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Re: [IMP-dev] maximum diameter restraints

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.

"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle
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