class TestResidueAttributes:
from pyrolyse.core.residue import _read_attributes, _read_write_attributes
test_attributes = list(_read_attributes)
test_attributes.remove('carbohydrate_info')
test_write_attr = list(_read_write_attributes)
ros_pose = get_pose('PYTEST')
lys_res = ros_pose.residue(2)
# Lazy but gets the work done.
@pytest.mark.parametrize('attr', test_attributes)
def test_get_readonly_attributes(self, attr):
# Can we get every read-only attribute without error?
print(attr)
getattr(self.lys_res, attr)
@pytest.mark.parametrize('attr', test_attributes)
def test_set_readonly_attributes(self, attr):
with pytest.raises(AttributeError):
setattr(self.lys_res, attr, None)
@pytest.mark.parametrize('attr', test_write_attr)
def test_get_readwrite_attributes(self, attr):
getattr(self.lys_res, attr)
@pytest.mark.parametrize('attr', test_write_attr)
def test_set_readwrite_attr(self, attr):
old_attr = getattr(self.lys_res, attr)
setattr(self.lys_res, attr, old_attr)
@pytest.mark.parametrize('attr', test_write_attr)
def test_set_readwrite_attr_wrong_type(self, attr):
wrong_type = None
with pytest.raises(TypeError):
setattr(self.lys_res, attr, wrong_type)
class TestPoseTorsionList:
pose = get_pose('PYTEST')
def test_get(self, get_torsion, set_torsion, torsion_list):
assert_array_equal(getattr(self.pose, torsion_list), [180.0] * 6)
@pytest.mark.parametrize('resid', list(range(-6, 6)))
def test_get_item_psis(self, get_torsion, set_torsion, torsion_list,
resid):
"""Test __getitem__ of parametrized TorsionList
Ex: say we test the first residue with attribute phis, the code would
be equivalent to:
>>> self.pose.set_psi(1, 0.)
>>> assert self.pose.psis[0] == self.pose.psi(1)
"""
if resid >= 0:
index = resid + 1
value = 0.
else:
index = self.pose.size + resid + 1
value = 33.
getattr(self.pose, set_torsion)(index, value)
assert (getattr(self.pose, torsion_list)[resid] == getattr(
self.pose, get_torsion)(index))
def test_get_slice_psis(self, get_torsion, set_torsion, torsion_list):
assert_array_equal(getattr(self.pose, torsion_list)[2:-1], [0.] * 3)
def test_set_psis(self, get_torsion, set_torsion, torsion_list):
setattr(self.pose, torsion_list, [60.] * 6)
for resid in range(1, self.pose.size):
assert getattr(self.pose, get_torsion)(resid) == 60.
@pytest.mark.parametrize('resid', list(range(-6, 6)))
def test_set_item_psis(self, get_torsion, set_torsion, torsion_list,
resid):
if resid >= 0:
index = resid + 1
value = -30.
else:
index = self.pose.size + resid + 1
value = -60.
getattr(self.pose, torsion_list)[resid] = value
assert getattr(self.pose, get_torsion)(index) == value
def test_set_range_psis(self, get_torsion, set_torsion, torsion_list):
getattr(self.pose, torsion_list)[2:-1] = [90.] * 3
for resid in range(3, 5):
assert getattr(self.pose, get_torsion)(resid) == 90.
assert_array_equal(getattr(self.pose, torsion_list),
[-30., -30., 90., 90., 90., -30.])
class TestPoseAttributes:
from pyrolyse.core.pose import _read_attributes
# Getting membrane_info returns an error as there is no membrane.
test_attributes = list(_read_attributes)
test_attributes.remove('membrane_info')
pose = get_pose('PYTEST')
# Lazy but gets the work done.
@pytest.mark.parametrize('attr', test_attributes)
def test_get_readonly_attributes(self, attr):
# Can we get every read-only attribute without error?
print(attr)
getattr(self.pose, attr)
@pytest.mark.parametrize('attr', test_attributes)
def test_set_readonly_attributes(self, attr):
with pytest.raises(AttributeError):
setattr(self.pose, attr, None)
@pytest.mark.parametrize('attr', ['fold_tree', 'pdb_info'])
def test_get_readwrite_attributes(self, attr):
getattr(self.pose, attr)
@pytest.mark.parametrize('attr', ['fold_tree', 'pdb_info'])
def test_set_readwrite_attr(self, attr):
old_attr = getattr(self.pose, attr)
setattr(self.pose, attr, old_attr)
@pytest.mark.parametrize('attr', ['fold_tree', 'pdb_info'])
def test_set_readwrite_attr_wrong_type(self, attr):
wrong_type = 1
with pytest.raises(TypeError):
setattr(self.pose, attr, wrong_type)
# Check data descriptors.
def test_residues(self):
assert self.pose.residues
def test_reslabels(self):
assert self.pose.reslabels
def test_scores(self):
# Killing two birds with one stone by also testing score functions.
sfxn = get_fa_scorefxn()
sfxn(self.pose)
assert self.pose.scores
class TestPDBInfoAttributes:
from pyrolyse.core.pdbinfo import (_read_attributes,
_read_write_attributes, _get_set_pairs)
test_attributes = list(_read_attributes)
test_write_attr = list(_read_write_attributes)
test_write_attr += [get_set[0] for get_set in _get_set_pairs]
pose = get_pose('PYTEST')
try:
pdbinfo = pose.pdb_info()
except TypeError:
pdbinfo = pose.pdb_info
# Lazy but gets the work done.
@pytest.mark.parametrize('attr', test_attributes)
def test_get_readonly_attributes(self, attr):
# Can we get every read-only attribute without error?
getattr(self.pdbinfo, attr)
@pytest.mark.parametrize('attr', test_attributes)
def test_set_readonly_attributes(self, attr):
with pytest.raises(AttributeError):
setattr(self.pdbinfo, attr, None)
@pytest.mark.parametrize('attr', test_write_attr)
def test_get_readwrite_attributes(self, attr):
getattr(self.pdbinfo, attr)
@pytest.mark.parametrize('attr', test_write_attr)
def test_set_readwrite_attr(self, attr):
old_attr = getattr(self.pdbinfo, attr)
setattr(self.pdbinfo, attr, old_attr)
@pytest.mark.parametrize('attr', test_write_attr)
def test_set_readwrite_attr_wrong_type(self, attr):
wrong_type = []
with pytest.raises(TypeError):
setattr(self.pdbinfo, attr, wrong_type)
def test_auto_get_pose(pose_input):
assert get_pose(pose_input).residue(1)
def test_get_pose(pose_input, kind):
assert get_pose(pose_input, kind).residue(1)