I think we may want to think about removing the list of particles from
the Restraint base class and providing several restraint subclasses
which use different containers to store the particles (this would be a
fairly minor change given the IMP_RESTRAINT macro and the current
interface). Then, we could have restraints which require a dynamic set
use a std::set, and ones which just have a static list or (like distance
restraint) a fixed number, use a vector or just member variables.
Agreed - although I suggest there's little point in doing that unless we
have specific restraints in mind which need such functionality.
I have ended up rolling my own version of ExclusionVolume. I have a
version which either enforces excluded volume, or, if the particles are
bonded, enforces the bond (it uses the BondDecorator def of bond). I
suspect something on those lines will be more useful in the long run as
we rarely have a set of particles where nothing is interacting tightly.
As you mention elsewhere, this is probably pretty slow. The usual way of
doing such a thing efficiently (at least in molecular mechanics
packages) is to have two restraints - one is the stereochemical
restraint, a simple loop over all bonds (in the Modeller case, this is
done just once and restraints are set up for each bond) while the second
is the excluded volume restraint, a loop over all nonbonded pairs. Part
of the nonbonded pair generation mechanism excludes bonded particles.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle