Draws a Ramachandran plot based on the input PDB file (e.g. 1mbn.pdb). Makes use of a Gaussian KDE (kernel density estimation) to plot the density of favoured torsion angles (φ and ψ).

Single mode	Batch mode

RamachanDraw is hosted on PyPi.

pip install ramachandraw

RamachanDraw includes useful functions to effortlessly draw a Ramachandran plot.

To draw a Ramachandran plot, we need a PDB file. RamachanDraw conveniently includes a function to automatically fetch and locally store the PDB file for the given PDB id.

from ramachandraw.utils import fetch_pdb

fetch_pdb(pdb_id, verbose)

• pdb_id (str|list|tuple): PDB id(s) corresponding to the PDB file(s) to be downloaded
• verbose (bool) (optional): set the verbosity, defaults to False
• Returns: path(s) to PDB file(s)

RamachanDraw extracts the φ and ψ torsion angles from the PDB file by taking advantage of the Biopython module. Additionally, aminoacid residues that were not drawn on the plot can be extract using the return_ignored argument.

from ramachandraw.parser import get_phi_psi

phi_psi(pdb_filepath, prune, hide_warnings)

• pdb_id (str|list|tuple): PDB filepath(s)
• prune (bool) (optional): prunes aminoacids with missing torsion angle(s), defaults to True
• hide_warnings (bool) (optional): sets the verbosity of the PDB structure parser, defaults to True
• Returns: Dictionary with keys as aminoacid residues and values as (φ, ψ) angles.

Makes use of the matplotlib module to draw a highly customizable Ramachandran plot.

from ramachandraw.utils import plot

plot(pdb_filepath, cmap="viridis", alpha=0.75, dpi=100, save=True, show=False, filename="plot.png")

• pdb_file (str|list|tuple): PDB id(s) corresponding to the PDB entry to be downloaded
• cmap (str) (optional): colormap to be used (from matplotlib) for the density of the favoured ("allowed") regions; default is viridis.
• alpha (float) (optional): sets the opacity of the colormap (value between 0-1); default is 0.75.
• dpi (int) (optional): resolution (in dots per inch); default is 100.
• save (bool) (optional):
  • True: saves the plot locally; default is True.
• show (bool) (optional):
  • True: shows the plot using the Qt5Agg backend; default is False.
• filename (str) (optional): filename to be used in case the plot is saved (i.e. save=True); default is plot.png.
• Returns: Ramachandran plot (matplotlib.axes.Axes object) that can be further customized if needed

Herein you will find an example from the PDB id corresponding to the myoglobin entry: 1MBN - in the Protein Data Bank.

from ramachandraw.parser import get_phi_psi
from ramachandraw.utils import fetch_pdb, plot

# PDB id
pdb_id = "1mbn"

# Draw the Ramachandran plot
plot(fetch_pdb(pdb_id))

# Generate a dictionary to store the (phi, psi) torsion angles
torsion_angles = get_phi_psi(fetch_pdb(pdb_id))

Feedback and constructive criticism is welcome. If necessary, open an issue in the issues tab.

MIT