def test_wrong_length(multi_mol_system_irregular, sequence):
"""
Many molecule and a sequence that has the wrong length raises an error.
"""
processor = dssp.AnnotateResidues('test', sequence)
with pytest.raises(ValueError):
processor.run_system(multi_mol_system_irregular)
def test_empty_system_error():
"""
There are no molecules, but there is a sequence. Should raise an error.
"""
system = vermouth.system.System()
sequence = 'not empty'
processor = dssp.AnnotateResidues('test', sequence)
with pytest.raises(ValueError):
processor.run_system(system)
def test_multi_molecules_cycle_one(self, multi_mol_system_irregular):
"""
Many molecules and a one element sequence to repeat.
"""
sequence = 'A'
expected = [sequence] * (15 * 3)
processor = dssp.AnnotateResidues('test', sequence)
processor.run_system(multi_mol_system_irregular)
found = self.sequence_from_system(multi_mol_system_irregular, 'test')
assert found == expected
def test_run_molecule(self, single_mol_system):
"""
The `run_molecule` method works.
"""
sequence = 'ABCDE'
expected = list(
itertools.chain(*([element] * 3 for element in sequence)))
processor = dssp.AnnotateResidues('test', sequence)
processor.run_molecule(single_mol_system.molecules[0])
found = self.sequence_from_system(single_mol_system, 'test')
assert found == expected
def test_empty_with_filter(multi_mol_system_irregular):
"""
There is a sequence, but no molecule are accepted by the molecule
selector. Should raise an error.
"""
sequence = 'not empty'
processor = dssp.AnnotateResidues('test',
sequence,
molecule_selector=lambda mol: False)
with pytest.raises(ValueError):
processor.run_system(multi_mol_system_irregular)
def test_empty_system_empty_sequence():
"""
There are no molecules, but the sequence is empty.
"""
system = vermouth.system.System()
sequence = ''
processor = dssp.AnnotateResidues('test', sequence)
try:
processor.run_system(system)
except ValueError:
pytest.fail('Should not have raised a ValueError.')
def test_single_molecules_cycle_one(self, single_mol_system):
"""
One molecule and a one element sequence to repeat over all residues of
the molecule.
"""
sequence = 'A'
expected = [sequence] * (5 * 3)
processor = dssp.AnnotateResidues('test', sequence)
processor.run_system(single_mol_system)
found = self.sequence_from_system(single_mol_system, 'test')
assert found == expected
def test_single_molecule(self, single_mol_system, sequence):
"""
The simple case with a single molecule and a sequence of the right size
works as expected.
"""
expected = list(
itertools.chain(*([element] * 3 for element in sequence)))
processor = dssp.AnnotateResidues('test', sequence)
processor.run_system(single_mol_system)
found = self.sequence_from_system(single_mol_system, 'test')
assert found == expected
def test_run_molecule_not_selected(self, single_mol_system):
"""
The molecule selector works with `run_molecule`.
"""
sequence = 'ABCDE'
processor = dssp.AnnotateResidues('test',
sequence,
molecule_selector=lambda mol: False)
processor.run_molecule(single_mol_system.molecules[0])
found = self.sequence_from_system(single_mol_system, 'test')
assert vermouth.utils.are_all_equal(found)
assert found[0] is None
def test_multi_molecules_cycle(self, multi_mol_system_regular, sequence):
"""
The case with multiple molecules with all the same size and one
sequence to repeat for each molecule works as expected.
"""
expected = list(
itertools.chain(*([element] * 3 for element in sequence)))
expected = expected * 3
processor = dssp.AnnotateResidues('test', sequence)
processor.run_system(multi_mol_system_regular)
found = self.sequence_from_system(multi_mol_system_regular, 'test')
assert found == expected
def test_multi_molecules_diff_sizes(self, multi_mol_system_irregular,
sequence):
"""
The case of many protein of various sizes and a sequence of the right
size works as expected.
"""
expected = list(
itertools.chain(*([element] * 3 for element in sequence)))
processor = dssp.AnnotateResidues('test', sequence)
processor.run_system(multi_mol_system_irregular)
found = self.sequence_from_system(multi_mol_system_irregular, 'test')
assert found == expected
def test_wrong_length_with_filter(multi_mol_system_irregular, sequence):
"""
Many molecules and a sequence that has the wrong length because of a
molecule selector.
"""
# We exclude the second molecule. The filter excludes it based on the
# number of nodes, which is 15 because it has 5 residues with 3 nodes
# each.
processor = dssp.AnnotateResidues(
'test', sequence,
molecule_selector=lambda mol: len(mol.nodes) != (5 * 3),
)
with pytest.raises(ValueError):
processor.run_system(multi_mol_system_irregular)
