hey Dainel - is the code checked in already? thanks, Keren.

On Mon, 1 Dec 2008, Daniel Russel 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) > 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 > > > >

Daniel Russel wrote: > No, something looks to be wrong with the repository and anything I try > to commit is rejected without an error message.

Indeed, there is a problem with our svn server this morning, which I will address.

Ben

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

Ben - I might be missing something here but the centroid changes at each optimization step - so this means that the particle will converge slower in the O(N) suggestion than in the O(N^2) suggestion - since the centroid of the previous iteration will hold it back. On Dec 3, 2008, at 7:36 PM, Ben Webb wrote:

> Friedrich Foerster wrote: >> 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. > > The solution already proposed by Daniel looks perfect to me as a > literal > solution to your problem, but is that really what you want to do: > constrain every particle pair in the protein to less than the > diameter? > If you have a lot of particles, that's going to become expensive > rather > quickly (O(N^2), obviously). Another option to consider would be to > constrain every particle to be less than the radius from the protein > center. That would give you far fewer restraints and scale as O(N). > You > could do this with a bunch of DistanceToSingletonScores if the protein > center is at a fixed point, or use a GravityCenterScoreState to > stick a > particle at the center of gravity of your protein, and then use > regular > distance restraints between each particle and that center. > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

currently, we do not have too many particles. but of course it'd be nice to have a faster restraint in any case ;)

tx

frido

On Wed, Dec 3, 2008 at 8:01 PM, Daniel Russel drussel@gmail.com wrote:

> Keren Lasker wrote: > > Ben - I might be missing something here but the centroid changes at > > each optimization step - so this means that the particle will converge > > slower in the O(N) suggestion than in the O(N^2) suggestion - since > > the centroid of the previous iteration will hold it back. > > > The score state is updated before the restraints are evaluated, so it > will always have the position of the current centroid. > > > On Dec 3, 2008, at 7:36 PM, Ben Webb wrote: > > > > > >> Friedrich Foerster wrote: > >> > >>> 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. > >>> > >> The solution already proposed by Daniel looks perfect to me as a > >> literal > >> solution to your problem, but is that really what you want to do: > >> constrain every particle pair in the protein to less than the > >> diameter? > >> If you have a lot of particles, that's going to become expensive > >> rather > >> quickly (O(N^2), obviously). Another option to consider would be to > >> constrain every particle to be less than the radius from the protein > >> center. That would give you far fewer restraints and scale as O(N). > >> You > >> could do this with a bunch of DistanceToSingletonScores if the protein > >> center is at a fixed point, or use a GravityCenterScoreState to > >> stick a > >> particle at the center of gravity of your protein, and then use > >> regular > >> distance restraints between each particle and that center. > >> > >> Ben > >> -- > >> ben@salilab.org http://salilab.org/~ben/http://salilab.org/%7Eben/ > >> "It is a capital mistake to theorize before one has data." > >> - Sir Arthur Conan Doyle > >> _______________________________________________ > >> 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 > >

Ben Webb wrote: > Friedrich Foerster wrote: > >> 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. >> > > The solution already proposed by Daniel looks perfect to me as a literal > solution to your problem, but is that really what you want to do: > constrain every particle pair in the protein to less than the diameter? > If you have a lot of particles, that's going to become expensive rather > quickly (O(N^2), obviously). Another option to consider would be to > constrain every particle to be less than the radius from the protein > center. That would give you far fewer restraints and scale as O(N). You > could do this with a bunch of DistanceToSingletonScores if the protein > center is at a fixed point, or use a GravityCenterScoreState to stick a > particle at the center of gravity of your protein, and then use regular > distance restraints between each particle and that center. > Good point. I hadn't suggested it since it is a looser bound than the diameter in general (not that the looseness is likely to matter :-). Also, since we already have code to compute an enclosing ball of a set of balls we can easily write a gravitycenter-analog which puts the point at the sphere center if you want something tighter than the gravity-center based bounds. Actually, I've been meaning to write such a class for a while.