Re: [IMP-dev] Harmonic cleanup

[Daniel Russel <drussel@salilab.org>]

> philosophically, i agree with with daniel that the name 'Harmonic'  
> requires a spring constant.
> to make everybody happy, i would propose a new name for functions  
> that call the harmonic functions, but have spatial parameters as an  
> input. for example LogGauss, LogUpperDistanceGauss or whatever you  
> agree with.
> is anybody be willing to contribute something like that to the  
> kernel (i am an official application guy, so the kernel is 'tabu'  
> for me)? i think the current workaround, i.e. introducing scaling  
> parameters through the back-door, is a bit unsatisfactory and will  
> confuse most users.
I agree that adding a new set of scoring functions in the most  
satisfactory response. There is still the question of whether we  
should use straight standard deviation (so the energy is simply  
delta^2/ (2*sigma^2)) or have scaling factors as in the old harmonic.