Haddock3 online user manual

[VGPReys]

Pull request related to the haddock3 user manual.

TODO:

• Make it an mdbook

TODO list:

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

[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.

[rvhonorato]

Moved to https://github.com/haddocking/haddock3-user-manual/pull/1