Daniel Russel wrote: > - 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.
Not having yet seen the Domino optimizer, I don't know why you'd want such behavior. But there are definitely restraints that don't act on pairs of particles (e.g. angle restraints). What would they do?
> - 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.
Sounds reasonable to me.
Ben