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Ramachandran plotting tool

Project description

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).

Usage

RamachanDraw includes useful functions to effortlessly draw a Ramachandran plot.

Fetch the PDB file from the online repository

To draw a Ramachandran plot, we need a PDB file. You can use a local PDB file by specifying the path. Alternatively, RamachanDraw conveniently includes a function to automatically fetch and locally store the PDB file for the given PDB id.

Arguments

fetch(pdb_file)
  • pdb_file (str): PDB id corresponding to the PDB entry to be downloaded.
  • Returns: path to PDB file.

Extract φ and ψ angles

RamachanDraw extracts the φ and ψ 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.

Arguments

phi_psi(pdb_file, return_ignored)
  • pdb_file (str): PDB id corresponding to the PDB entry to be downloaded.
  • return_ignored (bool):
    • True returns a list of tuple with the format (aminoacid, (phi, psi))
  • Returns: Dictionary with keys as aminoacid residues and values as (phi, psi) angle values.

Ramachandran plot

Makes use of the matplotlib module, using the Qt5Agg backend (PyQt5) to draw a highly customizable Ramachandran plot.

Arguments

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

Example

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

from RamachanDraw import fetch, phi_psi, plot

# PDB id to be downloaded
PDB_id = '1MBN'

# Drawing the Ramachandran plot
plot(fetch(PDB_id))

# Generating a dictionary to store the phi and psi angles
# And returning the ignored aminoacid residues
phi_psi_dict, ignored_res = phi_psi(fetch(PDB_id), return_ignored=True)

Contributing

Feedback and constructive criticism is welcome: a.dias.cirilo@umail.leidenuniv.nl.

License

MIT

Project details


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This version

0.2.1

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