8.1.1.2.1.7. skimpy.core.reactor¶

[———]

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.

8.1.1.2.1.7.1. Classes¶

Reactor

8.1.1.2.1.7.2. Functions¶

make_reactor_ode_fun(reactor, sim_type[, pool, ...])

This function generates the symbolic expressions for a reactor model

8.1.1.2.1.7.3. Module Contents¶

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

Bases: abc.ABC

extracellular_compartment = 'e'¶

medium¶

biomass_reactions¶

biomass_scaling¶

biomass_variables¶

models¶

boundary_conditions¶

initial_conditions¶

_modified = True¶

custom_variables¶

property variables¶

property parameters¶

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

add_boundary_condition(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(element, kind)¶

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

Parameters:

sim_type
ncpu

Returns:

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

solve_ode(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)¶

This function generates the symbolic expressions for a reactor model

Parameters:

reactor
sim_type
pool

Returns: