I find confusing the term non-sphere, since it is too fuzzy (ie. it can be almost anything !)
I suggest to use sphere object as it is (which of course has a radii attribute that must be larger than zero) and to have a point object (which either by definition has a radii value of zero or it does not have such an attribute at all. In the former case, just by defining a point object, the system should immediately define a zero value for the radii attribute and we should not bother the user to enter dummy values).
I think, for completeness, we should have both type of objects (sphere and point). 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. 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.
Pancho. On Mar 24, 2008, at 8:52 PM, Daniel Russel wrote:
Does it makes sense to have sphere and non-sphere versions of nonbonded lists (ones with and without non-zero radii)? I know there are contexts where you can get away with the latter, but it seems like we mostly want spheres and the added confusion and maintenance burden might overwhelm the advantage. Thoughts? I don't see myself using the non-sphere version. If the radii are zero, the difference comes down to fetching a zero attribute and adding it to each radius. And making sure that each particle has such an attribute. _______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev