Re: [IMP-dev] Proposal: replace BasicScoreFuncParams with PairPotential

[Daniel Russel <>]

On Jan 4, 2008, at 11:59 AM, Ben Webb wrote:

> Daniel Russel wrote:
> > > Maybe some pseudocode
> > > would elucidate this.
> > So lets look at evaluating an excluded volume potential for all  
> > nearby
> > pairs.
> ...
>
> OK, looks reasonable, but could you show it with derivatives as  
> well? I
> want to see how you propose combining these.
Ummm, sure. I don't see how that complicates anything. Separate email.

> > If we decided we want to move to a realish Leonard Jones potential
>
> The reason I chose a harmonic term for the example is because both the
> mean and the standard deviation would have to be tweaked, and I don't
> see how you propose to do that with your proposal.
I skipped changing the mean because you don't really have to. If the  
case if a repulsive potential, what you really want is a harmonic  
lower bound on the distance between the two spheres (not between their  
centers). So I passed the distance between the two spheres to the  
ScoreFunc instead of changing the mean.

My proposal has to be made more complicated if you want to change the  
standard deviation on a per-pair basis (rather than on a per-restraint  
basis), but I think if you are doing that you have moved beyond a  
general ScoreFunc into something more specific. We can always add  
subclasses of ScoreFunc which take extra parameters if needed (and the  
replacement for SphereDistanceScore could get the values for these  
parameters from the particles as it does with the radius).

> (And it's odd that you say LJ isn't a simple function of distance,
> because Modeller does have a 6-12 math form, so there's nothing to  
> stop
> you restraining an angle with a 6-12 form if you were sufficiently
> inclined.)
What I meant is that the shape changes as you change the radius of the  
particles, it is not just a shift of the minimum. So you can't just  
shift the origin for computations as you can in the harmonic case. You  
could have a 6-12 ScoreFunc and pass it the ratio of the radii to the  
distance, but this would require (in my proposal) a different  
PairScoreFunction, or in the current model, a whole new restraint.