8.1.1.2.1.3. skimpy.core.kinmodel¶

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8.1.1.2.1.3.1. Classes¶

KineticModel

This class contains the kinetic model as described by reaction and

8.1.1.2.1.3.2. Module Contents¶

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:

name = 'Unnamed'¶

reactions¶

boundary_conditions¶

constraints¶

initial_conditions¶

logger¶

_simtype = None¶

_modified = True¶

_recompiled = False¶

compartments¶

property reactants¶

property parameters¶

property moieties¶

add_reaction(reaction)¶

Adds a SKiMPy reaction to the model

Parameters:: reaction (skimpy.core.Reaction) – The reaction to add
Returns:

add_compartment(compartment)¶

Parameters:: compartment
Returns:

add_constraint(constraint)¶

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)¶

parametrize_by_reaction(param_dict)¶

If has input: apply as dict to reactions in the model by: reaction.parametrize(args)

Returns:

parametrize(param_dict)¶

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

property sim_type¶

prepare(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(type=NUMERICAL, sim_type=QSSA, ncpu=1)¶

compile_ode(sim_type=QSSA, ncpu=1)¶

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>`_.

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(parameter_list=[], mca_type=NET, sim_type=QSSA, ncpu=1)¶: Compile MCA expressions: elasticities, jacobian and control coeffcients