[attract] as a sampling module

[AnnaKravchenko]

Desired feature/enhancement

Add a rigid fragment-based protein-ssRNA doking pipeline, performed by the ATTRACT docking engine, as a sampling module of HADDOCK.

Motivation

1. Introduces a dedicated docking workflow for protein-ssRNA complexes within HADDOCK, eliminating the need for CNS-based sampling;
2. Could potentially be executed in an anchored manner, when a single fragment is docked using restraints (obtained using experimental data, etc.), and consecutive fragments are docked using restraints towards the previous fragment(s);
3. Could potentially be expanded to protein-protein and protein-DNA docking (supported by ATTRACT but outside of my current competency).

Description

[attract] module should handle the full docking workflow, consisting of the following steps:

1. Preparation of the input folder, protein coarse-graining
2. Sampling, a per-fragment rigid-body energy minimisation, with or without restraints
3. Scoring with ATTRACT scoring function or with HIPPO
4. Assembly of RNA fragments into a full-chain docking models
5. Conversion of a limited number of models back to all-atom representation

Additional context

Paper about fragment-based protein-ssRNA doking
Paper about anchored docking