Haddock3 online user manual

[VGPReys]

Pull request related to the haddock3 user manual.

Contribute to the book

The book source code is located in software/haddock3/src/.
From here, consider only relative paths for things to be functional.

Compile the book

This manual is ment to be compiled by mdbook.

To generate it, mdbook must be installed (see how to install mdbook).

Then run the following command, once in the software/haddock3/ directory:

mdbook build haddock3-manual --dest-dir ../manual
# or
/Applications/mdbook build haddock3-manual --dest-dir ../manual

Summary

note: Check when reviewed

• Make it an mdbook
• [x] Manual.md
• [x] 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
  • [X] haddock3-dmn # not described, to obscure, useless
  • [x] haddock3-pp
  • [X] haddock3-bm. # not described, obsolete, replaced by haddock-runner
• [x] Preparing input files
  • [x] Haddock3 requirements (chains, no resid duplicates, no altloc, etc...)
  • [x] pdb tools to manipulate input structures
• [x] Generating restraints for HADDOCK
  • [x] General introduction
  • [x] haddock-restraints command line interface
    • [x] calc_accessibility
    • [x] passive_from_active
    • [x] active_passive_to_ambig
    • [x] restrain_bodies
    • [x] z-restraints
  • [X] Symmetry restraints
  • [x] Ab-initio docking mode
  • [x] Flexibility
    • [x] Molecules Segments
    • [x] Semi-flexible
    • [x] Fully-flexible
• [x] Generating a docking protocol
  • [x] Configuration file
  • [x] Global parameters
  • [x] Concept of modules / 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] FAQ
• [x] Tutorials
  • [x] Access to various tutorials
  • [x] Best practice guide
    • [x] Structure preparation
    • [x] Generating restraints
    • [x] Small-molecules / Ligands
    • [x] Glycans
    • [x] Peptides
    • [x] DNA / RNA
    • [x] Proteins
    • [x] Clustering
    • [x] Analysing results
• [x] Online lectures
• [x] haddock3 source code architecture
• [x] Citing haddock3
• [x] 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.