conkit.plot.contactdensity module¶

A module to produce a domain boundary plot

class ContactDensityFigure(hierarchy, bw_method=’bowman’, **kwargs)[source]¶

Bases: conkit.plot._figure.Figure

A Figure object specifically for a contact density illustration.

This figure is an adaptation of the algorithm published by Sadowski (2013) [1].

[1]	Sadowski M. (2013). Prediction of protein domain boundaries from inverse covariances. Proteins 81(2), 253-260.

Examples

>>> import conkit
>>> cmap = conkit.io.read('toxd/toxd.mat', 'ccmpred').top_map
>>> conkit.plot.ContactDensityFigure(cmap)

Attributes

`hierarchy`	A ConKit `ContactMap`
`bw_method`	The method to estimate the bandwidth

Methods

redraw() Re-draw the plot with updated parameters

bw_method¶

The method to estimate the bandwidth

For a full list of options, please refer to calculate_contact_density()