def test_align_flat_rmsd(self):
for cout in xrange(20):
x = perturb(randomize_mol(methane))
y = perturb(randomize_mol(methane))
y = x.copy()
aligned_y = cm.align(x.copy(), y.copy())
self.assertAlmostEqual(cm.rmsd(x, y), cm.flat_rmsd(x, aligned_y), 5)
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)
