def test_com_methane(self):
"""The center of mass for methane should be as expected."""
global tolerance, methane
expected_com = np.array([0.25] * 3)
com = cm.center_of_geometry(methane)
diff = expected_com - com
assert np.linalg.norm(diff) < tolerance, "com is wrong: \ncom = \n%s, \nexpected = \n%s." % (com, expected_com)
def rmsd(self, x, y):
x = cm.translate(x, -cm.center_of_geometry(x))
y = cm.translate(y, -cm.center_of_geometry(y))
rot = cm.rmsd_rotation(x, y)
y = cm.transform(y, rot)
return cm.flat_rmsd(x, y)