The helper module contains various atom.Hierarchy-specific code
(get_bounding_box, clone, destroy, and the functions for creating
simplified versions). Externally, this doesn't make much sense, but
code is there since some of it internally uses em for computations. In
addition, Elina's new code for simplified restraint management forms a
nice, coherent set of functionality which could take over the helper
module by itself. As a result, I propose
- helper.get_bound_box, helper.clone and helper.destroy be moved to
atom.
- the helper.create_simplified function be renamed
em.create_simplified_from_density putting it in the em module and
making it more clear why it is there (there current name is too vague
anyway). It should also create the rigid bodies it needs internally.
- helper.create_simplified_by_residue needs to be thought about since
its current method of asigning radii doesn't make sense for anything
other than density based restraints (so it may make sense to move it
to em).
I don't think any of the code is too widely used, so changing things
now should be minimally disruptive. Thoughts?