To make my previous email more concrete (and revise things slightly),
deactivating particles would involve:
- telling the Model to delete the particle. That removes the pointer
in the model and frees the index up to be recycled
- the ParticleIterators in the model skip delete particles (skip null
pointers)
- the particle is marked as invalid and any accesses to it throw
exceptions
- all pointers to the particle are reference counted and the particle
object is deleted when all of them go away
This sounds reasonable to me. I agree that the most sensible way to do
this properly is to have a reference counted Particle-pointer attribute
for Particles. But don't worry too much about the reference counting in
Python - I can look at that. However, I suggest rather than a single
pointer attribute we use a vector<Particle pointer> attribute. This
would certainly make things like hierarchies much easier to implement
(plus, much faster, since you could just cache a 'child'
ParticleVectorKey rather than having to do a lot of lookups for child1,
child2, child3 etc.) Pointers to single particles are probably
sufficiently unusual that the overhead of a single-element list is
negligible.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle