equilibrator-api is a command-line API with minimal dependencies for calculation of standard
thermodynamic potentials of biochemical reactions using the same data found on
It can be used without a network connection (after installation and initialization).
Calculation of standard Gibbs potentials of reactions (together with a represnetation of uncertainties by a full covariance matrix).
Calculation of standard Gibbs potentials of transport reactions (i.e. between cellular compartments).
Calculation of standard reduction potentials of half-cells.
Adjustment of Gibbs free energies to pH, ionic strength, and pMg (Magnesium ion concentration).
Pathway analysis tools such as Max-min Driving Force and Enzyme Cost Minimization (requires the equilibrator-pathway package).
Adding new compounds that are not among the 500,000 currently in the MetaNetX database (requires the equilibrator-assets package).
How to cite us¶
If you plan to use results from
equilibrator-api in a scientific publication,
please cite our paper: Consistent Estimation of Gibbs Energy Using Component Contributions 1
How to install¶
You can simply
pip install equilibrator-api and start eQuilibrating. For more details, see Installation.
How to use¶
Alternatively, if you are looking for a quick-and-dirty guide, you can take a look at the Code examples section.
Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, and Ronan M. T. Fleming. Consistent Estimation of Gibbs Energy Using Component Contributions. PLOS Computational Biology, 9(7):e1003098, July 2013. URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003098 (visited on 2017-12-13), doi:10.1371/journal.pcbi.1003098.