Since I think such a new module is a good idea, I'll make it more concrete. Let's have a new module called IMP.helper. Its primary purpose is to contain functions that perform common tasks that - involve creation of more than one restraint or score state
- creation of a restraint or score state followed by non-trivial manipulation of it - functions to create standard particle sets
Examples would include existing code such as: - creating a rigid body and associated score states
- restraining the diameter of a set of particles - creating a hard sphere excluded volume restraint which intelligently handles rigid bodies - creating a coarse grained model of a protein with known number of amino acids, but no known structure
Having it in a module means that there is a clear first place to look for such things. The low level functionality in core is clearly differentiated from functions that use it.
On Fri, May 15, 2009 at 1:46 PM, Daniel Russel <">> wrote:
We now have several different layers of functionality in IMP, which are kind of jumbled together in core. For example, with rigid bodies, you can create one by - decorating a particles - creating a couple of score states from relatively general purpose singleton modifiers and container based score states
- adding them to the model or - use a create_rigid_body function to do it all for you
Having all of these together clutters the documentation and makes it harder to find out what you should be doing. That said, we need at least some of the detail bit available to users, so we can't really hide them away as internal.
One option would be to pull these into their own module (I can't think of the right name offhand, perhaps helpers), and reserve core for very general purpose things like PairsRestraint.