def test_peptides_not_equal_mods(self):
peptide = Peptide('ATSMPLK', 2, [
ModSite(23.01, 'nterm', 'testmod'),
ModSite(19.24, 2, 'testmod2')
])
peptide2 = Peptide('ATSMPLK', 3, [ModSite(23.01, 'nterm', 'testmod')])
self.assertNotEqual(peptide, peptide2)
def test_custom_ion_types(self):
peptide = Peptide('AAA', 2, [])
peptide.fragment(ion_types={IonType.b: []})
self.assertIsNotNone(peptide.fragment_ions)
self.assertTrue(
all(ion.startswith('b') for _, ion, _ in peptide.fragment_ions))
def test_b_ions(self):
peptide = Peptide('AFCWK', 1, [])
peptide.fragment(ion_types={IonType.b: []})
expected = {
'b1[+]': 72.0444,
'b2[+]': 219.1128,
'b3[+]': 322.1220,
'b4[+]': 508.2013,
}
self._test_ions(expected, ions_to_dict(peptide.fragment_ions))
def test_a_ions(self):
peptide = Peptide('AFCWK', 1, [])
peptide.fragment(ion_types={IonType.a: []})
expected = {
'a1[+]': 44.0495,
'a2[+]': 191.1179,
'a3[+]': 294.1271,
'a4[+]': 480.2064,
}
self._test_ions(expected, ions_to_dict(peptide.fragment_ions))
def test_x_ions(self):
peptide = Peptide('AFCWK', 1, [])
peptide.fragment(ion_types={IonType.x: []})
expected = {
'x1[+]': 173.0921,
'x2[+]': 359.1714,
'x3[+]': 462.1806,
'x4[+]': 609.2490,
}
self._test_ions(expected, ions_to_dict(peptide.fragment_ions))
def test_z_ions(self):
peptide = Peptide('AFCWK', 1, [])
peptide.fragment(ion_types={IonType.z: []})
expected = {
'z1[+]': 131.0941,
'z2[+]': 317.1734,
'z3[+]': 420.1826,
'z4[+]': 567.2510,
}
self._test_ions(expected, ions_to_dict(peptide.fragment_ions))
def test_peptides_equal_hash(self):
peptide = Peptide('ATSMPLK', 2, [
ModSite(23.01, 'nterm', 'testmod'),
ModSite(19.24, 2, 'testmod2')
])
peptide2 = Peptide('ATSMPLK', 2, [
ModSite(23.01, 'nterm', 'testmod'),
ModSite(19.24, 2, 'testmod2')
])
self.assertEqual(hash(peptide), hash(peptide2))
def test_c_ions(self):
peptide = Peptide('AFCWK', 1, [])
peptide.fragment(ion_types={IonType.c: []})
expected = {
'c1[+]': 89.0709,
'c2[+]': 236.1394,
'c3[+]': 339.1485,
'c4[+]': 525.2279,
}
self._test_ions(expected, ions_to_dict(peptide.fragment_ions))
def test_y_ions(self):
peptide = Peptide('AFCWK', 1, [])
peptide.fragment(ion_types={IonType.y: []})
expected = {
'y1[+]': 147.1128,
'y2[+]': 333.1921,
'y3[+]': 436.2013,
'y4[+]': 583.2697,
}
self._test_ions(expected, ions_to_dict(peptide.fragment_ions))
def test_all_ion_types(self):
peptide = Peptide('AAAMLPK', 2, [])
peptide.fragment(
ion_types={
IonType.b: [],
IonType.y: [],
IonType.a: [],
IonType.c: [],
IonType.z: [],
IonType.precursor: [],
IonType.imm: []
})
self.assertIsNotNone(peptide.fragment_ions)
def test_radical(self):
peptide = Peptide('AAA', 2, [], radical=True)
peptide.fragment(
ion_types={
IonType.b: [],
IonType.y: [],
IonType.a: [],
IonType.c: [],
IonType.z: [],
IonType.precursor: [],
IonType.imm: []
})
self.assertIsNotNone(peptide.fragment_ions)
def test_mod_site_out_of_range(self):
"""
Tests behaviour when a modification has a site beyond the peptide's
length.
