Ramachandran plotting tool

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

Installation

RamachanDraw is hosted on PyPi.

pip install ramachandraw

Usage

RamachanDraw includes useful functions to effortlessly draw a Ramachandran plot.

Fetch the PDB file

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.

Example

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)

Extract φ and ψ torsion angles

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.

Example

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.

Ramachandran plot

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

Example

from ramachandraw.utils import plot

plot(pdb_filepath, cmap="viridis", alpha=0.75, dpi=100, save=True, show=False, filename="plot.png", title=None)

• 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.
• title (str|None) (optional): custom title for the plot. If None, defaults to the PDB filepath.
• Returns: Ramachandran plot (matplotlib.axes.Axes object) that can be further customized if needed

Example

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

Single PDB

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))

Batch of PDBs

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


# PDB id
pdb_ids = ["1mbn", "4hhb"]

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

# Generate a list of dictionaries to store the (phi, psi) torsion angles
torsion_angles = get_phi_psi(fetch_pdb(pdb_ids))

Contributing

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

License

MIT