def fail_test(self):
cc = pyqms.ChemicalComposition()
failing_sequence_list = ['#Oxidation_w/o_pos', '#Oxidation_with_pos:1']
for failing_sequence in failing_sequence_list:
with self.assertRaises(SystemExit) as system_exit_check:
cc._parse_sequence_unimod_style(failing_sequence)
self.assertEqual(system_exit_check.exception.code, 1)
cc.clear()
cc._parse_sequence_unimod_style('#;')
assert len(cc.keys()) == 0
return
def check_unimod_pep_input(test_dict):
if 'aa_compositions' not in test_dict.keys():
test_dict['aa_compositions'] = pyqms.knowledge_base.aa_compositions
cc = pyqms.ChemicalComposition(
test_dict['input'], aa_compositions=test_dict['aa_compositions'])
print('hill:', cc.hill_notation_unimod())
print(cc.composition_of_aa_at_pos)
print(cc.composition_of_mod_at_pos)
assert cc.hill_notation_unimod() == test_dict['output']
if 'mod_pos_info' in test_dict.keys():
for mod_dict in test_dict['mod_pos_info']:
cc_mods = cc.composition_of_mod_at_pos.get(mod_dict['pos'], None)
assert cc_mods == mod_dict['cc_mods']
if 'aa_pos_info' in test_dict.keys():
for aa_dict in test_dict['aa_pos_info']:
cc_aa = cc.composition_of_aa_at_pos.get(aa_dict['pos'], None)
assert cc_aa == aa_dict['cc_mods']
def check_unimod_pep_input(test_dict):
if "aa_compositions" not in test_dict.keys():
test_dict["aa_compositions"] = pyqms.knowledge_base.aa_compositions
cc = pyqms.ChemicalComposition(
test_dict["input"], aa_compositions=test_dict["aa_compositions"])
print("hill:", cc.hill_notation_unimod())
print(cc.composition_of_aa_at_pos)
print(cc.composition_of_mod_at_pos)
assert cc.hill_notation_unimod() == test_dict["output"]
if "mod_pos_info" in test_dict.keys():
for mod_dict in test_dict["mod_pos_info"]:
cc_mods = cc.composition_of_mod_at_pos.get(mod_dict["pos"], None)
assert cc_mods == mod_dict["cc_mods"]
if "aa_pos_info" in test_dict.keys():
for aa_dict in test_dict["aa_pos_info"]:
cc_aa = cc.composition_of_aa_at_pos.get(aa_dict["pos"], None)
assert cc_aa == aa_dict["cc_mods"]
def setUp(self):
self.lib = pyqms.ChemicalComposition()
self.water1 = pyqms.ChemicalComposition('+H2O')
self.water_unimod_style_chemical_formula = pyqms.ChemicalComposition(
'+H(2)16O(1)')
def generate_cc_test(self):
cc = pyqms.ChemicalComposition('+H2O')
cc_returned = cc.generate_cc_dict()
assert len(cc_returned.keys()) == 2
return
def test__mass_with_cc_even_though_you_should_not_use_it(self):
cc = pyqms.ChemicalComposition('+H2O')
self.assertAlmostEqual(cc._mass(cc=cc), 18.0105646844)
def test_clear_removes_everything(self):
cc = pyqms.ChemicalComposition('KLEINERTEST')
cc.clear()
self.assertEqual(str(cc), '')
def test_add_chemical_formulas(self):
water1 = pyqms.ChemicalComposition('+H2O')
water2 = pyqms.ChemicalComposition('+H2O')
two_waters = water1 + water2
self.assertEqual(two_waters.hill_notation(), 'H4O2')
def check_hill_notation(aa, chemformula):
cc = pyqms.ChemicalComposition(aa)
cc.subtract_chemical_formula('H2O')
print(aa, chemformula)
print(cc)
assert cc.hill_notation() == chemformula
def test__mass_with_heavy_isotopes_TMT6Plex_example(self):
cc = pyqms.ChemicalComposition('#TMT6plex:0')
self.assertAlmostEqual(cc._mass(cc=cc), 229.162932, 6)