10.1.1.1.3. freeflux.analysis.inst_simulate
Define the InstSimulator class.
10.1.1.1.3.2. Classes
InstSimulator
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Provided fluxes should be in the unit of umol/gCDW/s if concentrations in the unit of |
10.1.1.1.3.3. Module Contents
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freeflux.analysis.inst_simulate.__author__ = 'Chao Wu'[source]
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class freeflux.analysis.inst_simulate.InstSimulator(model)[source]
Bases: freeflux.analysis.simulate.Simulator
Provided fluxes should be in the unit of umol/gCDW/s if concentrations in the unit of
umol/gCDW and timepoints in the unit of s.
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set_concentration(metabid, value)[source]
Set metabolite concentration in unit of umol/gCDW.
- Parameters:
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set_concentrations_from_file(file)[source]
Read metabolite concentrations (umol/gCDW) from file.
- Parameters:
file (file path) – tsv or excel file with fields “metabolite_ID” and “value”.
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_unset_concentrations(metabids)[source]
- Parameters:
metabids (str or list of str) – Metabolite ID(s).
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set_timepoints(timepoints)[source]
Set timepoints in unit of s.
Parameters
timepoints: list of float
Timepoints when MDVs are simulated.
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_unset_timepoints()[source]
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_lambdify_matrix_Ms()[source]
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_unset_matrix_Ms()[source]
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_calculate_initial_matrix_Xs()[source]
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_unset_initial_matrix_Xs()[source]
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_calculate_initial_matrix_Ys()[source]
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_unset_initial_matrix_Ys()[source]
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_build_initial_sim_MDVs()[source]
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_unset_initial_sim_MDVs()[source]
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prepare(n_jobs=1)[source]
- Parameters:
n_jobs (int) – If n_jobs > 1, decomposition job will run in parallel.
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_check_dependencies()[source]
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simulate()[source]
- Returns:
instTargetMDVs – EMU IDs => {measurement timepoints => simulated MDVs}
- Return type:
dict of dict