NutMEG.culture.base_organism.synthesis package

Submodules

NutMEG.culture.base_organism.synthesis.BioMolecule module

class NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule(name, Mr, conc_mol_per_cell=None, conc_mol_per_l=None, thermo=True, gamma=1.0, T=298.15, P=101325.0)

Bases: object

class for storing amino acid properties, or any other useful biological molecule really

GetThermoParams(T, P)
Mr = 0.0
conc_mol_per_cell = None
conc_mol_per_l = None
copies_per_cell = None
counter = 0

INITIALISATION METHODS

frequency = None
gamma = 1.0
name = ''
probrange = None
std_formation_R = None
std_formation_gibbs = None
thermo = True

NutMEG.culture.base_organism.synthesis.cell_synthesis module

class NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis

Bases: object

static AAsynthCost(TK)

Get the cost of synthesising all of the amino acids in one dry g of cells using the method from McCollom and Amend (2005). This is currently fixed to E Coli.

#TODO: Export the list of lists to be in a csv file in /data/, then import it here. This will allow for other model organisms to be simulated. #TODO: Work in methods for oxic environments

static ProteinSynthCost(TK, host_drymass, host_volume)

Calculate and return the cost of protein synthesis per gram. Assumes amino acids already synthesised.

Parameters

  • TK (float, int) – Temperature in Kelvin

  • host_drymass (float) – dry mass of organism in kg/cell

  • host_volume (float) – total (wet) volume of one organism.

static a_e(T, Eh=- 0.27)

Calculate the activity of an electron Assumes neutral conditons for Eh

static add_AAP_to_db(T, AAsynth, Psynth, filename='EColiSynth')

Add results to an SQL database to save having to recompute them.

Parameters

  • T (Temperature in K) –

  • AAsynth (cost of amino acid synthesis in J per dry g cells) –

  • Psynth (cost of 1 dry g protein synthesis from amino acids) –

  • #TODO (Perhaps would be more intuitive as a csv rather than db.) –

static extract_AAP_from_db(T, filename='EColiSynth')

Extract amino acid and protein synthesis from database

static get_ESynth_density(T, compute=None, AA=False)

Calculate the energy cost to synthesise one dry g of cells.

If you want to compute ESynth density for a new organism, pass compute as a dictionary in the following format: {‘dbfilename’:None (or path/to_database), ‘host’:base_organism}

static getreplistAA(AAList, listlen)

Get a representative list of Amino acids to build proteins which matches average cell composition.

static lnProteinReactionQuotient(PC, AAList)

NutMEG.culture.base_organism.synthesis.importers module

functions for importing data

NutMEG.culture.base_organism.synthesis.importers.AAreader(host_drymass, host_volume, filename='EColiSynth_AminoAcids.csv')
NutMEG.culture.base_organism.synthesis.importers.copies_moles(filename='EColiSynth_Ishihama2008_dataset3.csv')

Module contents