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