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)