reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters
SimulationData mass data
- class reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.GrowthRateParameters(raw_data, sim_data)[source]
Bases:
object
- class reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass(raw_data, sim_data)[source]
Bases:
object
- get_avg_cell_dry_mass(doubling_time)[source]
Gets the dry mass for an average cell at the given doubling time.
- Parameters:
doubling_time (Unum) – expected doubling time
- Returns:
average cell dry mass
- Return type:
Unum
- get_basal_rna_fractions()[source]
Measured RNA subgroup mass fractions. Fractions should change in other conditions with growth rate (see transcription.get_rna_fractions()).
- get_dna_critical_mass(doubling_time)[source]
Returns the critical mass for replication initiation. Faster growing cells maintain a consistent initiation mass but slower growing cells are smaller and will never reach this mass so it needs to be adjusted lower for them.
- Parameters:
doubling_time (Unum) – expected doubling time of cell
- Returns:
Critical mass for DNA replication initiation
- Return type:
Unum
- reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters._get_fit_parameters(list_of_dicts, key)[source]
- reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters._get_linearized_fit(x, y, **kwargs)[source]
- reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters._loadRow(key, list_of_dicts)[source]
- reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters._loadTableIntoObjectGivenDoublingTime(obj, list_of_dicts)[source]
- reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters._useFitParameters(x_new, function, x_units, y_units, dtype)[source]
- reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters._use_linearized_fit(x, params)[source]
- reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.linear_regression(x, y, r_tol=0.999, p_tol=1e-05)[source]
Perform linear regression on a data set and check that statistics are within expected values to confirm a good linear fit.
- Parameters:
- Returns:
- 2-element tuple containing
slope: linear fit slope
intercept: linear fit intercept
- Return type: