8.1.1.2.1.3. skimpy.core.kinmodel

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8.1.1.2.1.3.1. Module Contents

8.1.1.2.1.3.1.1. Classes

KineticModel

This class contains the kinetic model as described by reaction and
class skimpy.KineticModel(reactions=None, boundary_conditions=None, constraints=None, name='Unnamed')

Bases: object

This class contains the kinetic model as described by reaction and boundary conditions and constratins.

:param : :return:

property reactants(self)
property parameters(self)
property moieties(self)
add_reaction(self, reaction)

Adds a SKiMPy reaction to the model

Parameters

reaction (skimpy.core.Reaction) – The reaction to add

Returns

add_compartment(self, compartment)
Parameters

compartment –

Returns

add_constraint(self, constraint)
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)
parametrize_by_reaction(self, param_dict)
If has input: apply as dict to reactions in the model by

reaction.parametrize(args)

Returns

parametrize(self, param_dict)
repair(self)

Link inhibitors and activators to reactants FIXME: Any idea to avoid this is dearly welcome :return:

property sim_type(self)
prepare(self, mca=True, ode=True, **kwargs)

Model preparation for different analysis types. The preparation is done before the compiling step to be able to curate the model in between

Parameters

  • mca –

  • ode –

Returns

compile_jacobian(self, type=NUMERICAL, sim_type=QSSA, ncpu=1)
compile_ode(self, sim_type=QSSA, ncpu=1)
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>`_.

Parameters

  • time_out (list(float) or similar) – The times at which the solution is evaluated

  • solver_type – must be among [‘cvode’,’ida’,’dopri5’,’dop853’]

  • kwargs –

Returns

compile_mca(self, parameter_list=[], mca_type=NET, sim_type=QSSA, ncpu=1)

Compile MCA expressions: elasticities, jacobian and control coeffcients