py> mtx

array([[ 0.88302225, 0.11697778, 0.45451948, 5. ],

[ 0.11697778, 0.88302225, -0.45451948, 10. ],

[ -0.45451948, 0.45451948, 0.76604444, 20. ],

[ 0. , 0. , 0. , 1. ]])

My usual way of transforming a set of coordinates with a 4x4 matrix is to use numpy:

py> xyz_1

array([[ 5., 10., 15., 1.],

[ 20., 15., 10., 1.]])

py> numpy.inner(xyz_1, mtx)

array([[ 17.40268126, 12.59731919, 33.76326397, 1. ],

[ 28.9603065 , 21.03969455, 25.38784698, 1. ]])

What is the equivalent in cctbx? Is there a way to avoid converting coordinates back and fourth between numpy arrays with atoms().extract_xyz() & .set_xyz() (as might be used from a iotbx_pdb_hierarchy_ext.root).