Here is a new patch which includes the get_interacting_particles code.
It is not implemented for NonbondedRestraint as that did not appear to
be currently needed and required a few changes to the nonbonded lists
and so was not entirely trivial.
In as r652 with bug fixes and testcases. Keren, why don't you take a
look at it in latest SVN and see if you can make DOMINO work with it?
I don't have the time to review the rest of this patch as a whole. If
there are parts that you think others can use in the kernel, then send
in more targeted patches for those, please. Experimental restraints and
scores and whatnot can go in a separate module, either in the IMP
repository (as per impEM and DOMINO) or elsewhere. Either way you can
play with them there without the degree of scrutiny reserved for the kernel.