conkit.plot.precisionevaluation module¶

A module to produce a precision evaluation plot

class PrecisionEvaluationFigure(hierarchy, min_cutoff=0.0, max_cutoff=100.0, cutoff_step=0.2, **kwargs)[source]¶

Bases: conkit.plot.figure.Figure

A Figure object specifically for a Precision evaluation.

This figure will illustrate the precision scores of a contact map at different precision scores. These can be determined at various start and end points with different stepwise increases in between.

hierarchy¶

The contact map hierarchy

Type:	`ContactMap`

cutoff_step¶

The cutoff step

Type:	float

min_cutoff¶

The minimum cutoff factor

Type:	float

max_cutoff¶

The maximum cutoff factor

Type:	float

Examples

>>> import conkit
>>> cmap = conkit.io.read('toxd/toxd.mat', 'ccmpred').top_map
>>> cmap.sequence = conkit.io.read('toxd/toxd.fasta', 'fasta').top_sequence
>>> pdb = conkit.io.read('toxd/toxd.pdb', 'pdb').top_map
>>> cmap.match(pdb, inplace=True)
>>> conkit.plot.PrecisionEvaluationFigure(cmap)

cutoff_step: The cutoff step

draw()[source]¶

hierarchy: A ConKit ContactMap

max_cutoff

The maximum cutoff factor

Raises:	`ValueError` – The maximum cutoff value is smaller than the the minimum

min_cutoff

The minimum cutoff factor

Raises:	`ValueError` – The minimum cutoff value is larger than or equal to the maximum