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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)

The argument guard

Most scripts here open with this, above the imports:

if __name__ == "__main__":
    # Argument guard -- see "The argument guard" in Scripts/README.md.
    import argparse as _argparse
    _argparse.ArgumentParser(
        description=__doc__,
        formatter_class=_argparse.RawDescriptionHelpFormatter).parse_args()

Why it exists. These scripts mutate the database. Without the guard an unknown flag or a mistyped mode was silently ignored and the script ran with its defaults: asking Estimate_Reaction_Reversibility.py for --help rewrote 122 files. The guard turns that into an argparse error before anything is read or written.

Why it sits above the imports. So --help still works on a machine where one of the script's dependencies is missing from the path. Move it below the imports and --help fails with an ImportError instead of printing the docstring.

Keep it first. Anything placed before it -- an import with a side effect, a module-level path lookup, a database open -- runs before the arguments have been checked, which is the failure the guard exists to prevent.

Scripts that take real arguments extend the same block with their own add_argument calls; Scripts/Structures/Run_Marvin_pKas.py is an example.