def test_peptide_unmodified(self):
# check that the total mass, mz and composition is correct
pep = peptide.Peptide('LIGPTSVVMGR')
self.assertAlmostEqual(pep.mass, 1128.63251433)
self.assertEqual(pep._getComposition(), {
'H': 86,
'C': 49,
'S': 1,
'O': 13,
'N': 14
})
self.assertAlmostEqual(pep.getMZ(1), 1129.63979083)
def test_peptide_with_modifications(self):
# check that the total mass, mz and composition is correct
# pep = peptide.Peptide('LIGPTSVVMGR', modifications={ 9: self.mods.mods_TPPcode['R[166]'] }) #M[147]
pep = peptide.Peptide('LIGPTSVVMGR',
modifications={
9: self.mods.mods_TPPcode['M[147]']
}) #M[147]
self.assertAlmostEqual(pep.mass, 1144.62742895)
self.assertEqual(pep._getComposition(), {
'H': 86,
'C': 49,
'S': 1,
'O': 14,
'N': 14
})
self.assertAlmostEqual(pep.getMZ(1), 1145.63470545)
def setUp(self):
self.mods = modifications.Modifications()
self.phospho = self.mods.mods_unimods[21]
self.oxi = self.mods.mods_unimods[35]
self.mypep = peptide.Peptide('LIGPTSVVMGR',
modifications={
9: self.mods.mods_TPPcode['M[147]']
}) #M[147]
self.mypep2 = peptide.Peptide('LIGPTSVVMGR')
self.mypep3 = peptide.Peptide('ELVISLIVESS',
modifications={
5: self.phospho,
10: self.phospho
})
self.isoform1 = peptide.Peptide('ELVISLIVESS',
modifications={
5: self.phospho,
11: self.phospho
})
self.isoform2 = peptide.Peptide('ELVISLIVESS',
modifications={
10: self.phospho,
11: self.phospho
})
self.mypep4 = peptide.Peptide('MHGGTGFAGIDSSSPEVK',
modifications={
1: self.oxi,
5: self.phospho
})
self.isoform4_1 = peptide.Peptide('MHGGTGFAGIDSSSPEVK',
modifications={
1: self.oxi,
5: self.phospho
})
self.isoform4_2 = peptide.Peptide('MHGGTGFAGIDSSSPEVK',
modifications={
1: self.oxi,
12: self.phospho
})
self.isoform4_3 = peptide.Peptide('MHGGTGFAGIDSSSPEVK',
modifications={
1: self.oxi,
13: self.phospho
})
self.isoform4_4 = peptide.Peptide('MHGGTGFAGIDSSSPEVK',
modifications={
1: self.oxi,
14: self.phospho
})
self.notisoform4 = peptide.Peptide('MHGGTGFAGIDSSSPEVK',
modifications={14: self.phospho})
def test_peptide_with_modifications_2(self):
mypep = peptide.Peptide('LMGPTSVVMGR',
modifications={
9: self.mods.mods_TPPcode['M[147]'],
2: self.mods.mods_TPPcode['M[147]']
}) #M[147]
def test_create_peptide(self):
p = peptide.Peptide('PEPTIDE')