"""
peptide = Peptide('ALPK', 2, [ModSite(1000., 100, 'TestMod')])
self.assertAlmostEqual(427.28, peptide.mass, 2)
def test_invalid_residue(self):
"""
Tests that invalid residues result in a KeyError.
"""
peptide = Peptide('AUA', 2, [])
with self.assertRaisesRegex(KeyError, r'Invalid residue detected: U'):
mass = peptide.mass
def test_peptide_mass_mono_cterm_mod(self):
"""
Tests that the calculated mono mass (with a C-terminal modification)
is correct.
"""
peptide = Peptide('AAA', 2, [ModSite(21.981943, 'cterm', 'Cation:Na')])
self.assertAlmostEqual(253.10, peptide.mass, 2)
self.assertAlmostEqual(127.56, peptide.mz, 2)
def test_peptide_mass_mono_nterm_mod(self):
"""
Tests that the calculated mono mass (with an N-terminal modification)
is correct.
"""
peptide = Peptide('AAA', 2,
[ModSite(304.20536, 'nterm', 'iTRAQ8plex')])
self.assertAlmostEqual(535.33, peptide.mass, 2)
self.assertAlmostEqual(268.67, peptide.mz, 2)
def test_neutral_losses(self):
peptide = Peptide('AAAK', 2, [])
peptide.fragment(
ion_types={
IonType.b: ['NH3', ('testLoss', 9.)],
IonType.precursor: ['CO2', ('testLoss2', 13.)],
IonType.imm: [('testLoss3', 2.04), 'H2O']
})
expected_ions = {(44.049475632459, 'imm(A)', 0),
(42.009475632459, '[imm1-testLoss3][+]', 1),
(26.038910948429, '[imm1-H2O][+]', 1),
(42.009475632459, '[imm2-testLoss3][+]', 2),
(26.038910948429, '[imm2-H2O][+]', 2),
(42.009475632459, '[imm3-testLoss3][+]', 3),
(26.038910948429, '[imm3-H2O][+]', 3),
(101.107324862499, 'imm(K)', 0),
(72.044390252029, 'b1[+]', 1),
(55.01784115090901, '[b1-NH3][+]', 1),
(63.044390252029004, '[b1-testLoss][+]', 1),
(143.081504037179, 'b2[+]', 2),
(126.054954936059, '[b2-NH3][+]', 2),
(134.081504037179, '[b2-testLoss][+]', 2),
(214.118617822329, 'b3[+]', 3),
(197.09206872120902, '[b3-NH3][+]', 3),
(205.118617822329, '[b3-testLoss][+]', 3),
(107.56294714460401, 'b3[2+]', 3),
(99.04967259404401, '[b3-NH3][2+]', 3),
(103.06294714460401, '[b3-testLoss][2+]', 3),
(99.06732486249899, '[imm4-testLoss3][+]', 4),
(83.096760178469, '[imm4-H2O][+]', 4),
(21.508376049669, '[imm3-testLoss3][2+]', 3),
(13.523093707653999, '[imm3-H2O][2+]', 3),
(360.22414552154896, '[M+H][+]', 4),
(316.234315521549, '[M-CO2][+]', 4),
(347.22414552154896, '[M-testLoss2][+]', 4),
(180.615710994214, '[M+H][2+]', 4),
(158.620795994214, '[M-CO2][2+]', 4),
(174.115710994214, '[M-testLoss2][2+]', 4),
(50.037300664689, '[imm4-testLoss3][2+]', 4),
(42.052018322674, '[imm4-H2O][2+]', 4)}
self.assertEqual(expected_ions, set(peptide.fragment_ions))
def test_peptide_repr(self):
peptide = Peptide('ATSMPLK', 2, [
ModSite(23.01, 'nterm', 'testmod'),
ModSite(19.24, 2, 'testmod2')
])
expected_repr = \
"<Peptide {'_seq': 'ATSMPLK', '_charge': 2, '_mods': " \
"[ModSite(mass=23.01, site='nterm', mod='testmod'), "\
"ModSite(mass=19.24, site=2, mod='testmod2')], 'mass_type': "\
"<MassType.mono: 0>, 'radical': False, 'fragment_ions': None}>"
self.assertEqual(expected_repr, repr(peptide))
def test_peptide_str(self):
peptide = Peptide('ATSMPLK', 2, [
ModSite(23.01, 'nterm', 'testmod'),
ModSite(19.24, 2, 'testmod2')
])
expected_str = \
"<Peptide {'seq': 'ATSMPLK', 'charge': 2, 'mods': " \
"[ModSite(mass=23.01, site='nterm', mod='testmod'), " \
"ModSite(mass=19.24, site=2, mod='testmod2')], 'mass_type': " \
"<MassType.mono: 0>, 'radical': False}>"
self.assertEqual(expected_str, str(peptide))
def test_peptide_multiple_mods(self):
"""
Tests that the calculated mono mass is correct for a peptide with many
modifications.
