sorry for my ignorance of this discussion for a while.
i presume most people will want to use imp in a probabilistic
framework rather than doing simulations with physical form-fields.
Who knows? But we should allow for both.
philosophically, i agree with with daniel that the name 'Harmonic'
requires a spring constant.
Yes, you are a bit late here - we changed that ages ago!
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.
Agreed - it's straightforward to introduce new unary functions. We can
just stick them in as and when necessary.
i think the current workaround, i.e. introducing scaling parameters
through the back-door, is a bit unsatisfactory and will confuse most
users.
I didn't realize that's what you were using scaling of restraints for,
but I don't think that was ever their intended purpose. Scaling has been
very useful for people tweaking their scoring functions - and I don't
see that going away - but for your purposes it certainly sounds like new
unary functions are a better bet.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle