On 7/14/25 5:55 AM, Michael Brunsteiner via IMP-users wrote:
> In the main loop there are appear to be two commands that do the majority of the work:
>
> ub_sampler->apply(dof_values[i]);
> kfss->do_before_evaluate();
>
> can you suggest which of those I will find what i am looking for ?
I am not that familiar with the IMP.kinematics module so cannot really
answer your question, but kfss is a ScoreState, namely an IMP class that
perturbs the model before or after scoring. Usually these are used to
maintain some kind of invariant or constraint, like a center of mass or
a rigid body. Here I think this is just converting the internal
representation (a set of angles) to Cartesian coordinates for PDB
output. That's not the actual scoring or sampling itself. For those you
probably want to look at the UniformBackboneSampler and RRT classes at
https://github.com/salilab/imp/tree/develop/modules/kinematics/include
and https://github.com/salilab/imp/tree/develop/modules/kinematics/src
Ben
--
https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle