This allows the motional pivot algorithm to work on atomic coordinates from different data pipes,
different structural models, and different molecules. The change allows the
Structure.test_find_pivot_molecules system test to now pass, as missing atomic data is now correctly
handled. The user function backend uses the new pipe_control.structure.main.assemble_coordinates()
function.
The Structure.test_find_pivot and Structure.test_find_pivot_molecules system tests have been updated
for the user function argument changes.
