def test_solve_intermittent(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='intermittent',
sample_time=0.06,
)
def actual_function_int(t):
A1 = 0.33
A2 = 0.33
A3 = 0.34
tau1 = 5
tau2 = 1
tau3 = 0.1
return A1 * np.exp(-t / tau1) + A2 * np.exp(
-t / tau2) + A3 * np.exp(-t / tau3)
hbond.solution['time'] = time = np.arange(0, 6.0, 0.01)
hbond.solution['results'] = actual_function_int(time)
hbond.solve()
assert_almost_equal(
hbond.solution['fit'],
np.array([0.33, 0.33, 5, 1, 0.1]),
)
def test_solve_continuous(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
sample_time=0.06,
)
def actual_function_cont(t):
A1 = 0.75
A2 = 0.25
tau1 = 0.5
tau2 = 0.1
return A1 * np.exp(-t / tau1) + A2 * np.exp(-t / tau2)
hbond.solution['time'] = time = np.arange(0, 0.06, 0.001)
hbond.solution['results'] = actual_function_cont(time)
hbond.solve()
assert_almost_equal(
hbond.solution['fit'],
np.array([0.75, 0.5, 0.1]),
)
def test_solve_intermittent(self):
hbond = HBAC(self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='intermittent',
sample_time=0.06,
)
def actual_function_int(t):
A1 = 0.33
A2 = 0.33
A3 = 0.34
tau1 = 5
tau2 = 1
tau3 = 0.1
return A1 * np.exp(-t/tau1) + A2 * np.exp(-t/tau2) + A3 * np.exp(-t/tau3)
hbond.solution['time'] = time = np.arange(0, 6.0, 0.01)
hbond.solution['results'] = actual_function_int(time)
hbond.solve()
assert_array_almost_equal(
hbond.solution['fit'],
np.array([0.33, 0.33, 5, 1, 0.1]),
)
def test_solve_before_run_VE(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
sample_time=0.06,
)
with pytest.raises(ValueError):
hbond.solve()
def test_solve_before_run_VE(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
sample_time=0.06,
)
with pytest.raises(ValueError):
hbond.solve()
def test_solve_continuous(self):
hbond = HBAC(self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='continuous',
sample_time=0.06,
)
def actual_function_cont(t):
A1 = 0.75
A2 = 0.25
tau1 = 0.5
tau2 = 0.1
return A1 * np.exp(-t/tau1) + A2 * np.exp(-t/tau2)
hbond.solution['time'] = time = np.arange(0, 0.06, 0.001)
hbond.solution['results'] = actual_function_cont(time)
hbond.solve()
assert_array_almost_equal(
hbond.solution['fit'],
np.array([0.75, 0.5, 0.1]),
)
'O10' : u.select_atoms('bynum 18')
}
oxygens = sum(list(oxygen_dict.values()))
hydrogens = sum(list(hydrogen_dict.values()))
nitrogens = sum(list(nitrogen_dict.values()))
""
"Run HBond Autocorrelation"
hb_ac = HydrogenBondAutoCorrel(u,
acceptors = oxygens,
hydrogens = hydrogens,
donors = nitrogens,
bond_type='continuous')
hb_ac.run()
hb_ac.solve()
tau = hb_ac.solution['tau']
time = hb_ac.solution['time']
results = hb_ac.solution['results']
estimate = hb_ac.solution['estimate']
"Max Range"
factor = 0.5
max_d = int(data[:,0].size * factor)
max_h = int(time.size * factor)
max_r = int(len(u.trajectory) * factor)
"Plot Results and Find Correlation"
fig, ax1 = plt.subplots()
color = 'red'
ax1.set_xlabel('Pull Distance ($\AA$)')