8.1.1.1.1.5.1.6. skimpy.analysis.oracle.minimum_fluxes¶

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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

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

8.1.1.1.1.5.1.6.1. Attributes¶

`BIGM`
`BIGM_THERMO`
`BIGM_DG`
`BIGM_P`
`EPSILON`
`BIGM`
`BIGM_THERMO`
`BIGM_DG`
`BIGM_P`
`EPSILON`

8.1.1.1.1.5.1.6.2. Classes¶

`MinFLuxVariable`	Class to represent a negative slack variable for relaxation problems
`MinFLux`	Class to represent thermodynamics constraints.

8.1.1.1.1.5.1.6.3. Functions¶

`add_min_flux_requirements`(tmodel, flux[, inplace, exclude])
`relax_min_flux`(tmodel[, reactions_to_ignore, solver, ...])

8.1.1.1.1.5.1.6.4. Module Contents¶

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.BIGM¶

skimpy.BIGM_THERMO¶

skimpy.BIGM_DG¶

skimpy.BIGM_P¶

skimpy.EPSILON¶

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