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Re: [IMP-dev] Nonbonded lists



Francisco Melo wrote:
is the non-sphere object representing something like a cube or other geometric object in the future ?

I find confusing the term non-sphere, since it is too fuzzy (ie. it can be almost anything !)
Yeah, we probably should have "Point" in the name of the non-sphere ones.
I do not know how to overcome the efficiency problem, but certainly we can imagine situations where a mixture of spheres and points are both components of a model that need to be optimized.
Currently there is not much difference in the code which gets executed. There is just one less pass through the Particles for the Point version. When we figure out a way to make the implementations quite different, then it would definitely make sense to have different ScoreStates (even then, I would be a fan of handling it internally to the Nonbonded list so the user doesn't have to worry about it).

Points are very generic in nature and they can be used to represent almost everything (not necessarily physical objects, they can represent average, momentum, etc in 3D space ....). Therefore, we should have them included.
Spheres are a natural subset of points, so any structure which handles spheres would handle points without any real changes. The other way around doesn't work. And I can see people accidentally using the wrong one and wondering why the right thing is not happening.