Restrain ligand

[VGPReys]

Checklist

• Tests added for the new code
• Documentation added for the code changes
• Modifications / enhancements are reflected on the haddock3 user-manual
• CHANGELOG.md is updated to incorporate new changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

As proposed by an external user, this PR introduce an additional subcommand restrain-ligand into the haddock3-restraints CLI.
This new sub-command allows to select a residue name from a PDB file and generate unambiguous restraints keeping it in place.
This is an adaptation of the script used in the shape restraint docking set of script (restrain_ligand.py), and also similar to what can be performed by the restrain command from the haddock-restraints package.

Usage:
    haddock3-restraints restrain_ligand <pdb_file> <ligand_name> -r <radius> -d <deviation> -n <max_nb_restraints>

positional arguments:
  pdb_file              Input PDB file.
  ligand_name           Residue name.

options:
  -h, --help            show this help message and exit
  -r RADIUS, --radius RADIUS
                        Radius used for neighbors search around center of mass of ligand.
                        (default: 10.0)
  -n MAX_RESTRAINTS, --max-restraints MAX_RESTRAINTS
                        Maximum number of restraints to return. (default: 200)
  -d DEVIATION, --deviation DEVIATION
                        Allowed deviation from actual distance. (default: 1.0)

Related Issue

Closes #1299
Description in user manual is made in PR13 of haddock3-user-manual

[AnnaKravchenko]

Question:
Does unambiguous restraints violation counts towards “Restraints Energy” in report.html?
Because I do not see this happening, and wonder if its normal or if smth wrong with my .cfg

[amjjbonvin]

It is part of the distance restraint energy term (ambig+unambig+hbond combined, i.e. all distance restraints).