FCC Clustering module

Submodules

Module contents

Fraction of Common Contacts (FCC) clustering module.

The module takes the models generated in the previous step and calculates the contacts between them. Then, the module calculates the FCC matrix and clusters the models based on their contact similarities.

For more details about this clustering method, please check Rodrigues, J. P. et al. Proteins: Struct. Funct. Bioinform. 80, 1810–1817 (2012)

Note that the output models are reordered by cluster rank and the rank within each cluster; this means that the order of output models of this cluster will be different than the input - this may be relevant for modules executed downstream.

For more details about this module, please refer to the haddock3 user manual

class haddock.modules.analysis.clustfcc.HaddockModule(order: int, path: Path, initial_params: Path | str = PosixPath('/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/haddock/modules/analysis/clustfcc/defaults.yaml'))[source]

Bases: BaseHaddockModule

HADDOCK3 module for clustering with FCC.

classmethod confirm_installation() → None[source]

Confirm if FCC is installed and available.

name: str = 'clustfcc'

Default Parameters

Easy

clust_cutoff

default: 0.6
type: float
title: Minimum fraction of common contacts to be considered in a cluster.
min: 0.0
max: 1.0
short description: Minimum fraction of common contacts to be considered in a cluster. By default 0.6.
long description: Minimum fraction of common contacts (fcc) to cluster complexes together. Complexes not sharing fraction of common contacts above the fraction_cutoff parameter cannot belong to the same cluster.
group: analysis
explevel: easy

contact_distance_cutoff

default: 5.0
type: float
title: Cutoff distance (A) for contact detection.
min: 2.0
max: 999.99
short description: Cutoff distance (A) for contact detection. By default 5.0 Angstroms.
long description: Cutoff distance between two atoms for contact detection. By default 5.0 Angstroms.
group: analysis
explevel: easy

min_population

default: 4
type: integer
title: Clustering population threshold.
min: 1
max: 9999
short description: Threshold employed to exclude clusters with less than this number of members. By default 4.
long description: Minimum set of grouped complexes to define a cluster. If a potential cluster is composed of less than this number of members, it will be considered as singleton and discarded from final clusters. If set to 1, all complexes will be part of a cluster. By default 4.
group: analysis
explevel: easy

plot_matrix

default: False
type: boolean
title: Plot matrix of members
short description: Plot matrix of members. By default is false.
long description: Plot matrix of members. By default is false.
group: analysis
explevel: easy

strictness

default: 0.75
type: float
title: Strictness factor.
min: 0.0
max: 1.0
short description: Strictness factor. It’s multiplied by the fraction_cutoff to obtain a new cutoff for the second half of the matrix. By default 0.75.
long description: Strictness factor. It’s multiplied by the fraction_cutoff to obtain a new cutoff for the second half of the matrix. Used to allow for some variability. By default 0.75.
group: analysis
explevel: easy

Expert

executable

default: ‘src/contact_fcc’
type: file
title: Relative path to contact_fcc executable.
short description: Relative path to contact_fcc executable.
long description: As contact_fcc is an external tool, its path must be provided. Basically, this parameter should not be changed, as the tool is downloaded at the same time as haddock3. Nevertheless, one could try to have the contact_fcc tool written in another programming language or whatever.
group: executable
explevel: expert