optimModels.unittests package

Submodules

optimModels.unittests.cbm_optim module

optimModels.unittests.cbm_optim.LEVELS = [0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50, 100.0, 500.0, 1000.0, 10000.0]

This file contains several functions to perform different strain design strategies using stoichiometric models

optimModels.unittests.cbm_optim.medium_Lactate_optim(isMultiProc=False, size=1, withCobraPy=False)
optimModels.unittests.cbm_optim.medium_SC_Etanol_Levels_optim(isMultiProc=False, size=1, withCobraPy=False)
optimModels.unittests.cbm_optim.medium_SC_Etanol_optim(isMultiProc=False, size=1, withCobraPy=False)
optimModels.unittests.cbm_optim.medium_SC_optim(isMultiProc=False, size=1, withCobraPy=False)
optimModels.unittests.cbm_optim.medium_optim(isMultiProc=False, size=1, withCobraPy=False)
optimModels.unittests.cbm_optim.medium_reac_ko_optim(isMultiProc=False, size=[5, 5], withCobraPy=False)
optimModels.unittests.cbm_optim.reac_ko_medium_optim_CM(isMultiProc=False, size=(1, 1), withCobraPy=False)
optimModels.unittests.cbm_optim.reac_ko_optim(isMultiProc=False, size=1, withCobraPy=False)
optimModels.unittests.cbm_optim.reac_ko_optim_CM(isMultiProc=False, size=1, withCobraPy=False)

optimModels.unittests.cbm_simulation module

optimModels.unittests.cbm_simulation.cbm_simualtion()
optimModels.unittests.cbm_simulation.cbm_simualtion_iAF()
optimModels.unittests.cbm_simulation.medium_test()

optimModels.unittests.framed_cobrapy module

optimModels.unittests.framed_cobrapy.cameo_optim(isMultiProc, size)
optimModels.unittests.framed_cobrapy.cobra_optim(isMultiProc, size)
optimModels.unittests.framed_cobrapy.framed_optim(isMultiProc, size)
optimModels.unittests.framed_cobrapy.print_drains_cobrapy()
optimModels.unittests.framed_cobrapy.print_results(fileName, population, optimConfig)

optimModels.unittests.gecko_optim module

optimModels.unittests.gecko_optim.prot_ko_optim(prot_measure_fractions=None, prot_measure_ggdw=None, constraints=None, isMultiProc=False, size=1)

optimModels.unittests.gecko_simulation module

optimModels.unittests.gecko_simulation.analysis_growth(resFileName)
optimModels.unittests.gecko_simulation.analysis_ko(resFileName)
optimModels.unittests.gecko_simulation.simulate_prot()
optimModels.unittests.gecko_simulation.simulate_wt()
optimModels.unittests.gecko_simulation.simulate_wt_multi()

optimModels.unittests.kinetic_optim module

optimModels.unittests.kinetic_optim.ko_chassagnole(isMultiProc=False, size=1)
optimModels.unittests.kinetic_optim.ko_jahan()
optimModels.unittests.kinetic_optim.ko_millard(isMultiProc=False, size=1)
optimModels.unittests.kinetic_optim.under_over_chassagnole(isMultiProc=False, size=1)
optimModels.unittests.kinetic_optim.under_over_millard(isMultiProc=False, size=1)

optimModels.unittests.kinetic_simulation module

class optimModels.unittests.kinetic_simulation.Params

Bases: object

get_params_set()
optimModels.unittests.kinetic_simulation.kinetic_sim()
optimModels.unittests.kinetic_simulation.toy_model()
optimModels.unittests.kinetic_simulation.toy_model2()

optimModels.unittests.presentation module

optimModels.unittests.presentation.analysis_growth(resFileName, scale=False)
optimModels.unittests.presentation.essential_prot()
optimModels.unittests.presentation.essential_prot_scale()
optimModels.unittests.presentation.prot_ko_optim(prot_measure_fractions=None, prot_measure_ggdw=None, constraints=None, isMultiProc=False, size=1)

optimModels.unittests.simplify_solutions module

optimModels.unittests.simplify_solutions.jahan_ko()
optimModels.unittests.simplify_solutions.jahan_model()
optimModels.unittests.simplify_solutions.jahan_uo()
optimModels.unittests.simplify_solutions.millard_ko()
optimModels.unittests.simplify_solutions.millard_model()
optimModels.unittests.simplify_solutions.millard_uo()
optimModels.unittests.simplify_solutions.simplify_solution(simulProblem, decoder, evalFunc, solutions)
optimModels.unittests.simplify_solutions.simulate_solutions(simulProblem, decoder, solutions)
optimModels.unittests.simplify_solutions.yield_solutions(simulationResults, productId, uptakeId)

Module contents