed_missing_percentage=allowed_missing_percentage)
spec2vec_scores = []
for match_id in library_ids[all_match_ids]:
spec2vec_scores.append(
spec2vec_similarity.pair(documents_library[match_id],
documents_query[i]))
matches_df["s2v_score"] = spec2vec_scores
found_matches.append(matches_df.fillna(0))
else:
found_matches.append([])
return found_matches