"""Model changes.
Model changes are structural changes to the model structure.
Changes of values and initial conditions are encoded via
the changes instead.
"""
from sbmlutils import log
from sbmlsim.model.rr_model import roadrunner
[docs]logger = log.get_logger(__name__)
[docs]class ModelChange(object):
"""ModelChange.
Structural change to a model.
"""
[docs] CLAMP_SPECIES = "clamp_species"
@staticmethod
[docs] def clamp_species(r: roadrunner.RoadRunner, species_id, formula=True, speed=1e4):
"""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.
"""
if formula is None:
# unclamping species.
formula = False
if formula is True:
# clamping to current model value
formula = r[species_id]
selections = r.timeCourseSelections
rid = f"{species_id}_clamp"
if formula:
r.addReaction(rid, [], [species_id], f"{speed}*({formula}-{species_id})")
# update selections
selections.append(rid)
r.selections = selections
else:
r.removeReaction(rid)
# update selections
r.selections = [key for key in selections if key != rid]