Heatmapper Functions

This module defines functions for supporting VMD plugin Heatmapper format files.

prody.dynamics.heatmapper.parseHeatmap(heatmap, **kwargs)

Returns a two dimensional array and a dictionary with information parsed from heatmap, which may be an input stream or an .hm file in VMD plugin Heat Mapper format.

prody.dynamics.heatmapper.showHeatmap(heatmap, *args, **kwargs)

Show heatmap, which can be an two dimensional array or a Heat Mapper .hm file.

Heatmap is plotted using imshow() function. Default values passed to this function are interpolation='nearest', aspect='auto', and origin='lower'.

prody.dynamics.heatmapper.writeHeatmap(filename, heatmap, **kwargs)

Returns filename that contains heatmap in Heat Mapper .hm file (extension is automatically added when not found). filename may also be an output stream.

Parameters:

• title (str) – title of the heatmap

• xlabel (str) – x-axis lab, default is 'unknown'

• ylabel (str) – y-axis lab, default is 'unknown'

• xorigin (float) – x-axis origin, default is 0

• xstep (float) – x-axis step, default is 1

• min (float) – minimum value, default is minimum in heatmap

• max (float) – maximum value, default is maximum in heatmap

• format (str) – number format, default is '%f'

Other keyword arguments that are arrays with length equal to the y-axis (second dimension of heatmap) will be considered as numbering.