haddock.clis.restraints.calc_accessibility module

haddock3-restraints calc_accessibility subcommand.

Given a pdb file, it will calculate the relative accessibility of the side chains and return a list of surface exposed residues.

Nucleic acids bases are considered to be always accessible.

Usage:

haddock3-restraints calc_accessibility

<input_pdb_file> Path to a PDB file to analyse [-c <cutoff>] Relative side-chain accessibility cutoff [–log_level <log_level>] DEBUG, INFO, WARNING, ERROR, or CRITICAL [–export_to_actpass] Flag to export accessible resiudes [–probe_radius <probe_radius>] Probe radius for the accessibility calculation

haddock.clis.restraints.calc_accessibility.add_calc_accessibility_arguments(calc_accessibility_subcommand)

Add arguments to the calc_accessibility subcommand.

haddock.clis.restraints.calc_accessibility.apply_cutoff(access_data: dict[str, dict[int, dict[str, float]]], cutoff: float) → dict[str, list[int]]

Apply a cutoff to the sidechain relative accessibility.

haddock.clis.restraints.calc_accessibility.calc_accessibility(input_pdb_file: Path | str, cutoff: float = 0.4, log_level: str = 'INFO', export_to_actpass: bool = False, probe_radius: float = 1.4) → None

Calculate the accessibility of the side chains and apply a cutoff.

Parameters:

• input_pdb_file (str) – Path to the PDB file.

• cutoff (float) – Relative cutoff for sidechain accessibility, default = 0.4

• log_level (str) – Logging level.

• export_to_actpass (bool) – Export the exposed residues as passive to an actpass file.

• probe_radius (float) – Probe radius for the accessibility calculation.

haddock.clis.restraints.calc_accessibility.export_passive(result_dict: dict[str, list[int]], prefix: str = '') → None

Export the exposed residues as passive to an actpass file.

haddock.clis.restraints.calc_accessibility.get_accessibility(pdb_f: Path | str, probe_radius: float = 1.4) → dict[str, dict[int, dict[str, float]]]

Compute per-residue accessibility values.

Calls FreeSASA using its Python API and returns per-residue accessibility values.

Parameters:

pdb_f (Union[Path, str]) – Path to the PDB file of interest.

Returns:

resid_access (dict[str, dict[int, dict[str, float]]]) – Dictionary containing a list of accessible residues for each chain(s).