Make sure charge isn't 0 during peak annotation

Fixes #11.
bittremieux · Jul 2, 2020 · 7ecb4d0 · 7ecb4d0
1 parent 0ab2989
commit 7ecb4d0
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/spectrum_utils/spectrum.py b/spectrum_utils/spectrum.py
@@ -1037,7 +1037,7 @@ def annotate_peptide_fragments(self, fragment_tol_mass: float,
         if self.peptide is None:
             raise ValueError('No peptide sequence available for the spectrum')
         if max_ion_charge is None:
-            max_ion_charge = self.precursor_charge - 1
+            max_ion_charge = max(1, self.precursor_charge - 1)
 
         theoretical_fragments = _get_theoretical_peptide_fragments(
             self.peptide, self.modifications, ion_types, max_ion_charge)

diff --git a/spectrum_utils/tests/spectrum_test.py b/spectrum_utils/tests/spectrum_test.py
@@ -646,18 +646,17 @@ def test_annotate_peptide_fragments():
     fragment_tol_mode = 'Da'
     peptides = ['SYELPDGQVITIGNER', 'MFLSFPTTK', 'DLYANTVLSGGTTMYPGIADR',
                 'YLYEIAR', 'VAPEEHPVLLTEAPLNPK']
-    for peptide in peptides:
+    for charge, peptide in enumerate(peptides, 1):
         fragment_mz = np.asarray([fragment.calc_mz for fragment in
                                   spectrum._get_theoretical_peptide_fragments(
-                                      peptide)])
+                                      peptide, max_charge=charge - 1)])
         fragment_mz += np.random.uniform(
             -0.9 * fragment_tol_mass, 0.9 * fragment_tol_mass,
             len(fragment_mz))
         num_peaks = 150
         mz = np.random.uniform(100, 1400, num_peaks)
         mz[: len(fragment_mz)] = fragment_mz
         intensity = np.random.lognormal(0, 1, num_peaks)
-        charge = 2
         spec = spectrum.MsmsSpectrum(
             'test_spectrum', mass.calculate_mass(sequence=peptide,
                                                  charge=charge),