Snek provides quality of Life Functions for CobraPy.
There are several reasons why this module is helpful for CobraPy users:
When setting bounds of a reaction or the objective function with the main CobraPy package, no error is raised when a spelling error occurs.
Reaction.lower_bound = 5
Reaction.lower_buond = 5 # no error raised, but the bound is not updated
This can happen frequently and is hard to debug. Thus following functions ensure correct spelling:
snek.set_bounds()snek.set_objective()
CobraPy gives the user a lot of freedom. However, here we implemented some basic checks that ensure that no unintended errors are made and prints warning if this is true.
snek.sensitive_optimize()snek.set_objective()
Certain functionalities are somewhat "hidden" in CobraPy. Here we implemented some basic functions that easily access this hidden functionalities.
snek.get_objective()snek.get_solver()
We added some new functions to easily search for reactions and metabolites as well.
snek.find_biomass_reaction()snek.find_reaction()snek.find_metabolite()
This module contains several functions for the elemental analysis of molecules and the calculation of molecular weights from sum formulas. Following functions are currently available:
snek.elements.count_atom()snek.elements.unique_elements()snek.elements.formula_to_dictionary()snek.elements.dictionary_to_formula()snek.elements.element_flux_coefficient()snek.elements.element_fluxes()snek.elements.molecular_weight()snek.elements.get_pDNA_formula()snek.elements.get_protein_formula()
More specialized functions to investigate CobraPy models and to look at fluxes. Following functions are currently available.
snek.analysis.get_constrained_reactions()snek.analysis.in_bounds()snek.analysis.in_flux()snek.analysis.investigate_network()snek.analysis.investigate_network_solution()snek.analysis.out_bounds()snek.analysis.out_flux()