Francisco Melo wrote: > is the non-sphere object representing something like a cube or other > geometric object in the future ?
Nonbonded lists currently come in two forms, as I understand it - one works for points (i.e. get a list of all point pairs within distance N) while the other works for spheres (i.e. get a list of all sphere pairs with surface-surface distances within N). The latter essentially takes the distance N and adds the radii of the two spheres.
> I find confusing the term non-sphere, since it is too fuzzy (ie. it > can be almost anything !)
By non-sphere in this context we mean a particle that does not have a radius, but does have xyz coordinates.
> 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).
We don't have objects since C++ is not dynamically typed, but the closest approximation to what you suggest is the XYZDecorator. Particles themselves can have any attributes you like, so you could certainly define particles to represent things which are not points or spheres. For example, we already have particles to store a protein hierarchy (residues, chains, whole proteins) and these don't have xyz coordinates or radii, of course.
Ben