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



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.

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 don't doubt that you can write a 6-12 term, but you cheated and changed the example. ;) (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.)

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle