8.1.1.1.1.5. `skimpy.analysis.oracle`¶

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Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

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8.1.1.1.1.5.1. Submodules¶

8.1.1.1.1.5.2. Package Contents¶

8.1.1.1.1.5.2.1. Classes¶

`MinFLuxVariable`	Class to represent a negative slack variable for relaxation problems
`MinFLux`	Class to represent thermodynamics constraints.
`ParameterValues`	Parameters set for kinetic models wich can be indexed with symbols or
`BinUseVariable`
`BinVariable`
`FluxRatioCons`	Class to represent thermodynamics constraints.

8.1.1.1.1.5.2.2. Functions¶

`add_min_log_displacement`(tmodel, min_log_displacement, tva_fluxes=None, inplace=True)
`add_undefined_delta_g`(_tmodel, solution, delta_g_std=-10, delta_g_std_err=2, add_displacement=True, inplace=True, exclude_reactions=[])
`add_dummy_delta_g`(tmodel, rxn, delta_g_std=-100, delta_g_std_err=2, add_displacement=True)
`add_min_flux_requirements`(tmodel, flux, inplace=True, exclude=[])
`relax_min_flux`(tmodel, reactions_to_ignore=(), solver=None, in_place=False)	param t_tmodel
`fix_directionality`(tmodel, solution, inplace=True)	Takes a flux solution and transfers its reaction directionality as
`sanitize_cobra_vars`(met_name)
`deltag0_to_keq`(deltag0, temp, unit=KCAL, gas_constant=None)
`load_fluxes`(solution_raw, tmodel, kmodel, density=None, ratio_gdw_gww=None, concentration_scaling=None, time_scaling=None, xmol_in_flux=0.001)
`load_concentrations`(solution_raw, tmodel, kmodel, concentration_scaling=None)
`load_equilibrium_constants`(solution_raw, tmodel, kmodel, concentration_scaling=None, in_place=False)
`impose_turnover_concentation_ratios`(tmodel, metabolites, tva, ratio, in_place=False, discretization=LOG, N=11)
`add_ratio_constraints`(model, lc, fwd, bwd, ratio, concentration_range=(MIN_C, MAX_C), discretization=LOG, N=11)

8.1.1.1.1.5.2.3. Attributes¶

`BIGM`
`BIGM_THERMO`
`BIGM_DG`
`BIGM_P`
`EPSILON`
`MAX_STOICH`
`BIGM`
`BIGM_THERMO`
`BIGM_DG`
`BIGM_P`
`EPSILON`
`MIN_C`
`MAX_C`
`BIGM`
`EPSILON`
`LOG`
`LIN`

skimpy.add_min_log_displacement(tmodel, min_log_displacement, tva_fluxes=None, inplace=True)¶

skimpy.BIGM¶

skimpy.BIGM_THERMO¶

skimpy.BIGM_DG¶

skimpy.BIGM_P¶

skimpy.EPSILON¶

skimpy.MAX_STOICH = 10¶

skimpy.add_undefined_delta_g(_tmodel, solution, delta_g_std=- 10, delta_g_std_err=2, add_displacement=True, inplace=True, exclude_reactions=[])¶

skimpy.add_dummy_delta_g(tmodel, rxn, delta_g_std=- 100, delta_g_std_err=2, add_displacement=True)¶

skimpy.BIGM¶

skimpy.BIGM_THERMO¶

skimpy.BIGM_DG¶

skimpy.BIGM_P¶

skimpy.EPSILON¶

class skimpy.MinFLuxVariable(reaction, **kwargs)¶

Bases: pytfa.optim.variables.ReactionVariable

Class to represent a negative slack variable for relaxation problems

prefix = MinFluxVar_¶

class skimpy.MinFLux(reaction, expr, **kwargs)¶

Bases: pytfa.optim.constraints.ReactionConstraint

Class to represent thermodynamics constraints. G: Flux_FW + Fluw_BW > min_flux

prefix = MF_¶

skimpy.add_min_flux_requirements(tmodel, flux, inplace=True, exclude=[])¶

skimpy.relax_min_flux(tmodel, reactions_to_ignore=(), solver=None, in_place=False)¶

Parameters

t_tmodel (pytfa.thermo.ThermoModel:) –
reactions_to_ignore – Iterable of reactions that should not be relaxed
solver – solver to use (e.g. ‘optlang-glpk’, ‘optlang-cplex’, ‘optlang-gurobi’

Returns

a cobra_model with relaxed bounds on standard Gibbs free energy

skimpy.fix_directionality(tmodel, solution, inplace=True)¶: Takes a flux solution and transfers its reaction directionality as constraints for the cobra_model :param inplace: :param tmodel: :param solution: :return:

skimpy.sanitize_cobra_vars(met_name)¶

skimpy.deltag0_to_keq(deltag0, temp, unit=KCAL, gas_constant=None)¶

class skimpy.ParameterValues(parameter_values, kmodel=None)¶

Bases: object

Parameters set for kinetic models wich can be indexed with symbols or

__getitem__(self, item)¶

__setitem__(self, item, value)¶

items(self)¶

keys(self)¶

values(self)¶

skimpy.load_fluxes(solution_raw, tmodel, kmodel, density=None, ratio_gdw_gww=None, concentration_scaling=None, time_scaling=None, xmol_in_flux=0.001)¶

skimpy.load_concentrations(solution_raw, tmodel, kmodel, concentration_scaling=None)¶

skimpy.load_equilibrium_constants(solution_raw, tmodel, kmodel, concentration_scaling=None, in_place=False)¶

skimpy.MIN_C = 1e-10¶

skimpy.MAX_C = 0.1¶

skimpy.BIGM¶

skimpy.EPSILON¶

skimpy.LOG = log¶

skimpy.LIN = lin¶

class skimpy.BinUseVariable(model, id_, **kwargs)¶

Bases: pytfa.optim.variables.ModelVariable, pytfa.optim.variables.BinaryVariable

prefix = BinUseVariable_¶

class skimpy.BinVariable(model, id_, **kwargs)¶

Bases: pytfa.optim.variables.ModelVariable

prefix = BinVariable_¶

class skimpy.FluxRatioCons(model, expr, id_, **kwargs)¶

Bases: pytfa.optim.constraints.ModelConstraint