Alanine Scanning module

Submodules

haddock.modules.analysis.alascan.scan module

Module contents

HADDOCK3 module for alanine scan.

This module is responsible for the alanine scan analysis of the models generated in the previous step of the workflow. For each model, the module will mutate the interface residues and calculate the energy differences between the wild type and the mutant, thus providing a measure of the impact of such mutation.

If cluster information is available, the module will also calculate the average energy difference for each cluster of models.

class haddock.modules.analysis.alascan.HaddockModule(order, path, *ignore, init_params=PosixPath('/home/runner/work/haddock3/haddock3/src/haddock/modules/analysis/alascan/defaults.yaml'), **everything)[source]

Bases: BaseHaddockModule

HADDOCK3 module for alanine scan.

classmethod confirm_installation()[source]: Confirm if module is installed.

name: str = 'alascan'

Default Parameters

Easy

int_cutoff

default: 5.0
type: float
title: Distance cutoff (Å) used to define interface contacts.
min: 1.0
max: 20.0
short description: Distance cutoff (Å) used to define interface contacts between two interacting molecules.
long description: Distance cutoff (Å) used to define interface contacts between two interacting molecules.
group: analysis
explevel: easy

output

default: False
type: boolean
title: Dump all the models in the output folder
short description: Dump all the models in the output folder with the delta_score written in the b-factor column.
long description: Dump all the models in the output folder with the delta_score written in the b-factor column.
group: analysis
explevel: easy

plot

default: False
type: boolean
title: Plot scanning data.
short description: Plot scanning data.
long description: Plot scanning data.
group: analysis
explevel: easy

scan_residue

default: ‘ALA’
type: string
title: Residue to be used for the scanning
choices: [‘ALA’, ‘ARG’, ‘ASN’, ‘ASP’, ‘CYS’, ‘GLN’, ‘GLU’, ‘GLY’, ‘HIS’, ‘ILE’, ‘LEU’, ‘LYS’, ‘MET’, ‘PHE’, ‘PRO’, ‘SER’, ‘THR’, ‘TRP’, ‘TYR’, ‘VAL’, ‘ALY’, ‘ASH’, ‘CFE’, ‘CSP’, ‘CYC’, ‘CYF’, ‘CYM’, ‘DDZ’, ‘GLH’, ‘HLY’, ‘HY3’, ‘HYP’, ‘M3L’, ‘MLY’, ‘MLZ’, ‘MSE’, ‘NEP’, ‘PNS’, ‘PTR’, ‘SEP’, ‘TOP’, ‘TYP’, ‘TYS’]
short description: Residue to be used for the scanning. The default is alanine.
long description: Residue to be used for the scanning. The default is alanine. Use bigger residues at your own risk.
group: analysis
explevel: easy

Expert

resdic 

default: []
type: list
title: List of residues to be mutated
short description: List of residues to be mutated. By default all the interface residues are mutated.
long description: List of residues to be mutated. By default all the interface residues are mutated. resdic_* is an expandable parameter. You can provide resdic_A, resdic_B, resdic_C, etc, where the last capital letter is the chain identifier.
group: analysis
explevel: expert