optimModels.unittests package¶
Submodules¶
optimModels.unittests.cbm_optim module¶
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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
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optimModels.unittests.cbm_optim.
medium_Lactate_optim
(isMultiProc=False, size=1, withCobraPy=False)¶
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optimModels.unittests.cbm_optim.
medium_SC_Etanol_Levels_optim
(isMultiProc=False, size=1, withCobraPy=False)¶
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optimModels.unittests.cbm_optim.
medium_SC_Etanol_optim
(isMultiProc=False, size=1, withCobraPy=False)¶
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optimModels.unittests.cbm_optim.
medium_SC_optim
(isMultiProc=False, size=1, withCobraPy=False)¶
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optimModels.unittests.cbm_optim.
medium_optim
(isMultiProc=False, size=1, withCobraPy=False)¶
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optimModels.unittests.cbm_optim.
medium_reac_ko_optim
(isMultiProc=False, size=[5, 5], withCobraPy=False)¶
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optimModels.unittests.cbm_optim.
reac_ko_medium_optim_CM
(isMultiProc=False, size=(1, 1), withCobraPy=False)¶
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optimModels.unittests.cbm_optim.
reac_ko_optim
(isMultiProc=False, size=1, withCobraPy=False)¶
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optimModels.unittests.cbm_optim.
reac_ko_optim_CM
(isMultiProc=False, size=1, withCobraPy=False)¶
optimModels.unittests.cbm_simulation module¶
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optimModels.unittests.cbm_simulation.
cbm_simualtion
()¶
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optimModels.unittests.cbm_simulation.
cbm_simualtion_iAF
()¶
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optimModels.unittests.cbm_simulation.
medium_test
()¶
optimModels.unittests.framed_cobrapy module¶
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optimModels.unittests.framed_cobrapy.
cameo_optim
(isMultiProc, size)¶
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optimModels.unittests.framed_cobrapy.
cobra_optim
(isMultiProc, size)¶
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optimModels.unittests.framed_cobrapy.
framed_optim
(isMultiProc, size)¶
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optimModels.unittests.framed_cobrapy.
print_drains_cobrapy
()¶
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optimModels.unittests.framed_cobrapy.
print_results
(fileName, population, optimConfig)¶
optimModels.unittests.gecko_optim module¶
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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¶
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optimModels.unittests.gecko_simulation.
analysis_growth
(resFileName)¶
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optimModels.unittests.gecko_simulation.
analysis_ko
(resFileName)¶
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optimModels.unittests.gecko_simulation.
simulate_prot
()¶
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optimModels.unittests.gecko_simulation.
simulate_wt
()¶
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optimModels.unittests.gecko_simulation.
simulate_wt_multi
()¶
optimModels.unittests.kinetic_optim module¶
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optimModels.unittests.kinetic_optim.
ko_chassagnole
(isMultiProc=False, size=1)¶
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optimModels.unittests.kinetic_optim.
ko_jahan
()¶
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optimModels.unittests.kinetic_optim.
ko_millard
(isMultiProc=False, size=1)¶
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optimModels.unittests.kinetic_optim.
under_over_chassagnole
(isMultiProc=False, size=1)¶
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optimModels.unittests.kinetic_optim.
under_over_millard
(isMultiProc=False, size=1)¶
optimModels.unittests.kinetic_simulation module¶
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optimModels.unittests.kinetic_simulation.
kinetic_sim
()¶
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optimModels.unittests.kinetic_simulation.
toy_model
()¶
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optimModels.unittests.kinetic_simulation.
toy_model2
()¶
optimModels.unittests.presentation module¶
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optimModels.unittests.presentation.
analysis_growth
(resFileName, scale=False)¶
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optimModels.unittests.presentation.
essential_prot
()¶
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optimModels.unittests.presentation.
essential_prot_scale
()¶
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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¶
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optimModels.unittests.simplify_solutions.
jahan_ko
()¶
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optimModels.unittests.simplify_solutions.
jahan_model
()¶
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optimModels.unittests.simplify_solutions.
jahan_uo
()¶
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optimModels.unittests.simplify_solutions.
millard_ko
()¶
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optimModels.unittests.simplify_solutions.
millard_model
()¶
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optimModels.unittests.simplify_solutions.
millard_uo
()¶
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optimModels.unittests.simplify_solutions.
simplify_solution
(simulProblem, decoder, evalFunc, solutions)¶
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optimModels.unittests.simplify_solutions.
simulate_solutions
(simulProblem, decoder, solutions)¶
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optimModels.unittests.simplify_solutions.
yield_solutions
(simulationResults, productId, uptakeId)¶