Commit 61f76aba authored by Avi Flamholz's avatar Avi Flamholz

Usage in readme.

parent 5d6c0396
......@@ -8,6 +8,38 @@ A command-line API with minimal dependencies for calculation of standard thermod
* Calculation of standard Gibbs potentials of reactions.
* Calculation of standard reduction potentials of half-cells.
# Example Usage
Import the API and create an instance.
```python
from equilibrator_api import EquilibratorAPI, Reaction
eq_api = EquilibratorAPI()
```
Now you can parse a reaction from a KEGG-style reaction string. The example given is ATP hydrolysis to ADP and Pi
```python
rxn_str = "C00002 + C00001 = C00008 + C00009"
rxn = Reaction.parse_formula(rxn_str)
```
Finally you can calculate various things for this reaction
```python
if not rxn.check_full_reaction_balancing():
print '%s is not balanced', rxn
# ionic_strength in molar units
dG0_prime, dG0_uncertainty = equilibrator.dG0_prime(
rxn, pH=6.5, ionic_strength=0.2)
# reversibility index is a measure of reaction reversibility
# that accounts for stoichiometry.
# https://doi.org/10.1093/bioinformatics/bts317
ln_RI = reaction.reversibility_index(pH=6.5, ionic_strength=0.2)
```
# dependenceis:
- python 2.7
- numpy (preferably >= 1.12.0)
......
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