Simplify cosine computation

[hubernhard]

Hi Nicolas,

while going through your code, I noticed that the cosine computation in _compare_spectra() can be simplified, as the if dm == 0. statement is not needed since all possible cases are already handled in the else part:

libmetgem/libmetgem/cosine.py

Lines 34 to 47 in 6281ffc

	if dm == 0.:
	for i in range(spectrum1_data.shape[0]):
	for j in range(spectrum2_data.shape[0]):
	diff = spectrum2_data[j, MZ] - spectrum1_data[i, MZ]
	if abs(diff) <= mz_tolerance:
	scores.append((spectrum1_data[i, INTENSITY] * spectrum2_data[j, INTENSITY], i, j, SpectraMatchState.fragment))
	else:
	for i in range(spectrum1_data.shape[0]):
	for j in range(spectrum2_data.shape[0]):
	diff = spectrum2_data[j, MZ] - spectrum1_data[i, MZ]
	if abs(diff) <= mz_tolerance:
	scores.append((spectrum1_data[i, INTENSITY] * spectrum2_data[j, INTENSITY], i, j, SpectraMatchState.fragment))
	elif abs(diff + dm) <= mz_tolerance:
	scores.append((spectrum1_data[i, INTENSITY] * spectrum2_data[j, INTENSITY], i, j, SpectraMatchState.neutral_loss))

And as it took me some time to figure out how the neutral loss computation actually works, I added a commet that explains the derivation in more detail.

And by the way, thank you for your work on MetGem! It really helps a lot.

Best regards,
Bernhard