def test_level_C(self):
"""Run Shrake-Rupley with level C."""
m = copy.deepcopy(self.model) # modifies atom.sasa
sasa = ShrakeRupley()
sasa.compute(m, level="C")
for c in m.get_chains():
atom_sum = sum(a.sasa for a in c.get_atoms())
self.assertAlmostEqual(atom_sum, c.sasa, places=2)
def test_level_R(self):
"""Run Shrake-Rupley with level R."""
m = copy.deepcopy(self.model) # modifies atom.sasa
sasa = ShrakeRupley()
sasa.compute(m, level="R")
for r in m.get_residues():
atom_sum = sum(a.sasa for a in r)
self.assertAlmostEqual(atom_sum, r.sasa, places=2)
def test_custom_radii(self):
"""Run Shrake-Rupley with custom radii."""
m = copy.deepcopy(self.model) # modifies atom.sasa
sasa = ShrakeRupley(radii_dict={"C": 5.00})
sasa.compute(m)
result = [a.sasa for a in m.get_atoms()][:5]
expected = [0.0, 190.45, 41.18, 0.0, 36.03]
for a, b in zip(result, expected):
self.assertAlmostEqual(a, b, places=2)
def test_default_algorithm(self):
"""Run Shrake-Rupley with default parameters."""
m = copy.deepcopy(self.model) # modifies atom.sasa
sasa = ShrakeRupley()
sasa.compute(m)
result = [a.sasa for a in m.get_atoms()][:5]
expected = [50.36, 31.40, 10.87, 12.86, 2.42]
for a, b in zip(result, expected):
self.assertAlmostEqual(a, b, places=2)
def test_higher_resolution(self):
"""Run Shrake-Rupley with 960 points per sphere."""
m = copy.deepcopy(self.model) # modifies atom.sasa
sasa = ShrakeRupley(n_points=960)
sasa.compute(m)
result = [a.sasa for a in m.get_atoms()][:5]
expected = [51.90, 31.45, 12.45, 12.72, 3.02]
for a, b in zip(result, expected):
self.assertAlmostEqual(a, b, places=2)
def test_fail_empty_entity(self):
"""Raise exception on invalid level parameter: S > C."""
sasa = ShrakeRupley()
r = copy.deepcopy(self.model["A"].child_list[0])
for a in list(r):
r.detach_child(a.name) # empty residue
self.assertEqual(len(r.child_list), 0)
with self.assertRaisesRegex(ValueError, "Entity has no child atoms"):
sasa.compute(r)
def test_fail_compute_level_2(self):
"""Raise exception on invalid level parameter: S > C."""
chain = self.model["A"]
with self.assertRaisesRegex(ValueError, "be equal or smaller than"):
sasa = ShrakeRupley()
sasa.compute(chain, level="S") # Chain is a child of Structure.
def test_fail_compute_level_1(self):
"""Raise exception on invalid level parameter: X."""
with self.assertRaisesRegex(ValueError, "Invalid level"):
sasa = ShrakeRupley()
sasa.compute(self.model, level="X")
def test_fail_compute_entity_level(self):
"""Raise exception on input Atom entity."""
atom = list(self.model.get_atoms())[0]
with self.assertRaisesRegex(ValueError, "Invalid entity type"):
sasa = ShrakeRupley()
sasa.compute(atom)
def test_fail_compute_entity_type(self):
"""Raise exception on unsupported entity type."""
with self.assertRaisesRegex(ValueError, "Invalid entity type"):
sasa = ShrakeRupley()
sasa.compute([1, 2, 3, 4, 5])
def test_fail_n_points(self):
"""Raise exception on bad n_points parameter."""
with self.assertRaisesRegex(ValueError, "must be larger than 1"):
sasa = ShrakeRupley(n_points=0)
def test_fail_probe_radius(self):
"""Raise exception on bad probe_radius parameter."""
with self.assertRaisesRegex(ValueError, "must be a positive number"):
sasa = ShrakeRupley(probe_radius=-1.40)