Refactor `kinmodel` set of scripts

[jaimergp]

Description

Start refactor of @pkiruba's kinmodel (first set of patches in this fork).

Todos

• [ ] Refactor scripts into library pieces and assemble the actual script as part of workflows
  • [ ] Structural alignment
  • [ ] Sequence alignment
  • [ ] Model building
  • [ ] Structure minimization
• [ ] Provide Rosetta alternatives using OpenMM and others.

Questions

• [ ] Availability of in-house datasets. Can we redistribute them with the code?

Status

• [ ] Ready to go