thanks! What I want is a similar thing to AngleTripletScore, but for a distance metric over rotation tensor between two reference frames. Computing the distance per se is not the hard part (this could be in Euler angles or between the quaternion or a geodesic on the unit sphere) - the painful part is computing the derivative in Cartesian coordinates form. I was hoping somebody went through this pain already... :)


On Tue, Mar 25, 2014 at 6:55 PM, Ben Webb <ben@salilab.org> wrote:
On 3/25/14, 6:47 PM, Barak Raveh wrote:
Does anybody know of an existing implementation of a harmonic restraint
on rotational degrees of freedom?

Sure, this is essentially how an angle restraint works in the CHARMM forcefield, for example.


Namely, I have two reference frame of two particles p1 and p2. For
simplicity, assume xyz(p1) = xyz(p2). I would like to add a harmonic
restraint over the delta in their reference frame, for some definition
of that delta.

You just need to encode that delta (e.g. as a PairScore) then plug it into the existing framework. For example, see core::AngleTripletScore.

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



--
Barak