It is committed now and there are some more comments in the example.
On Dec 1, 2008, at 10:59 AM, Friedrich Foerster wrote:
> thanks a lot. looks like what i need. > can you add some comments at the crucial lines below? > > frido > > On Mon, Dec 1, 2008 at 4:39 PM, Daniel Russel drussel@gmail.com > wrote: > I have some code for you, but the repository appears to be broken. > > Here is the example: > import IMP > import IMP.core > > # This example addes a restraint on bipartite nonbonded interactions > # after excluding a set of bonded interactions. > > m= IMP.Model() > # The set of particles > lc= > IMP.core.ListSingletonContainer(IMP.core.create_xyzr_particles(m, > 20, 1.0)) > ps = IMP.core.AllPairsPairContainer(lc) > > # Set up the nonbonded list > h=IMP.core.HarmonicUpperBound(10,1) > d=IMP.core.DistancePairScore(h) > is that line the actual maximum distance restraint? i guess it is > now a max diameter of 10? > r= IMP.core.PairsRestraint(d, ps) > m.add_restraint(r) > > # Set up optimizer > o= IMP.core.ConjugateGradients() > o.set_model(m) > > o.optimize(100) > > for i in range(0, ps.get_number_of_particle_pairs()): > p= ps.get_particle_pair(i) > print IMP.core.distance(IMP.core.XYZDecorator(p[0]), > IMP.core.XYZDecorator(p[1])) > > On Dec 1, 2008, at 12:11 AM, Friedrich Foerster wrote: > >> hi impians, >> >> for the 26s project i would like to use a maximum diameter restraint >> on the shape of proteins. so it'd be a restraint similar to the >> connectivity restraint: all distances in a protein are evaluated and >> if the largest distance is above a specified threshold, a harmonic >> restraint would be applied on the respective pair. >> did anybody already put something like that into imp? and if no, is >> anybody familiar with the core also interested in that and willing to >> code it? it'd take me ages and the code would be ugly ;) >> >> thanks >> >> frido >> >> -- >> >> Friedrich Foerster >> Max-Planck Institut fuer Biochemie >> Am Klopferspitz 18 >> D-82152 Martinsried >> >> Tel: +49 89 8578 2651 >> Fax: +49 89 8578 2641 >> >> foerster@biochem.mpg.de >> >> www.tomotronic.org >> >> >> >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev