def setUp(self):
self.host = load_structure()
self.guest = load_molecule()
self.complex = Complex(self.host, self.guest)
self.fitness = MinDistanceFitness(threshold=1.5)
self.num_steps = 100
self.temperature = 0.1
self.mcdocker = MonteCarloDocker(
self.host, self.guest,
fitness=self.fitness, temperature=self.temperature
)
class TestMCDocker(ut.TestCase):
def setUp(self):
self.host = load_structure()
self.guest = load_molecule()
self.complex = Complex(self.host, self.guest)
self.fitness = MinDistanceFitness(threshold=1.5)
self.num_steps = 100
self.temperature = 0.1
self.mcdocker = MonteCarloDocker(
self.host, self.guest,
fitness=self.fitness, temperature=self.temperature
)
def test_run(self):
cpx = self.mcdocker.run(self.complex.copy(), self.num_steps)
self.assertTrue(cpx.distance_matrix.min() > 1.5)
def test_dock(self):
cpxs = self.mcdocker.dock(self.num_steps)
self.assertIsInstance(cpxs, list)
self.assertIsInstance(cpxs[0], Complex)
def test_copy(self):
newdocker = self.mcdocker.copy()
self.assertEqual(newdocker.temperature, self.mcdocker.temperature)
self.assertEqual(newdocker.host, self.mcdocker.host)
self.assertEqual(newdocker.guest, self.mcdocker.guest)
def dock_at_point(self, point, attempts):
hcoords = self.translate_host(point)
complexes = [
Complex(self.new_host(newcoords=hcoords),
self.new_guest(newcoords=self.rotate_guest()))
for _ in range(attempts)
]
return complexes
def dock(self, attempts):
cpx = Complex(self.host.copy(), self.guest.copy())
for trial in range(attempts):
cpx = self.run(cpx, 1)
if self.fitness(cpx) >= 0:
print(f"{trial + 1} attempts to success")
return [cpx]
return []
def setUp(self):
self.host = load_structure()
self.guest = load_molecule()
self.complex = Complex(self.host.copy(), self.guest.copy())
def create_new_complex(self, host_coords, guest_coords):
return Complex(self.new_host(newcoords=host_coords),
self.new_guest(newcoords=guest_coords),
add_transform=False)
def dock(self, attempts):
cpx = Complex(self.host.copy(), self.guest.copy())
cpx = self.run(cpx, attempts)
return self.rank_complexes([cpx])