Though the AmbiguousConstraint format will blow up the constraint file considerably (certainly depending on the implementation), it should do exactly what I was looking for.
Thank you (once again) for your quick and useful answer.
By the way, does Rosetta handle AmbiguousNMRDistance constraints in the same way? I.e. evaluating all given ones and only scoring the lowest or applicable ones? I observed that if I give my constraints in the AtomPair format the scores are way off and the structures do not converge. With AmbiguousNMRDistance this is not the case but not all constraints seem to be considered. Is this all about the “curvature” option?
AmbiguousNMRDistance atom_name_i res_no_i atom_name_j res_no_j BOUNDED min_dist max_dist curvature
In the literature this value is often set to 0.3.