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()