Metadata-Version: 2.1
Name: HabitabilityTheOry
Version: 0.0.3
Summary: This package contains some useful functions to assess habitability of Chemostat-like environments to energy-limited microbes.
Author-email: Antonin Affholder <aaffholder@arizona.edu>
Project-URL: Homepage, https://gitlab.com/antonin.affholder/HaThOr_pkg
Project-URL: Bug Tracker, https://gitlab.com/antonin.affholder/HaThOr_pkg/-/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# HaThOr
## Habitable TheOry

### Rationale and goals
Here, we use habitable theory to build a tool to assess habitability at a large spectrum

We have a model frame for growth:

\[
k_g = A \lambda \tau e^{-\frac{\Delta G_{ac}}{RT}} - A e^{-\frac{\Delta G_{am}}{RT}}
\]
where
 - $k_g$ is the specific growth rate (s$^{-1}$)
 - $A$ pre-exponential factor (s$^{-1}$)
 - $\lambda = - \Delta_rG_c/E_{ana}$ the catabolic yield
 - $\tau$ active biomass fraction (mol enzyme per mole biomass)
 - $\Delta G_{ac}$ activation gibbs free energy of the catabolic reaction (J/mol)
 - $\Delta G_{am}$ activation gibbs free energy of the maintenance reaction (J/mol)
 - $R=8.314$ (J/(K mol)) is the perfect gas constant
 - $T$ absolute temperature (K)
 
Some of these parameters can be estimated from growth curves (see Guyot and Affholder _in prep_).


Structure of the package HaThOr:
 - chem_helper contains some helper functions and stoichiometric data for some organisms
 - Metabolisms contains the classes metabolism and organism that are designed to build objects representing a functional type with a given metabolism and a given set of parameters
 - Chemostat contains the chemostat class, used to define an environment and calculate biomass etc.
