def test_hes_custom_weights(self, ens1, ens2):
results, details = encore.hes([ens1, ens2], weights='mass')
results_custom, details_custom = encore.hes([ens1, ens2],
weights=(ens1.select_atoms('name CA').masses,
ens2.select_atoms('name CA').masses))
result_value = results[0, 1]
result_value_custom = results_custom[0, 1]
assert_almost_equal(result_value, result_value_custom)
def test_hes_custom_weights(self):
results, details = encore.hes([self.ens1, self.ens2], weights='mass')
results_custom, details_custom = encore.hes(
[self.ens1, self.ens2],
weights=(self.ens1.atoms.CA.masses, self.ens2.atoms.CA.masses))
result_value = results[0, 1]
result_value_custom = results_custom[0, 1]
assert_almost_equal(result_value, result_value_custom)
def test_hes_custom_weights(self, ens1, ens2):
results, details = encore.hes([ens1, ens2], weights='mass')
results_custom, details_custom = encore.hes(
[ens1, ens2],
weights=(ens1.select_atoms('name CA').masses,
ens2.select_atoms('name CA').masses))
result_value = results[0, 1]
result_value_custom = results_custom[0, 1]
assert_almost_equal(result_value, result_value_custom)
def test_hes_align(self, ens1, ens2):
# This test is massively sensitive!
# Get 5260 when masses were float32?
results, details = encore.hes([ens1, ens2], align=True)
result_value = results[0,1]
expected_value = 2047.05
assert_almost_equal(result_value, expected_value, decimal=-3,
err_msg="Unexpected value for Harmonic Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, expected_value))
def test_hes_to_self(self, ens1):
results, details = encore.hes([ens1, ens1])
result_value = results[0, 1]
expected_value = 0.
assert_almost_equal(
result_value,
expected_value,
err_msg="Harmonic Ensemble Similarity to itself not zero: {0:f}".
format(result_value))
def test_hes(self):
results, details = encore.hes([self.ens1, self.ens2], weights='mass')
result_value = results[0, 1]
min_bound = 1E5
self.assertGreater(
result_value,
min_bound,
msg=
"Unexpected value for Harmonic Ensemble Similarity: {0:f}. Expected {1:f}."
.format(result_value, min_bound))
def test_hes_error_estimation(self, ens1):
expected_average = 10
expected_stdev = 12
averages, stdevs = encore.hes([ens1, ens1], estimate_error = True, bootstrapping_samples=10, selection="name CA and resnum 1-10")
average = averages[0,1]
stdev = stdevs[0,1]
assert_almost_equal(average, expected_average, decimal=-2,
err_msg="Unexpected average value for bootstrapped samples in Harmonic Ensemble imilarity")
assert_almost_equal(stdev, expected_stdev, decimal=-2,
err_msg="Unexpected standard daviation for bootstrapped samples in Harmonic Ensemble imilarity")
def test_hes_align(self, ens1, ens2):
# This test is massively sensitive!
# Get 5260 when masses were float32?
results, details = encore.hes([ens1, ens2], align=True)
result_value = results[0, 1]
expected_value = 2047.05
assert_almost_equal(
result_value,
expected_value,
decimal=-3,
err_msg=
"Unexpected value for Harmonic Ensemble Similarity: {0:f}. Expected {1:f}."
.format(result_value, expected_value))
def test_hes_error_estimation(self, ens1):
expected_average = 10
expected_stdev = 12
averages, stdevs = encore.hes([ens1, ens1],
estimate_error=True,
bootstrapping_samples=10,
selection="name CA and resnum 1-10")
average = averages[0, 1]
stdev = stdevs[0, 1]
assert_almost_equal(
average,
expected_average,
decimal=-2,
err_msg=
"Unexpected average value for bootstrapped samples in Harmonic Ensemble imilarity"
)
assert_almost_equal(
stdev,
expected_stdev,
decimal=-2,
err_msg=
"Unexpected standard daviation for bootstrapped samples in Harmonic Ensemble imilarity"
)
def test_hes(self, ens1, ens2):
results, details = encore.hes([ens1, ens2], weights='mass')
result_value = results[0, 1]
min_bound = 1E5
assert result_value > min_bound, "Unexpected value for Harmonic " \
"Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, min_bound)
def test_hes(self, ens1, ens2):
results, details = encore.hes([ens1, ens2], weights='mass')
result_value = results[0, 1]
min_bound = 1E5
assert result_value > min_bound, "Unexpected value for Harmonic " \
"Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, min_bound)
def test_hes_to_self(self, ens1):
results, details = encore.hes([ens1, ens1])
result_value = results[0, 1]
expected_value = 0.
assert_almost_equal(result_value, expected_value,
err_msg="Harmonic Ensemble Similarity to itself not zero: {0:f}".format(result_value))
