def test_two_particles_cannot_be_in_same_positions(self):
master = Master(100, 1)
master.create_nanoparticles_and_ligands(2, 10, 10, 1)
master.agents[0].position = np.array([1, 1, 1])
position = np.array([1, 1, 1])
self.assertFalse(master._check_space_available_nanoparticle(position))
def test_correct_number_of_nanoparticles_are_created(self):
master = Master(100, 1)
master.create_nanoparticles_and_ligands(10, 1, 1, 1)
self.assertEqual(10, master.number_of_nanoparticles)
agents = [i for i in master.agents if isinstance(i, Nanoparticle)]
self.assertEqual(10, len(agents))
def test_no_nanoparticles_are_touching(self):
master = Master(1000, 1)
master.create_nanoparticles_and_ligands(100, 10, 10, 1)
positions = [i.position for i in master.agents]
combs = combinations(positions, 2)
distance = [np.linalg.norm(a - b) for (a, b) in combs]
self.assertTrue(all([i > 22 for i in distance]))
def test_two_particles_can_be_far_away(self):
master = Master(100, 1)
master.create_nanoparticles_and_ligands(2, 10, 10, 1)
master.agents[0].position = np.array([1, 1, 1])
position = np.array([50, 50, 50])
self.assertTrue(master._check_space_available_nanoparticle(position))
def test_all_receptors_have_correct_length(self):
master = Master(100, 1)
master.create_nanoparticles_and_ligands(10, 1, 1, 1)
master.create_receptors(10, 1)
[
self.assertEqual(1, a.receptor_length) for a in master.agents
if isinstance(a, Receptor)
]
def test_correct_number_ligands_are_created(self):
master = Master(100, 1)
master.create_nanoparticles_and_ligands(100, 10, 1, 1)
self.assertEqual(master.ligand_length, 1)
self.assertEqual(master.number_of_ligands, 10)
ligands = [i.ligands for i in master.agents]
for l in ligands:
self.assertEqual(10, len(l))
def test_no_nanoparticles_outside_area(self):
master = Master(1000, 1)
master.create_nanoparticles_and_ligands(100, 10, 10, 1)
positions = [i.position for i in master.agents]
self.assertTrue(
all([(i[0] < 1000 and i[1] < 1000 and i[2] < 1000)
for i in positions]))
self.assertTrue(
all([(i[0] > 0 and i[1] > 0 and i[2] > 0) for i in positions]))
def test_two_particles_can_be_really_close_without_touching(self):
master = Master(100, 1)
master.create_nanoparticles_and_ligands(2, 10, 10, 1)
master.agents[0].position = np.array([1, 1, 1])
position = np.array([23, 1, 1])
self.assertTrue(master._check_space_available_nanoparticle(position))
x = 22 / np.sqrt(3) + 1
position = np.array([x, x, x])
self.assertTrue(master._check_space_available_nanoparticle(position))
def test_two_particles_cannot_be_touching(self):
master = Master(100, 1)
master.create_nanoparticles_and_ligands(2, 10, 10, 1)
master.agents[0].position = np.array([1, 1, 1])
position = np.array([23 - 1e-10, 1, 1])
self.assertFalse(master._check_space_available_nanoparticle(position))
x = 22 / np.sqrt(3) + 1 - 1e-10
position = np.array([x, x, x])
self.assertFalse(master._check_space_available_nanoparticle(position))
def binding_energy():
print('Binding Energy -------------')
d = np.linspace(5, 25, 5).tolist()
data = {}
means = []
errors = []
time_data = []
for i in d:
variable_finals = []
for _ in range(3):
number_of_seconds = 1 # i.e. 1 hour = 3600 seconds
model = Master(dimension=1000,
binding_energy=int(i),
time_unit=10e-3,
number_of_receptors=2,
receptor_length=100,
number_of_nanoparticles=1,
nanoparticle_radius=50,
number_of_ligands=2,
ligand_length=7,
binding_distance=4,
receptor_radius=3,
ligand_radius=3,
cell_diffusion_coef=1)
model.create_receptors() # 100 nm for receptor
model.create_nanoparticles_and_ligands(
) # 1-2 nm for ligand # 95 particles
print(
f'{model.dimension/1000} μm\u00b3 system, {model.binding_energy} binding energy, {model.number_of_nanoparticles} Nanoparticles,\n'
f'{model.nanoparticle_radius} nm Nanoparticle Radius, {model.number_of_ligands} Ligands, Ligand length {model.ligand_length} nm,\n'
f'{model.number_of_receptors} Receptors, {model.receptor_length} nm Receptor length, {model.binding_distance} Binding distance'
)
model.run(steps=number_of_seconds) # 3600 for 1 hour
print(f'The surface coverage is {model.surface_coverage}')
variable_finals.append(model.surface_coverage)
time_data.append(np.array(model.coverage))
mean_time = np.mean(time_data, axis=0)
error_time = np.std(time_data, axis=0)
data[f'{model.binding_energy} KT binding energy '] = np.array(
[list(range(0, model.time + 1)), mean_time, error_time])
mean_coverage = np.mean(np.array(variable_finals))
print(f'The mean surface coverage is {mean_coverage}')
errors.append(np.std(np.array(variable_finals)))
means.append(np.mean(np.array(variable_finals)))
plt.xlabel('Time (milliseconds)')
plt.ylabel('Surface Coverage')
for key, value in data.items():
plt.plot(value[0], value[1], label=key)
plt.fill_between(value[0],
value[1] - value[2],
value[1] + value[2],
alpha=0.2)
plt.legend()
plt.show()
second_variable_plot('Binding energy (kt)', 'Surface Coverage', d, means,
errors)
def test_no_receptor_tips_are_touching(self):
for _ in range(100):
master = Master(100, 1)
master.create_nanoparticles_and_ligands(10, 1, 1, 1)
master.create_receptors(100, 1)
positions = [
a.tip_position for a in master.agents
if isinstance(a, Receptor)
]
combs = combinations(positions, 2)
distance = [np.linalg.norm(a - b) for (a, b) in combs]
[self.assertNotAlmostEqual(d, 0) for d in distance]
def test_no_receptor_bases_outside_area(self):
for _ in range(100):
master = Master(500, 1)
master.create_nanoparticles_and_ligands(100, 10, 10, 1)
positions = [
i.base_position for i in master.agents
if isinstance(i, Receptor)
]
self.assertTrue(
all([(i[0] < 1000 and i[1] < 1000 and i[2] < 1000)
for i in positions]))
self.assertTrue(
all([(i[0] > 0 and i[1] > 0 and i[2] > 0) for i in positions]))
