Haddock3 online user manual

[VGPReys]

Pull request related to the haddock3 user manual.

TODO list:

• [x] Manual.md
• [ ] Introduction
  • [x] HADDOCK
  • [x] Haddock3 modularity
• [ ] Installation
  • [ ] GitHub repository
  • [ ] CNS
  • [ ] Virtual environments (conda / venv)
• [x] Command Line Interfaces (CLI)
  • [x] haddock3
  • [x] haddock3-cfg
  • [x] haddock3-restraints
  • [x] haddock3-score
  • [ ] haddock3-analyse
  • [ ] haddock3-traceback
  • [ ] haddock3-re
  • [x] haddock3-copy
  • [ ] haddock3-clean
  • [ ] haddock3-unpack
  • [ ] haddock3-mpitask
  • [ ] haddock3-dmn
  • [ ] haddock3-pp
  • [ ] haddock3-bm
• [ ] Preparing input files
  • [ ] Haddock3 requirements (chains, no resid duplicates, no altloc, etc...)
  • [ ] pdb tools to manipulate input structures
• [ ] Generating restraints for HADDOCK
  • [ ] General introduction
  • [ ] haddock-restraints command line interface
    • [ ] calc_accessibility
    • [ ] passive_from_active
    • [ ] active_passive_to_ambig
    • [ ] restrain_bodies
  • [ ] Symmetry restraints
  • [ ] Ab-initio docking mode
  • [x] Flexibility
    • [x] Molecules Segments
    • [x] Semi-flexible
    • [x] Fully-flexible
• [ ] Generating a docking protocol
  • [ ] Global parameters
  • [ ] Concept of modules / parameters
• [ ] Available modules
  • [ ] Topology
  • [ ] Sampling
  • [ ] Refinements
  • [ ] Scoring
  • [ ] Analysis
• [ ] Docking scenario examples
• [ ] Getting support / How to ask for help
• [ ] Citing haddock3
• [ ] Acknowledgement

[amjjbonvin]

It's start! Nice.

[amjjbonvin]

I would also add sections about:

• flexibility options
• ab-initio docking mode (for CM restraints and random airs)
• symmetry restraints

May-be as part of a general section about restraints in HADDOCK3 and this is also where the haddock-restraints part should be residing

[AnnaKravchenko]

Question about flexibility options. It is about explaining how to make molecule/part of molecule flexible/semi-flexible in haddokc3, only practical things, right?
Or would you like to see a more theoretical explanation about flexibility in haddock, i.e. that semi-flexible refinement is happening in torsion angle space etc.?

[VGPReys]

Question about flexibility options. It is about explaining how to make molecule/part of molecule flexible/semi-flexible in haddokc3, only practical things, right? Or would you like to see a more theoretical explanation about flexibility in haddock, i.e. that semi-flexible refinement is happening in torsion angle space etc.?

flexref is a module and will have its own documentation.

In my opinion, it is more about explaining how to make molecules/segments flexible/semi-flexible.
Detailed explanation on the various parameters used to define it, and in which modules they can be used.