Clipper Programming Question:

I'm writing this library to solve my own problems, and to help CCP4 developers transition to OO programming. You should find the best tool for the problem you need to solve, and use that. If Clipper fits the task, then I am happy to provide advice on implementation and make changes which do not lose generality.
Having said that, it is certainly possible to use CLipper in association with CCTBX.