"""
peptide = Peptide('AYHGMLPWK', 3, [
ModSite(304.20536, 'nterm', 'iTRAQ8plex'),
ModSite(44.985078, 2, 'Nitro'),
ModSite(15.994915, 5, 'Oxidation'),
ModSite(15.994915, 7, 'Oxidation'),
ModSite(31.989829, 8, 'Dioxidation'),
ModSite(21.981943, 'cterm', 'Cation:Na')
])
self.assertAlmostEqual(1536.70, peptide.mass, 2)
self.assertAlmostEqual(513.24, peptide.mz, 2)
def test_basic_mod(self):
peptide = Peptide('AAYK', 2, [ModSite(1., 2, 'testmod')])
ions = peptide.fragment()
self.assertIsNotNone(ions)
def test_peptides_not_equal_non_instance(self):
peptide = Peptide('ATSMPLK', 2, [
ModSite(23.01, 'nterm', 'testmod'),
ModSite(19.24, 2, 'testmod2')
])
self.assertNotEqual(peptide, ('ATSMPLK', 2))
def test_basic_mod_numpy(self):
peptide = Peptide('AAYK', 2, [ModSite(1., np.int32(2), 'testmod')])
with self.assertRaisesRegex(
RuntimeError,
r'Modification site was not an integer or a string'):
peptide.fragment()
def test_fragment_invalidation(self):
peptide = Peptide('AAA', 2, [])
peptide.fragment()
self.assertIsNotNone(peptide.fragment_ions)
peptide.seq = 'AA'
self.assertIsNone(peptide.fragment_ions)
def test_unknown_string_neutral_loss(self):
peptide = Peptide('AAAK', 2, [])
with self.assertRaises(KeyError):
peptide.fragment(ion_types={IonType.b: ['test']})
def test_peptide_mass_avg_no_mods(self):
"""Tests that the calculated average mass is correct."""
peptide = Peptide('AAA', 2, [], mass_type=MassType.avg)
self.assertAlmostEqual(231.24, peptide.mass, 2)
self.assertAlmostEqual(116.63, peptide.mz, 2)
def test_invalid_residue(self):
peptide = Peptide('AUA', 2, [])
with self.assertRaisesRegex(KeyError, r'Invalid residue detected: U'):
peptide.fragment()
def test_basic(self):
peptide = Peptide('AAA', 2, [])
peptide.fragment()
self.assertIsNotNone(peptide.fragment_ions)
peptide.clean_fragment_ions()
self.assertIsNone(peptide.fragment_ions)
def test_basic_numpy(self):
peptide = Peptide('AAA', np.int32(2), [])
ions = peptide.fragment()
self.assertIsNotNone(ions)
def test_basic(self):
peptide = Peptide('AAA', 2, [])
ions = peptide.fragment()
self.assertIsNotNone(ions)
def test_peptide_mass_mono_no_mods(self):
"""Tests that the calculated mono mass is correct."""
peptide = Peptide('AAA', 2, [])
self.assertAlmostEqual(231.12, peptide.mass, 2)
self.assertAlmostEqual(116.57, peptide.mz, 2)