============= BRENDA Parser

This Python module provides classes that encapsulate information provided by the BRENDA database__ and a parser that generates relevant content from the text file that can be downloaded for free.

.. __: http://www.brenda-enzymes.org/

Copyright

:Author: Moritz Emanuel Beber :License: Please see the LICENSE.rst file distributed with this module.

Recent Changes

• Parser no longer hick-ups on empty lines, continued lines not starting with a tab, and other format breaking content.
• Parser now prints progress to stdout.
• Soon, support for the SOAP interface will be added.
• If desired, a setup script could be added.

Usage

If you want to use this module outside its directory, you will have to add it to your PYTHONPATH environment variable (unix).

.. code:: python

>>> from brenda import BRENDAParser
>>> with BRENDAParser("brenda_download.txt") as bp:
...     content = bp.parse()

The method parse returns a dictionary with all enzymes that were parsed. Every key in the dictionary is a string representing an EC number starting form the 6 general classes down to the individual enzymes. The values in the dictionary are always lists, as an example:

.. code:: python

>>> len(content["1"])
1348
>>> len(content["1.1.1.1"])
1

Warning

The API changed slightly.

Notes

There is one additional key "file_encoding" which contains the argument used for the parser when reading the file.