haddock.clis.restraints.restrain_ligand module

haddock3-restraints restrain_ligand subcommand.

Given an input PDB file and a residue name (ligands), the tool will create unambiguous restraints to keep this ligand in place during the refinements.

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)

haddock.clis.restraints.restrain_ligand.add_restrain_ligand_arguments(restrain_ligand_subcommand)

Add arguments to the random removal subcommand.

haddock.clis.restraints.restrain_ligand.main(pdb_file: str | Path, ligand_name: str, radius: float = 10.0, deviation: float = 1.0, max_restraints: int = 20) → None

Simple wrapper of the restrain_ligand function.

haddock.clis.restraints.restrain_ligand.restrain_ligand(pdbfile: str | Path, ligand_name: str, radius: float = 10.0, deviation: float = 1.0, max_restraints: int = 20) → str

Generate unambiguous restraints to keep a ligand in place.

Parameters:

• pdbfile (Union[str, Path]) – Path to a PDB file containing a ligand

• ligand_name (str) – Residue name of the ligand to work with

• radius (float, optional) – Radius used for neighbors search around center of mass of ligand, by default 10.0

• deviation (float, optional) – Allowed deviation from actual distance, by default 1.0

• max_restraints (int, optional) – Maximum number of restraints to return, by default 20

Returns:

unambig_str (str) – The actual unambiguous restraints as a string.