def test_simple_dnacc(self):
cases = [
dict(beta_DeltaG0=-10, weights=None, binding_free_energy=-9.01, p_bound_0_1=0.99327740159843414),
dict(
beta_DeltaG0=-10,
weights=[0.8, 0.6, 3.7],
binding_free_energy=-5.54,
p_bound_0_1=0.8 * 1.2497165073687115 * 0.6,
),
dict(beta_DeltaG0=-1, weights=None, binding_free_energy=-1.05, p_bound_0_1=0.55013119441689895),
dict(
beta_DeltaG0=-1,
weights=[0.8, 0.6, 3.7],
binding_free_energy=-0.59,
p_bound_0_1=0.8 * 0.69788894233575782 * 0.6,
),
]
for case in cases:
N = 3
boltz_bind = SymDict()
boltz_bind[0, 1] = exp(-case["beta_DeltaG0"])
boltz_bind = csr_matrix_from_dict((N, N), boltz_bind)
dnacc = Generic(boltz_bind, case["weights"])
self.assertAlmostEqual(dnacc.binding_free_energy, case["binding_free_energy"], 2)
self.assertAlmostEqual(dnacc.p_bound[0, 1], case["p_bound_0_1"])
self.assertAlmostEqual(dnacc.p_bound[0, 1], dnacc.p_bound[1, 0])
self.assertEqual(dnacc.p_bound[0, 0], 0.0)
self.assertEqual(dnacc.p_bound[1, 2], 0.0)
self.assert_(dnacc.avg_num_bonds >= 0)
def test_count_bonds(self):
N = 3
boltz_bind = SymDict()
boltz_bind[0, 1] = boltz_bind[0, 2] = boltz_bind[1, 2] = 100.0
boltz_bind = csr_matrix_from_dict((N, N), boltz_bind)
dnacc = Generic(boltz_bind)
self.assertAlmostEqual(dnacc.count_bonds(set((0,)), set((1,))), 0.4658727174875526)
def test_count_bonds(self):
N = 3
boltz_bind = SymDict()
boltz_bind[0, 1] = boltz_bind[0, 2] = boltz_bind[1, 2] = 100.0
boltz_bind = csr_matrix_from_dict((N, N), boltz_bind)
dnacc = Generic(boltz_bind)
self.assertAlmostEqual(dnacc.count_bonds(set((0,)), set((1,))), 0.46587246970021012)
self.assertAlmostEqual(dnacc.count_bonds(set(range(N)), set(range(N))), dnacc.avg_num_bonds, delta=1e-5)
def setUp(self):
self.p_free = np.arange(5, 10).astype("float64")
d = SymDict()
d[1, 2] = 600.0
d[2, 3] = 6000.0
self.mtx = csr_matrix_from_dict((5, 5), d)
self.prefactor = 32.0
self.maxDelta = 1e-7
self.maxSteps = 10001
self.weights = np.array([5.0, 6.0, 7.0, 8.0, 9.0])
def test_count_bonds(self):
N = 3
boltz_bind = SymDict()
boltz_bind[0, 1] = boltz_bind[0, 2] = boltz_bind[1, 2] = 100.0
boltz_bind = csr_matrix_from_dict((N, N), boltz_bind)
dnacc = Generic(boltz_bind)
self.assertAlmostEqual(dnacc.count_bonds(set((0,)), set((1,))),
0.46587246970021012)
self.assertAlmostEqual(dnacc.count_bonds(set(range(N)), set(range(N))),
dnacc.avg_num_bonds, delta=1e-5)
def test_simple_dnacc(self):
cases = [
dict(beta_DeltaG0=-10, weights=None,
binding_free_energy=-9.01,
p_bound_0_1=0.99327740159843414),
dict(beta_DeltaG0=-10, weights=[0.8, 0.6, 3.7],
binding_free_energy=-5.54,
p_bound_0_1=0.8 * 1.2497165073687115 * 0.6),
dict(beta_DeltaG0=-1, weights=None,
binding_free_energy=-1.05,
p_bound_0_1=0.55013119441689895),
dict(beta_DeltaG0=-1, weights=[0.8, 0.6, 3.7],
binding_free_energy=-0.59,
p_bound_0_1=0.8 * 0.69788894233575782 * 0.6)]
for case in cases:
N = 3
boltz_bind = SymDict()
boltz_bind[0, 1] = exp(-case['beta_DeltaG0'])
boltz_bind = csr_matrix_from_dict((N, N), boltz_bind)
dnacc = Generic(boltz_bind, case['weights'])
self.assertAlmostEqual(dnacc.binding_free_energy,
case['binding_free_energy'], 2)
self.assertAlmostEqual(dnacc.p_bound[0, 1],
case['p_bound_0_1'])
self.assertAlmostEqual(dnacc.p_bound[0, 1],
dnacc.p_bound[1, 0])
self.assertEqual(dnacc.p_bound[0, 0], 0.0)
self.assertEqual(dnacc.p_bound[1, 2], 0.0)
self.assert_(dnacc.avg_num_bonds >= 0)
