Surface Accessibility Scoring module

Submodules

haddock.modules.scoring.sasascore.sasascore module

Module contents

Surface accessibility scoring module.

This module performs a solvent accessibility analysis based on some user-defined residues that should be buried or accessible.

If a supposedly buried (resp. accessible) residue is accessible (resp. buried), the score should increase by one. The lower the final score the more consistent the model with the user data.

To run this module, the user must provide a dictionary with the buried and/or accessible residues. The keys of the dictionary should be the chain identifiers and the values should be lists of residue numbers.

Example:

>>> resdic_buried_A: [1, 2, 3]
>>> resdic_accessible_B: [4, 5, 6]

class haddock.modules.scoring.sasascore.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/scoring/sasascore/defaults.yaml'))[source]

Bases: ScoringModule

HADDOCK3 module to perform accessibility scoring.

classmethod confirm_installation() → None[source]: Confirm module is installed.

name: str = 'sasascore'

Default Parameters

Easy

cutoff

default: 0.4
type: float
title: relative side chain surface accessibility cutoff
min: 0.0
max: 1.0
short description: relative side chain surface accessibility cutoff
long description: relative side chain surface accessibility cutoff. Residues with a relative side chain surface accessibility below this value are considered buried.
group: scoring
explevel: easy

resdic_accessible 

default: []
type: list
title: List of residues supposed to be accessible
short description: List of residues supposed to be accessible
long description: resdic_* is an expandable parameter. You can provide resdic_accessible_A, resdic_accessible_B, resdic_accessible_C, etc, where the last capital letter is the chain identifier.
group: analysis
explevel: easy

resdic_buried 

default: []
type: list
title: List of residues supposed to be buried
short description: List of residues supposed to be buried
long description: resdic_buried_* is an expandable parameter. You can provide resdic_buried_A, resdic_buried_B, resdic_buried_C, etc, where the last capital letter is the chain identifier.
group: analysis
explevel: easy

Expert

probe_radius

default: 1.4
type: float
title: Probe radius
min: 0.0
max: 10.0
short description: Probe radius
long description: Sets the probe radius (in Angstrom) used to compute solvent accessible surface area.
group: analysis
explevel: expert