sbmlsim.model.model_change

Model changes.

Model changes are structural changes to the model structure. Changes of values and initial conditions are encoded via the changes instead.

Module Contents

Classes

ModelChange

ModelChange.

Attributes

logger

sbmlsim.model.model_change.logger[source]
class sbmlsim.model.model_change.ModelChange[source]

Bases: object

ModelChange.

Structural change to a model.

CLAMP_SPECIES = clamp_species[source]
static clamp_species(r, species_id, formula=True, speed=10000.0)[source]

Clamp/free species to certain value or formula.

This is only an approximative clamp, i.e. not working instantenious. Depending on the model kinetics different speed settings are required. FIXME: time cannot be used in formula due to https://github.com/sys-bio/roadrunner/issues/601 FIXME: concentrations and amounts are not handled (uses native species setting

i.e., amount or concentration definition.

Parameters

r (sbmlsim.model.rr_model.roadrunner.RoadRunner) –