When you get a Restraint back from a RestraintSet, python doesn't know that the thing returned is a ConnectivityRestraint and so the only methods available are those for a generic Restraint. You can cast the resulting object to, eg, a ConnectivityRestraint by doing IMP.core.ConnectivityRestraint.get_as(the_restraint). This will throw an exception if the cast does not succeeed.
On Sep 15, 2011, at 8:32 AM, Pia Unverdorben wrote:
> Dear all, > > I try to access the connected pairs of a connectivity restraint via get_connected_pairs(). Directly after defining the restraint, everything works fine. Now my problem is, that after adding it to a RestraintSet and retrieving it, the same function always gives an attribute error. Show() tells me in both cases that it is a connectivity restraint, so get_connected_pairs should work the same way? > My test case is below (modified from the connectivity restraint example). What is wrong? Is there any possibility to get this connected pairs out of the restraint set? > Any help is greatly appreciated! > > Thanks, > Pia > > > import IMP > import IMP.core > import IMP.misc > import IMP.algebra > import IMP.atom > > m=IMP.Model() > hs=[] > # create the molecules, with 5 particles for each of 10 molecules > for i in range(0,10): > p=IMP.Particle(m) > d= IMP.atom.Hierarchy.setup_particle(p) > for j in range(0,5): > p=IMP.Particle(m) > cd= IMP.atom.Fragment.setup_particle(p) > d.add_child(cd) > xd= IMP.core.XYZR.setup_particle(p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(3*i,j,0), 1)) > hs.append(p) > > ps= IMP.core.SphereDistancePairScore(IMP.core.HarmonicUpperBound(0,1)) > cps= IMP.core.ChildrenRefiner(IMP.atom.Hierarchy.get_traits()) > > # score based on the one closest particle from each set of balls > lrps = IMP.misc.LowestRefinedPairScore(cps, ps) > #lrps = IMP.core.KClosePairsPairScore(ps, cps, 1) > # connect all 10 molecules together > cr = IMP.core.ConnectivityRestraint(lrps) > cr.set_particles(hs) > rs_set=IMP.RestraintSet('connectivity') > m.add_restraint(rs_set) > rs_set.add_restraint(cr) > cr.show() > print len(cr.get_connected_pairs()) > print m.evaluate(False) > > > for i in range(0,rs_set.get_number_of_restraints()): > res=rs_set.get_restraint(i) > res.show() > if res.get_is_part_of_model(): > print "is part of model" > pairs=res.get_connected_pairs() > print len(pairs) > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users