def test_precursor_ion_calculated_correctly(): fragger = PeptideFragment0r('MK', charges=[1]) # no series, only precursor fragments = fragger.fragment_peptide(ion_series=[]) assert isinstance(fragments, DataFrame) assert len(fragments) == 1 row = fragments.iloc[0]
def test_fragment_three_aa_peptide_b_series(): """Test b3 fragmentation""" fragger = PeptideFragment0r('KKK', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['b']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 3 row = fragments.iloc[2] assert row['name'] == 'b3' assert row['cc'] == 'C(18)H(36)N(6)O(3)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 385.29216550997
def test_fragment_three_aa_peptide_a_series(): """Test a2 fragmentation""" fragger = PeptideFragment0r('MKK', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['a']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 3 row = fragments.iloc[1] assert row['name'] == 'a2' assert row['cc'] == 'C(10)H(21)N(3)O(1)S(1)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 232.14780994897004
def test_fragment_two_aa_peptide_b_series(): """Test b2 fragmentation""" fragger = PeptideFragment0r('KK', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['b']) assert isinstance(fragments, DataFrame) row = fragments.iloc[1] assert row['name'] == 'b2' assert row['cc'] == 'C(12)H(24)N(4)O(2)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 257.19720249556997
def test_fragment_two_aa_peptide_a_series(): """Test a1 fragmentation""" fragger = PeptideFragment0r('MK', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['a']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 2 row = fragments.iloc[0] assert row['name'] == 'a1' assert row['cc'] == 'C(4)H(9)N(1)S(1)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 104.05284693456998
def test_fragment_three_aa_peptide_x_series(): """Test x2 fragmentation""" fragger = PeptideFragment0r('MKK', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['x']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 3 row = fragments.iloc[1] assert row['name'] == 'x2' assert row['cc'] == 'C(13)H(24)N(4)O(4)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 301.18708
def test_fragment_two_aa_peptide_b_series_with_mod(): """Test y2 fragmentation""" fragger = PeptideFragment0r('MKK#Oxidation:1', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['b']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 3 row = fragments.iloc[1] assert row['name'] == 'b2' assert row['cc'] == 'C(11)H(21)N(3)O(3)S(1)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 276.1376
def test_fragment_three_aa_peptide_z_series(): """Test z2 fragmentation""" fragger = PeptideFragment0r('MKK', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['z']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 3 row = fragments.iloc[1] assert row['name'] == 'z2' # assert row['cc'] == 'C(11)H(24)N(4)O(2)S(1)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 258.18236
def test_fragment_two_aa_peptide_y_series(): """Test y2 fragmentation""" fragger = PeptideFragment0r('KK', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['y']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 2 row = fragments.iloc[1] assert row['name'] == 'y2' assert row['cc'] == 'C(12)H(26)N(4)O(3)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 274.2004907132)
def test_fragment_one_aa_peptide_y_series(): """Test y1 fragmentation""" fragger = PeptideFragment0r('K', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['y']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 1 row = fragments.iloc[0] assert row['name'] == 'y1' assert row['cc'] == 'C(6)H(14)N(2)O(2)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 147.11280646
def test_fragment_three_aa_peptide_c_series(): """Test c1/2 fragmentation""" fragger = PeptideFragment0r('MKK', charges=[1]) fragments = fragger.fragment_peptide(ion_series=['c']) assert isinstance(fragments, DataFrame) # assert len(fragments) == 3 row = fragments.iloc[0] assert row['name'] == 'c1' assert row['cc'] == 'C(5)H(12)N(2)O(1)S(1)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 149.07436 row = fragments.iloc[1] assert row['name'] == 'c2' assert row['cc'] == 'C(11)H(24)N(4)O(2)S(1)' assert row['charge'] == 1 assert pytest.approx(row['mz'], 5e-6) == 277.16932
def test_fragment_one_aa_peptide_internal(): fragments = PeptideFragment0r('RKKR', charges=[1], ions=['I']).df # fragments = fragger.fragment_peptide(ion_series=['internal b-y']) assert isinstance(fragments, DataFrame) print(fragments)
def __init__(self, *args, **kwargs): """Summary.""" logger.info("Initialize PeptideFragmentor") self.args = args self.kwargs = kwargs self.fragger = PeptideFragment0r()