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ModelSEED Biochemistry Database Script Environment

We've developed a small python library for loading and manipulating the biochemistry database according to our needs and we written a set of scripts that uses the library for our needs.

The main set of scripts that we used for the most recent publication of the ModelSEED Biochemistry Database are:

In the last case, the scripts were used to generate some of the figures and tables in our latest publication.

Python Environment

All these scripts run in a Python 3 environment, and some require additional packages which we explain here:

  1. Install Conda https://conda.io/projects/conda/en/latest/user-guide/install/index.html

  2. Set up a python 3 conda environment

 conda create -n msd-env python=3
  1. Activate
 conda activate msd-env
  1. Install rdkit and openbabel for handling biochemical structures
 conda install -c rdkit rdkit
 conda install -c openbabel openbabel
  1. Install eQuilibrator for retrieving thermodynamics data
conda install wxPython
pip install quilt
pip install equilibrator_api

(you might not need to install wxPython, I had trouble with dependencies on a mac)

  1. Export path to local python libraries
export PYTHONPATH=$PYTHONPATH:<path-to-repository>/ModelSEEDDatabase/Libs/Python/
  1. Test
./Biochemistry/Reprint_Biochemistry.py
git status -s

(The script should run without throwing any errors and there should be no change in the biochemistry data)