rpThermo

Calculate the formation energy of chemical species and the Gibbs free energy for each reaction and for the heterologous pathway itself. This tool uses the component contribution method for determining the formation energy of chemical species that are either not annotated, or cannot be found in the internal database.

For each species, the challenge is to find the corresponding compound in the eQuilibrator cache. To find the good compound, one tries to exact match species ID, InChIKey, InChI or SMILES and stops with the first hit. Then, if no compound has been found, in the last resort, the first part of species InChIKey is looked for within the cache. If the result (a list) is not empty, the first compound is taken.

Because we are interested in the thermodynamics of the pathway when the production of the target is optimized, we have modified coefficients of each reaction. We used a linear system solver (from SciPy) by giving the reaction that produces the target as objective and elimination of intermediate species as constraints.

Input

Required:

• -input: (string) Path to the input file
• -input_format: (string) Valid options: tar, sbml. Format of the input file

Advanced Options:

• -pathway_id: (string, default=rp_pathway) ID of the heterologous pathway

Output

• -output: (string) Path to the output file

Installation Guide

Overview

rpthermo depends on rplibs, which depends on cobra, which requires python-libsbml.
On Apple Silicon (arm64) macOS, python-libsbml is not available as a native Conda package.

Therefore, installation must be done using an Intel (osx-64) Conda environment under Rosetta.

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General case

conda install -c conda-forge rpthermo

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Apple Silicon macOS (M1/M2/M3)

1. Install Rosetta 2

softwareupdate --install-rosetta --agree-to-license

2. Install rpThermo

CONDA_SUBDIR=osx-64 conda install -c conda-forge rpthermo

Or with mamba:

CONDA_SUBDIR=osx-64 mamba install -c conda-forge rpthermo

3. Persist platform setting

conda config --env --set subdir osx-64

4. Verify installation

python -c "import rpthermo; print('rpthermo installed successfully')"

5. (Optional) Dev installation

CONDA_SUBDIR=osx-64 conda env create -f environment.yaml

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Troubleshooting

Solver fails on Apple Silicon

Make sure you are using:

CONDA_SUBDIR=osx-64

Wrong architecture environment

Check:

conda config --show subdir

Expected output:

subdir: osx-64

Run

rpThermo process

From Python code

from rptools.rplibs import rpSBML
from rptools.rpthermo import runThermo

pathway = rpSBML(inFile='lycopene/rp_003_0382.sbml').to_Pathway()

runThermo(pathway)

print(pathway.get_thermo_dGm_prime().get('value'))
print(pathway.get_fba_dGm_prime())

>>> -3079.477259696032
>>> {'value': -3079.477259696032, 'error': 7.250256007547839, 'units': 'kilojoule / mole'}

From CLI

python -m rptools.rpthermo <input_sbml> <outfile>

Tests

Test can be run with the following commands:

Natively

cd tests
pytest -v

CI/CD

For further tests and development tools, a CI toolkit is provided in ci folder (see ci/README.md).

Authors

• Joan Hérisson
• Melchior du Lac

Acknowledgments

• Thomas Duigou

Licence

rpThermo is released under the MIT licence. See the LICENCE file for details.