Contact Map module

Submodules

Module contents

Compute contacts and generate heatmaps.

class haddock.modules.analysis.contactmap.HaddockModule(order: int, path: Path, *ignore: Any, init_params: str | Path = PosixPath('/home/runner/work/haddock3/haddock3/src/haddock/modules/analysis/contactmap/defaults.yaml'), **everything: Any)[source]

Bases: BaseHaddockModule

HADDOCK3 module to compute complexes contacts and generate heatmap.

classmethod confirm_installation() → None[source]

Confirm if contact executable is compiled.

name: str = 'contactmap'

Default Parameters

Easy

ca_ca_dist_threshold

default: 9.0
type: float
title: Ca-Ca distance defining a contact.
min: 4.0
max: 1000.0
short description: Distance between Ca atoms of two residues defining a contact.
long description: Distance between Ca atoms of two residues defining a contact.
group: analysis
explevel: easy

chordchart_datatype

default: ‘shortest-dist’
type: string
title: Type of data to be used in the chordchart.
choices: [‘ca-ca-dist’, ‘shortest-dist’]
short description: Type of data to be used in the chordchart.
long description: ca-ca-dist and shortest-dist are averages distances observed in cluster.
group: analysis
explevel: easy

cluster_heatmap_datatype

default: ‘shortest-cont-probability’
type: string
title: Type of data to be used in the heatmap.
choices: [‘ca-ca-dist’, ‘ca-ca-cont-probability’, ‘shortest-dist’, ‘shortest-cont-probability’]
short description: Type of data to be used in the heatmap.
long description: ca-ca-dist & shortest-dist are averages distances observed in cluster. ca-ca-cont-probability & shortest-cont-probability are probability of the distances to be observed under their respective thresholds.
group: analysis
explevel: easy

color_ramp

default: ‘Greys’
type: string
title: Color ramp used to color heatmap.
choices: [‘Greys’, ‘Purples’, ‘BuPu’, ‘Blues’, ‘BuGn’, ‘Greens’, ‘deep’, ‘tempo’, ‘algae’, ‘dense’, ‘amp’]
short description: Color ramp used to color heatmap.
long description: Color ramp used to color heatmap. Please refer to plotly builtin-colorscales for more information
group: analysis
explevel: easy

generate_chordchart

default: True
type: boolean
title: Generate chordchart.
short description: Generate plotly chordchart representation of the contacts.
long description: Uses generated contact matrices files to generate chord chart.
group: analysis
explevel: easy

generate_heatmap

default: True
type: boolean
title: Generate contact heatmap.
short description: Generate plotly heatmap matrix representation of the contacts.
long description: Uses generated contact matrices files to generate heatmap.
group: analysis
explevel: easy

shortest_dist_threshold

default: 4.5
type: float
title: Distance defining a contact between two residues.
min: 2.0
max: 1000.0
short description: Shortest distance between any atom of two residues defining a contact.
long description: Shortest distance between any atom of two residues defining a contact.
group: analysis
explevel: easy

single_model_analysis

default: False
type: boolean
title: Analyse contacts at single model level.
short description: Analyse contacts at single model level.
long description: In addition to cluster analysis, also perform single model analyses.
group: analysis
explevel: easy

Expert

topX

default: 10
type: integer
title: Number of unclustered models to analyse.
min: 1
max: 100
short description: Number of unclustered models to analyse.
long description: Top X unclustered models to analyse. Models are sorted based on their score (if accessible) and only a subset defined by this variable are analysed. If no score available, a random set of topX models are analysed.
group: analysis
explevel: expert