Contact Map module
Submodules
Module contents
Compute contacts between chains in complexes.
The [contactmap] module aims at generating heatmaps and chordcharts of
the contacts observed in the input complexes.
If complexes are clustered, the analysis of contacts will be performed based on all structures from each cluster.
Heatmaps are describing the probability of contacts (<5A) between two residues (both intramolecular and intermolecular).
Chordcharts are describing only intermolecular contacts in circles, connecting with chords the two residues that are contacting.
- class haddock.modules.analysis.contactmap.HaddockModule(order: int, path: Path, *ignore: Any, init_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/analysis/contactmap/defaults.yaml'), **everything: Any)[source]
Bases:
BaseHaddockModuleHADDOCK3 module to compute complexes contacts and generate heatmap.
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