8.1.1.2.1.7. `skimpy.core.reactor`¶

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8.1.1.2.1.7.1. Module Contents¶

8.1.1.2.1.7.1.1. Classes¶

Reactor

8.1.1.2.1.7.1.2. Functions¶

make_reactor_ode_fun(reactor, sim_type, pool=None, add_dilution=False, custom_ode_update=None)

This function generates the symbolic expressions for a reactor model

class skimpy.Reactor(models, biomass_reactions, biomass_scaling, boundary_conditions=None, extracellular_compartment='e', custom_variables=[])¶

Bases: abc.ABC

property variables(self)¶

property parameters(self)¶

parametrize(self, value_dict, model_name)¶: Set the parameters of a specified model :param value_dict: :param model_name: :return:

add_boundary_condition(self, boundary_condition)¶

Enforces a boundary condition (e.g. a constant concentration) on the kinetic model

Parameters: boundary_condition (skimpy.core.BoundaryCondition) – the boundary condition to enforce
Returns

add_to_tabdict(self, element, kind)¶

compile_ode(self, sim_type=QSSA, ncpu=1, add_dilution=False, custom_ode_update=None)¶

Parameters

sim_type –
ncpu –

Returns

initialize(self, value_dict, model_name)¶: Set the initial conditions for a single strain (excluding medium) :param value_dict: :param model_name: :return:

solve_ode(self, time_out, solver_type='cvode', **kwargs)¶: The solver types are from ::scikits.odes::, and can be found at <https://scikits-odes.readthedocs.io/en/latest/solvers.html>`_. :param time_out: The times at which the solution is evaluated :type time_out: list(float) or similar :param solver_type: must be among [‘cvode’,’ida’,’dopri5’,’dop853’] :param kwargs: :return:

skimpy.make_reactor_ode_fun(reactor, sim_type, pool=None, add_dilution=False, custom_ode_update=None)¶