Re: [IMP-dev] performance of Connectivity restraint

[Keren Lasker <>]

just for the records,
Ben suggested compiling with release=true, which reduced the running  
time to ~7 seconds.
I still think we should consider a faster implementation. Maybe use  
geometric hashing to query close particles in space.
On Jan 26, 2009, at 9:43 PM, Keren Lasker wrote:

> 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.
>
>
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