# Source code for matchms.similarity.ModifiedCosine

```import logging
from typing import Tuple
import numpy as np
from matchms.filtering.add_precursor_mz import _convert_precursor_mz
from matchms.typing import SpectrumType
from .BaseSimilarity import BaseSimilarity
from .spectrum_similarity_functions import (collect_peak_pairs,
score_best_matches)

logger = logging.getLogger("matchms")

[docs]class ModifiedCosine(BaseSimilarity):
"""Calculate 'modified cosine score' between mass spectra.

The modified cosine score aims at quantifying the similarity between two
mass spectra. The score is calculated by finding best possible matches between
peaks of two spectra. Two peaks are considered a potential match if their
m/z ratios lie within the given 'tolerance', or if their m/z ratios
lie within the tolerance once a mass-shift is applied. The mass shift is
simply the difference in precursor-m/z between the two spectra.
See Watrous et al. [PNAS, 2012, https://www.pnas.org/content/109/26/E1743]
for further details.

For example

.. testcode::

import numpy as np
from matchms import Spectrum
from matchms.similarity import ModifiedCosine

spectrum_1 = Spectrum(mz=np.array([100, 150, 200.]),
intensities=np.array([0.7, 0.2, 0.1]),
spectrum_2 = Spectrum(mz=np.array([104.9, 140, 190.]),
intensities=np.array([0.4, 0.2, 0.1]),

# Use factory to construct a similarity function
modified_cosine = ModifiedCosine(tolerance=0.2)

score = modified_cosine.pair(spectrum_1, spectrum_2)

print(f"Modified cosine score is {score['score']:.2f} with {score['matches']} matched peaks")

Should output

.. testoutput::

Modified cosine score is 0.83 with 1 matched peaks

"""
# Set key characteristics as class attributes
is_commutative = True
# Set output data type, e.g. ("score", "float") or [("score", "float"), ("matches", "int")]
score_datatype = [("score", np.float64), ("matches", "int")]

[docs]    def __init__(self, tolerance: float = 0.1, mz_power: float = 0.0,
intensity_power: float = 1.0):
"""
Parameters
----------
tolerance:
Peaks will be considered a match when <= tolerance apart. Default is 0.1.
mz_power:
The power to raise mz to in the cosine function. The default is 0, in which
case the peak intensity products will not depend on the m/z ratios.
intensity_power:
The power to raise intensity to in the cosine function. The default is 1.
"""
self.tolerance = tolerance
self.mz_power = mz_power
self.intensity_power = intensity_power

[docs]    def pair(self, reference: SpectrumType, query: SpectrumType) -> Tuple[float, int]:
"""Calculate modified cosine score between two spectra.

Parameters
----------
reference
Single reference spectrum.
query
Single query spectrum.

Returns
-------

Tuple with cosine score and number of matched peaks.
"""
def get_valid_precursor_mz(spectrum):
"""Extract valid precursor_mz from spectrum if possible. If not raise exception."""
message_precursor_missing = \
"Precursor_mz missing. Apply 'add_precursor_mz' filter first."
message_precursor_no_number = \
"Precursor_mz must be of type int or float. Apply 'add_precursor_mz' filter first."
message_precursor_below_0 = "Expect precursor to be positive number." \
"Apply 'require_precursor_mz' first"

precursor_mz = spectrum.get("precursor_mz", None)
if not isinstance(precursor_mz, (int, float)):
logger.warning(message_precursor_no_number)
precursor_mz = _convert_precursor_mz(precursor_mz)
assert precursor_mz is not None, message_precursor_missing
assert precursor_mz > 0, message_precursor_below_0
return precursor_mz

def get_matching_pairs():
"""Find all pairs of peaks that match within the given tolerance."""
zero_pairs = collect_peak_pairs(spec1, spec2, self.tolerance, shift=0.0,
mz_power=self.mz_power,
intensity_power=self.intensity_power)
precursor_mz_ref = get_valid_precursor_mz(reference)
precursor_mz_query = get_valid_precursor_mz(query)

mass_shift = precursor_mz_ref - precursor_mz_query
nonzero_pairs = collect_peak_pairs(spec1, spec2, self.tolerance, shift=mass_shift,
mz_power=self.mz_power,
intensity_power=self.intensity_power)

if zero_pairs is None:
zero_pairs = np.zeros((0, 3))
if nonzero_pairs is None:
nonzero_pairs = np.zeros((0, 3))
matching_pairs = np.concatenate((zero_pairs, nonzero_pairs), axis=0)
if matching_pairs.shape[0] > 0:
matching_pairs = matching_pairs[np.argsort(matching_pairs[:, 2])[::-1], :]
return matching_pairs

spec1 = reference.peaks.to_numpy
spec2 = query.peaks.to_numpy
matching_pairs = get_matching_pairs()
if matching_pairs.shape[0] == 0:
return np.asarray((float(0), 0), dtype=self.score_datatype)
score = score_best_matches(matching_pairs, spec1, spec2,
self.mz_power, self.intensity_power)
return np.asarray(score, dtype=self.score_datatype)
```