Subject: Re: [IMP-dev] maximum diameter restraints
From: Daniel Russel <>
Date: Wed, 3 Dec 2008 14:43:41 -0800
Reply-to: List for IMP development <>
For small numbers of particles, the quadratic approach should be faster. What small means is less clear :-)
On Dec 3, 2008, at 2:41 PM, "Friedrich Foerster" <">> wrote:
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 <">">> 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
>> --
>> ">">http://salilab.org/~ben/
>> "It is a capital mistake to theorize before one has data."
>> - Sir Arthur Conan Doyle
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