Keren Lasker wrote:
Sure - if we're going to allow particle deletion, there's no
reason to
have active/inactive.
We might need it for discrete optimization via MC or inference.
I would prefer if you'll leave it till we sort out the discrete
optimization framework.
Currently, once a particle is deactivated, various things will skip
over
it/remove it so trying to reactivate it afterwards would be a bit of a
mess. The problem is that either we have to put checks everywhere in
the
code or we have to remove inactive particles from various lists (like
the set of particles to be checked for nonbonded interactions).
As a result, we should probably remove the methods now. If we want
them
later, we can put them back and change the other code.