[IMP-dev] performance of Connectivity restraint

hi all,

I am writing a test case for adding hierarchy support in DOMINO, and it seems that the connectivity restraint works incredibly sssllllooowww between two proteins each of ~100 residues.

i=0 ub = IMP.core.HarmonicUpperBound(1.0, 0.1) ss= IMP.core.DistancePairScore(ub) r= IMP.core.ConnectivityRestraint(ss) ps = IMP.Particles() ps_refined=[] for j in xrange(2):

ps_refined.append(IMP.core.hierarchy_get_leaves(self.h_particles[i+j])) ps.append(self.particles[i+j]) for e in ps_refined: r.add_particles(e)

beg = time.time() r.evaluate(None) end = time.time() dt = end - beg print 'connectivity restraint calculation took %9.6f Seconds' % (dt)

The evaluate function takes ~20 seconds.

am I missing something here? is there a faster implementation using some external library ?

thanks, Keren.