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¶