Efficiently rotate a set of points with a rotation matrix in numpy

You can multiply A with the transpose of the rotation matrix:

A = dot(A, R.T)

There's a couple of minor updates/points of clarification to add to Aapo Kyrola's (correct) answer. First, the syntax of the matrix multiplication can be slightly simplified using the recently added matrix multiplication operator @:

A = A @ R.T

Also, you can arrange the transformation in the standard form (rotation matrix first) by taking the transpose of A prior to the multiplication, then transposing the result:

A = (R @ A.T).T

You can check that both forms of the transformation produce the same results via the following assertion:

np.testing.assert_array_equal((R @ A.T).T, A @ R.T)