a Python package to parse and manipulate the BRENDA database

What is Brendapyrser?

This project provides python classes and functions to parse the JSON file containing the entire BRENDA enzyme database (https://www.brenda-enzymes.org)

Note: Since the 2024.x releases, BRENDA is distributed as a structured JSON document (schema 2.0.0) rather than the legacy flat text file. BRENDApyrser >= 0.1.0 parses this JSON format. For the old text format, use BRENDApyrser 0.0.4.

This is an ongoing project!

Installation

1. pip install brendapyrser

or

2. Git clone project to local directory.

   In terminal navigate to directory and enter: python setup.py install

Usage

Due to BRENDA's license, BRENDA's database cannot be downloaded directly by the parser, instead, the user is asked to download the database as a JSON file after accepting usage conditions here.

The parser accepts the JSON file directly, as well as .json.gz and the .json.tar.gz archive in which BRENDA ships the database — no manual extraction required:

from brendapyrser import BRENDA

brenda = BRENDA("brenda_2026_1.json.tar.gz")

reaction = brenda.reactions.get_by_id("1.1.1.1")
print(reaction.name)            # alcohol dehydrogenase
print(reaction.organisms[:3])   # source organisms
print(reaction.KMvalues)        # KM values keyed by substrate
print(reaction.bibliography)    # structured references (PMID, authors, year, ...)

You can find a jupyter notebook with usage examples here.

Contribute

Contributions are always more than welcome! Feel free to fork, make changes and pull requests. If you don't know where to start, you can always browse open issues. Thanks!

Citation

If you use this software, please cite it as below:

Robaina-Estévez, S. (2026). BRENDApyrser: a Python package to parse and manipulate the BRENDA database (Version 0.1.0)[Computer software]. https://doi.org/10.5281/zenodo.7026555