rstoolbox.plot.plot_ramachandran¶

rstoolbox.plot.plot_ramachandran(df, seqID, fig, grid=None, positions=None, **kwargs)¶

Generates a ramachandran plot in RAMPAGE style.

For more details and sources please refert to ramachandran plot for python

Background distribution data taken from git repository

The phi - psi dihedrals should be present in the DesignSerie. If this is not the case, consider computing them using for example the get_sequence_and_structure(). Note that this function will only plot the ramachandran for a single decoy. If one would like to compute it for mutiple decoys, please see the example below.

Parameters for scatter() can be provided with prefix scatter_.

Parameters for plot() can be provided with prefix line_.

Parameters:	df (Series) – Data container, where ONE column cotains the phi and a second column the psi angles. seqID (str) – Identifier of the sequence of interest fig (Figure) – Figure into which the data is going to be plotted. grid (tuple) – Grid of the figure. By default assumes the figure has nothing else and so, the grid is (2, 2). positions (list() of tuple) – Positions in the grid (in case the image will contain more than the Ramachandran). By default, it assumes a (2, 2) grid and fills all positions.
Returns:	list() of Axes
Raises:	ValueError: If the grid does not provide at least 4 positions. ValueError: If there number of positions is not 4.

See also

plot_ramachandran_single() get_sequence_and_structure() get_dihedrals() get_phi() get_psi()

Example

In [1]: import rstoolbox as rb
   ...: import pandas as pd
   ...: plt.style.use('ggplot')
   ...: definitions = {
   ...:                "scores": ["score"],
   ...:                "sequence" : "A",
   ...:                "psipred" : "*",
   ...:                "structure" : "*",
   ...:                "dihedrals": "*"
   ...:                }
   ...: dsf = rb.io.parse_rosetta_file(
   ...:     "../rstoolbox/tests/data/input_3ssepred.minisilent.gz",
   ...:     definitions )
   ...: figure = plt.figure(figsize=(15,10))
   ...: rb.plot.plot_ramachandran(dsf.iloc[0], "A", figure)
   ...: plt.tight_layout()
   ...: fig.subplots_adjust(top=1.2)
   ...: 

In [2]: plt.show()

In [3]: plt.close()