Core clipping step

[giacomomutti]

Hello, thanks for this amazing tool!
I have been trying to reproduce the foldtree pipeline in my personal scripts, however I do not understand how the "Structure trimming to find the core region" step (presented in the supp mat of the preprint) is implemented.

From what I see in the foldtree.py pipeline there is an option to clip it whereas this is not possible in the snakemake pipeline, even though the clip_core.py script seems to have been developed for this.

So, my doubts are: 1) in order to reproduce the pipeline of the preprint should I clip or not? 2) Will you implement this option in the smk version?

Thanks!