- For the Domino optimizer, the right addition on restraints may be to
have them return a list of pairs of interacting particles. This way we
don't have to worry about the granularity of the restraint and
nonbonded lists can just return their current list of nonbonded pairs.
- The ChainPair restraint could be simplified to only contain one
chain now that we have reference counting on the PairScores (so you
can share pairscores via shared objects rather than having one
restraint). This simplifies the restraint code a bit.
- I think ObjectPointer should be made part of the API now that we
have reference counting and renamed to IMP::Pointer and it is pretty
stable.