Daniel Russel wrote:
> For a while I have been thinking it would be nice to add another layer
> of indirection for particle storage in IMP. The idea would be that we
> add some base classes like:
> class ParticleContainer {
> //provide virtual get_number, get, find etc.
> }
> class ParticlePairContainer;
> class ParticleSetContainer;
Sounds like a reasonable interface to me.
> Then restraints would internally have a appropriate particle
> container. The nice thing would be that you could then choose to share
> containers between restraints and states as needed, reducing the
> number of things that need to be updated when something changes.
>
> This could be implemented without changing the existing API since we
> could leave the exiting get/set methods in the restraints. And just
> add a method to set the container if you want it shared.
>
> NonbondedListRestraint would go away we we would just have
> PairListRestraint (you just set the ParticlePairContainer in the
> restraint to be the NonbondedList). Likewise, the BondedList base
> class goes away and the BondDecoratorListRestraint.
There definitely needs to be a little more flexibility in the nonbonded
list implementations. For example, it is often necessary to exclude
pairs other than bonded pairs, for example 1-3 (angle) or 1-4 (dihedral)
pairs, or specifically listed pairs (e.g. protein-ligand close
contacts). Seems like it would make sense to allow this functionality in
whatever container is used by the nonbonded list.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle