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, 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_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_save_without_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.save_results()
def test_save_without_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.save_results()
def test_save(self):
hbond = HBAC(self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
with tempdir.in_tempdir():
hbond.save_results('hbondout.npz')
loaded = np.load('hbondout.npz')
assert_('time' in loaded)
assert_('results' in loaded)
def test_continuous(self):
hbond = HBAC(self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
assert_array_almost_equal(
hbond.solution['results'],
np.array([ 1. , 0.92668623, 0.83137828,
0.74486804, 0.67741936, 0.60263932],
dtype=np.float32)
)
def test_intermittent(self):
hbond = HBAC(self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='intermittent',
sample_time=0.06,
)
hbond.run()
assert_array_almost_equal(
hbond.solution['results'],
np.array([ 1. , 0.92668623, 0.84310848,
0.79325515, 0.76392961, 0.72287393],
dtype=np.float32)
)
def test_intermittent_timecut(self):
hbond = HBAC(self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='intermittent',
time_cut=0.01, # time cut at traj.dt == continuous
sample_time=0.06,
)
hbond.run()
assert_array_almost_equal(
hbond.solution['results'],
np.array([ 1. , 0.92668623, 0.83137828,
0.74486804, 0.67741936, 0.60263932],
dtype=np.float32)
)
def test_save(self, u, hydrogens, oxygens, nitrogens, tmpdir):
hbond = HBAC(u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
tmpfile = os.path.join(str(tmpdir), 'hbondout.npz')
hbond.save_results(tmpfile)
loaded = np.load(tmpfile)
assert 'time' in loaded
assert 'results' in loaded
def test_save(self):
hbond = HBAC(
self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
with tempdir.in_tempdir():
hbond.save_results('hbondout.npz')
loaded = np.load('hbondout.npz')
assert_('time' in loaded)
assert_('results' in loaded)
def test_intermittent(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='intermittent',
sample_time=0.06,
)
hbond.run()
assert_almost_equal(
hbond.solution['results'],
np.array([
1., 0.92668623, 0.84310848, 0.79325515, 0.76392961, 0.72287393
],
dtype=np.float32))
def test_save(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
with tempdir.in_tempdir():
hbond.save_results('hbondout.npz')
loaded = np.load('hbondout.npz')
assert 'time' in loaded
assert 'results' in loaded
def test_continuous(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
assert_almost_equal(
hbond.solution['results'],
np.array([
1., 0.92668623, 0.83137828, 0.74486804, 0.67741936, 0.60263932
],
dtype=np.float32))
def test_intermittent_excl(self):
hbond = HBAC(
self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='intermittent',
exclusions=self.excl_list,
sample_time=0.06,
)
hbond.run()
assert_array_almost_equal(
hbond.solution['results'],
np.array([
1., 0.92668623, 0.84310848, 0.79325515, 0.76392961, 0.72287393
],
dtype=np.float32))
def test_continuous_excl(self):
hbond = HBAC(
self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='continuous',
exclusions=self.excl_list,
sample_time=0.06,
)
hbond.run()
assert_array_almost_equal(
hbond.solution['results'],
np.array([
1., 0.92668623, 0.83137828, 0.74486804, 0.67741936, 0.60263932
],
dtype=np.float32))
def test_save(self, u, hydrogens, oxygens, nitrogens, tmpdir):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
tmpfile = os.path.join(str(tmpdir), 'hbondout.npz')
hbond.save_results(tmpfile)
loaded = np.load(tmpfile)
assert 'time' in loaded
assert 'results' in loaded
def test_intermittent_timecut(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='intermittent',
time_cut=0.01, # time cut at traj.dt == continuous
sample_time=0.06,
)
hbond.run()
assert_almost_equal(
hbond.solution['results'],
np.array([
1., 0.92668623, 0.83137828, 0.74486804, 0.67741936, 0.60263932
],
dtype=np.float32))
def test_intermittent_excl(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='intermittent',
exclusions=(np.arange(len(hydrogens)), np.array(
range(len(oxygens)))),
sample_time=0.06,
)
hbond.run()
assert_almost_equal(
hbond.solution['results'],
np.array([ 1. , 0.92668623, 0.84310848,
0.79325515, 0.76392961, 0.72287393],
dtype=np.float32)
)
def test_continuous_excl(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
exclusions=(np.arange(len(hydrogens)), np.array(
range(len(oxygens)))),
sample_time=0.06,
)
hbond.run()
assert_almost_equal(
hbond.solution['results'],
np.array([ 1. , 0.92668623, 0.83137828,
0.74486804, 0.67741936, 0.60263932],
dtype=np.float32)
)
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]),
)
'O6' : u.select_atoms('bynum 36'),
'O7' : u.select_atoms('bynum 23'),
'O8' : u.select_atoms('bynum 23'),
'O9' : u.select_atoms('bynum 64'),
'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)