def test_rotated(self):
"""Rotating a molecule around the first euler angle should not affect its rmsd."""
global tolerance, num_test
for idx in xrange(num_test):
some_methane = methane_sample()
before = self.rmsd(some_methane, some_methane)
after = self.rmsd(some_methane, cm.rotate_euler(some_methane, random.random() * math.pi, random.random() * math.pi, random.random() * math.pi))
assert abs(before - after) <= tolerance, "rotating the molecule affected its rmsd. before = %s, rmsd = %s, idx = %s" % (before, after, idx)
def test_known_rotated(self):
"""RMSD for a specific case should evaluate as I expect."""
global tolerance, num_test
for idx in xrange(num_test):
first_mol = randomize_mol(np.array([0.0, 0.0, -1.0, 0.0, 0.0, 1.0]))
second_mol = randomize_mol(np.array([0.0, 0.0, -2.0, 0.0, 0.0, 3.0]))
# translation_vector = np.array([random.random() * 10.0 + 5.0 for i in xrange(3)])
rmsd = self.rmsd(first_mol, cm.rotate_euler(second_mol, random.random() * math.pi, random.random() * math.pi, random.random() * math.pi))
expected = 1.5
assert abs(rmsd - expected) < tolerance, "rmsd was not as expected: %s != %s" % (rmsd, 1.0)
def randomize_mol(mol):
"""Randomly move a molecule around."""
translation_vector = np.array([random.random() * 10.0 + 5.0 for i in xrange(3)])
(rot_alpha, rot_beta, rot_gamma) = [random.random() * 2 * math.pi for i in xrange(3)]
return cm.translate(cm.rotate_euler(mol, rot_alpha, rot_beta, rot_gamma), translation_vector)
