def test_with_set_not_matching_set_number_regex(self, mock_pfunc,
mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
user_mod = ['Set blah:2:3:4']
with self.assertRaises(ValueError):
flips.parse_flips(user_mod)
def test_unparseable_score(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
user_mod = ['Single : A 89 SER OG : rot 180:bad score section']
with self.assertRaises(ValueError):
flips.parse_flips(user_mod)
def test_unparseable_score(self, mock_pfunc, mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
user_mod = ['Single : A 89 SER OG : rot 180:bad score section']
with self.assertRaises(ValueError):
flips.parse_flips(user_mod)
def test_user_mod_with_too_many_sections(self, mock_pfunc,
mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
user_mod = ['Set:2:3:4:5']
with self.assertRaises(ValueError):
flips.parse_flips(user_mod)
def test_single_other_calls_parse_other_score(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_other_score.return_value = [1, 2]
user_mod = ['Single : A 89 SER OG : rot 180:sc= 0']
flips.parse_flips(user_mod)
assert mock_parse_other_score.called
def test_single_canflip_calls_parse_canflip_score(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_canflip_score.return_value = [1, 2, 3, 4, 5, 6, 7]
user_mod = ['Single : A 41 ASN :FLIP amide:sc= -0.0583 X(o=-0.064,f=-0.058)']
flips.parse_flips(user_mod)
assert mock_parse_canflip_score.called
def test_single_methyl_calls_parse_methyl_score(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_methyl_score.return_value = [1, 2, 3, 4]
user_mod = ['Single : A 57 LYS NZ :NH3+ 180:sc= 0 (180deg=0)']
flips.parse_flips(user_mod)
assert mock_parse_methyl_score.called
def test_single_other_calls_parse_other_score(self, mock_pfunc,
mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_other_score.return_value = [1, 2]
user_mod = ['Single : A 89 SER OG : rot 180:sc= 0']
flips.parse_flips(user_mod)
assert mock_parse_other_score.called
def test_single_canflip_calls_parse_canflip_score(self, mock_pfunc,
mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_canflip_score.return_value = [1, 2, 3, 4, 5, 6, 7]
user_mod = [
'Single : A 41 ASN :FLIP amide:sc= -0.0583 X(o=-0.064,f=-0.058)'
]
flips.parse_flips(user_mod)
assert mock_parse_canflip_score.called
def test_single_methyl_calls_parse_methyl_score(self, mock_pfunc,
mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_methyl_score.return_value = [1, 2, 3, 4]
user_mod = [
'Single : A 57 LYS NZ :NH3+ 180:sc= 0 (180deg=0)'
]
flips.parse_flips(user_mod)
assert mock_parse_methyl_score.called
def test_calls_parse_func_group(self, mock_pfunc, mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_canflip_score.return_value = [1, 2, 3, 4, 5, 6, 7]
user_mod = self.single
res = flips.parse_flips(user_mod)
mock_pfunc.assert_called_once_with(' A 41 ASN ')
def test_calls_parse_func_group(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_canflip_score.return_value = [1, 2, 3, 4, 5, 6, 7]
user_mod = self.single
res = flips.parse_flips(user_mod)
mock_pfunc.assert_called_once_with(' A 41 ASN ')
def test_with_non_single_non_set(self, mock_pfunc, mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
'''Parsing USER MOD with no flip lines should return an empty list.'''
user_mod = ['blah'] # not Set or Single
res = flips.parse_flips(user_mod)
mock_pfunc.assert_not_called()
mock_parse_methyl_score.assert_not_called()
mock_parse_canflip_score.assert_not_called()
mock_parse_other_score.assert_not_called()
self.assertEqual(res, [])
def test_with_non_single_non_set(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
'''Parsing USER MOD with no flip lines should return an empty list.'''
user_mod = ['blah'] # not Set or Single
res = flips.parse_flips(user_mod)
mock_pfunc.assert_not_called()
mock_parse_methyl_score.assert_not_called()
mock_parse_canflip_score.assert_not_called()
mock_parse_other_score.assert_not_called()
self.assertEqual(res, [])
def test_with_single(self, mock_pfunc, mock_parse_methyl_score,
mock_parse_canflip_score, mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_canflip_score.return_value = [1, 2, 3, 4, 5, 6, 7]
user_mod = self.single
res = flips.parse_flips(user_mod)
assert type(res) is list
assert len(res) == 1
f = res[0]
assert f.flip_class == 'single'
assert f.set is None
assert f.set_index is None
def test_sets_flip_func_group_info(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = ['A', '100B', 'THR', 'OG1', '']
mock_parse_canflip_score.return_value = [1, 2, 3, 4, 5, 6, 7]
user_mod = self.single
res = flips.parse_flips(user_mod)
f = res[0]
assert f.chain == 'A'
assert f.resi == '100B'
assert f.resn == 'THR'
assert f.name == 'OG1'
assert f.alt == ''
def test_with_single(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = [1, 2, 3, 4, 5]
mock_parse_canflip_score.return_value = [1, 2, 3, 4, 5, 6, 7]
user_mod = self.single
res = flips.parse_flips(user_mod)
assert type(res) is list
assert len(res) == 1
f = res[0]
assert f.flip_class == 'single'
assert f.set is None
assert f.set_index is None
def test_sets_flip_func_group_info(self, mock_pfunc,
mock_parse_methyl_score,
mock_parse_canflip_score,
mock_parse_other_score):
mock_pfunc.return_value = ['A', '100B', 'THR', 'OG1', '']
mock_parse_canflip_score.return_value = [1, 2, 3, 4, 5, 6, 7]
user_mod = self.single
res = flips.parse_flips(user_mod)
f = res[0]
assert f.chain == 'A'
assert f.resi == '100B'
assert f.resn == 'THR'
assert f.name == 'OG1'
assert f.alt == ''
def test_user_mod_with_too_many_sections(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
user_mod = ['Set:2:3:4:5']
with self.assertRaises(ValueError):
flips.parse_flips(user_mod)
def test_with_set_not_matching_set_number_regex(self, mock_pfunc,
mock_parse_methyl_score, mock_parse_canflip_score,
mock_parse_other_score):
user_mod = ['Set blah:2:3:4']
with self.assertRaises(ValueError):
flips.parse_flips(user_mod)