secstructartist 1.1.3

Module to visualize protein secondary structure in matplotlib

secstructartist

This package allows to include pretty secondary structure schemes in matplotlib plots.

Table of content

• Installation
  • Prerequisites
  • Installation from PyPI
  • Installation from GitHub
• Usage
  • A simple example
  • Customizing your plots
• License
• Contributing
• Authors

Installation

Prerequisites

• General prerequisites:
  • Python 3.8 or higher
  • pip
• Third-party python packages:
  • matplotlib
  • numpy

Installation from PyPI

This is the recommended way to install the package.

1. Create a virtual environment (optional but recommended):

   python3 -m venv secstructartist
   source secstructartist/bin/activate
   

2. Install python module

   pip install secstructartist
   

Installation from GitHub

Here, you will download the repository, and manually build and install the package.

1. Create a virtual environment (optional but recommended):

   python3 -m venv secstructartist
   source secstructartist/bin/activate
   

2. Clone the repository:

   git clone https://github.com/bickeld/secstructartist.git
   cd secstructartist
   

3. Build package and install

   make build
   make install
   

Usage

In the examples/ directory there is a Jupyter notebook (link) with plenty of code examples for simple and advanced use cases. Therefore, only the basics usage will be shown here.

A simple example

The simplest possible use case:

import matplotlib.pyplot as plt
import secstructartist as ssa

secstruct_str = "LLLSSSSSLLLLLHHHHHHHHLLLHHHHHHHHLLLLLLLLLSSSSSSLLLL"
fig, _objs = ssa.draw(secstruct_str)
fig.savefig("example0.png")

Customizing your plots

Plots can be modified by initializing a custom SecStructArtist.

import matplotlib.pyplot as plt
import secstructartist as ssa

secstruct_str = "LLLSSSSSLLLLLHHHHHHHHLLLHHHHHHHHLLLLLLLLLSSSSSSLLLL"
nres = len(secstruct_str)

# Initialize a custom SecStructArtist istance to modify settings 
artist = ssa.SecStructArtist()
# Set global settings
artist.height = .7
artist.linewidth = .8
# Set settings of "H" - Helices
artist["H"].fillcolor = (.9, 0., 0.)
artist["H"].shadecolor = (.7, 0., 0.)
artist["H"].ribbon_period = 3.6
artist["H"].ribbon_width = 2.2
# Set settings of "S" - beta-Sheets
artist["S"].arrow_length = 2.7
artist["S"].fillcolor = "#ddcc00"
artist["S"].height = .5
# Set settings of "L" - loop
artist["L"].linecolor = "blue"
artist["L"].linewidth = 1.8

# Generate figure and axis
fig, ax = plt.subplots(figsize=(4,.4), dpi=150)

# Include secondary structure scheme above the plot
artist.draw(secstruct_str, xpos=list(range(3, 3+nres)), ypos=3.5, ax=ax)

ax.set_xlabel("Residue index")
ax.set_ylim([3, 4])

fig.savefig("example1.png")

License

Distributed under the GNU General Public License v3 (GPLv3) License.

Contributing

If you find a bug, please open a bug report. If you have an idea for an improvement or new feature, please open a feature request.

Authors

- David Bickel