def test_can_handle_all_residues(self):
content = 'ALA CYS ASP GLU PHE GLY HIE ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR'
result = parse.get_sequence_from_AA3(contents=content)
self.assertEqual(
result,
'NALA CYS ASP GLU PHE GLY HIE ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP CTYR'
)
def test_can_handle_all_residues(self):
content = "ALA CYS ASP GLU PHE GLY HIE ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR"
result = parse.get_sequence_from_AA3(content=content)
self.assertEqual(
result,
"NALA CYS ASP GLU PHE GLY HIE ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP CTYR",
)
def test_raises_error_on_bad_residue(self):
content = 'ALA XXX ALA'
with self.assertRaises(RuntimeError):
parse.get_sequence_from_AA3(contents=content)
def test_can_handle_alternate_protonation_states(self):
content = 'ALA ASH GLH LYN HIE HIP HID ALA'
result = parse.get_sequence_from_AA3(contents=content)
self.assertEqual(result, 'NALA ASH GLH LYN HIE HIP HID CALA')
def test_can_handle_comment(self):
content = 'ALA ALA\n#comment\nALA ALA\n'
result = parse.get_sequence_from_AA3(contents=content)
self.assertEqual(result, 'NALA ALA ALA CALA')
def test_can_parse_simple_sequence(self):
content = 'ALA ALA ALA ALA'
result = parse.get_sequence_from_AA3(contents=content)
self.assertEqual(result, 'NALA ALA ALA CALA')
def test_raises_error_on_bad_residue(self):
content = 'ALA XXX ALA'
with self.assertRaises(RuntimeError):
parse.get_sequence_from_AA3(contents=content)
def test_can_handle_alternate_protonation_states(self):
content = 'ALA ASH GLH LYN HIE HIP HID ALA'
result = parse.get_sequence_from_AA3(contents=content)
self.assertEqual(result, 'NALA ASH GLH LYN HIE HIP HID CALA')
def test_can_handle_comment(self):
content = 'ALA ALA\n#comment\nALA ALA\n'
result = parse.get_sequence_from_AA3(contents=content)
self.assertEqual(result, 'NALA ALA ALA CALA')
def test_can_parse_simple_sequence(self):
content = 'ALA ALA ALA ALA'
result = parse.get_sequence_from_AA3(contents=content)
self.assertEqual(result, 'NALA ALA ALA CALA')
