NutMEG.applications package

Submodules

NutMEG.applications.NutMEmatcher module

class NutMEG.applications.NutMEmatcher.NutMEmatcher(org, loc)

Bases: object

Class for matching parameters to outputs, specifically nutrients and maintenance. Cycle through implementations of ecosystem’s predict_growth, until one gets the desired output.

exparam(param, SimID, OrgID)

Return the requested simulation paramter in the exopnential phase of S=simulation SimID.

higherorlower(param, value, result)

For passed param, see if we have an acceptable result. Currently only works for GrowthRate and FinBM.

iterateMF(MFrange, target)

Iteration instructions for changing the maintenance fraction

iterate_to_target(iterables, target)

Perform the iteration for the passed values.

match(level='Basic', paramsdict={'MaintenanceFrac': [0, 1]}, target={'GrowthRate': 0.0003})

Find an organism that matches the target output by varying paramsdict values.

Parameters

  • level (str) – level of complexity to output. Basic: only efficiency. NutME: efficiency and the theoretical calculations which sould make it up.

  • paramsdict (dict) – Which parameters to iterate through when matching. If a list with two entries is passed, iterate between those values. If a single value, stick to it, if more values use ONLY these values and return the best fit. TODO: options 2 and 3 here.

  • target (dict) – Target paramter(s) to get to. At the moment this only supports growth rate, but others will be added. TODO: add other targets (final biomass? final conc?)

net_powers(SimID, OrgID)

Return the power supply and maintenance fraction in the exponential phase of the simulation SimID.

print_theory_estimates(SimID, OrgID)

Print estimates at maintenance efficiency available in NutMEG.

simulate_growth(org2, loc2)

Perfrom a growth prediction with the horde and locale passed

NutMEG.applications.theory_estimates module

class NutMEG.applications.theory_estimates.theory_estimates(org, loc)

Bases: object

Class to easily work out some theory estimates for maintenance powers in specific environments

org

The type of organism to use

Type

base_organism like

loc

The type of reactor (environment) to use

Type

reactor like

classmethod fromOrgLoc(OrgID, LocID, dbpath='/Users/pete/github2/NutMEG/NutMEG/util/../../NutMEG_db')

Initialise from organisms or reactors already saved with IDs OrgID and LocID respectively.

classmethod fromSim(SimID, dbpath='/Users/pete/github2/NutMEG/NutMEG/util/../../NutMEG_db')

Initialise from a Simulation already performed with ID SimID.

temperature_defenses(T, per_cell=True)

Return some expected temperature defense costs at temperature T which are built in to NutMEG, in units W/cell.

Returns them in a dictionary, so far we have Lever10pc: Lever et al. (2015) ith protein replacement at 10% racemization, Lever2pc: the same with replacement at 2% racemization. and Tijhuis et al (1993)’s trend with empirical data.

Module contents