sbmlsim.simulation.timecourse
¶
Definition of timecourses and timecourse simulations.
Module Contents¶
Classes¶
Simulation definition. |
|
Timecourse simulation consisting of multiple concatenated timecourses. |
Attributes¶
- class sbmlsim.simulation.timecourse.Timecourse(start, end, steps, changes=None, model_changes=None, model_manipulations=None, discard=False)[source]¶
Bases:
sbmlsim.serialization.ObjectJSONEncoder
Simulation definition.
Definition of all information necessary to run a single timecourse simulation.
A single simulation consists of multiple changes which are applied, all simulations are performed and collected.
Changesets and selections are deep copied for persistence.
- Parameters
start (float) –
end (float) –
steps (int) –
changes (Dict[str, pint.Quantity]) –
model_changes (Dict[str, pint.Quantity]) –
model_manipulations (dict) –
discard (bool) –
- add_change(self, sid, value)[source]¶
Add change.
- Parameters
sid (str) –
value (float) –
- Return type
None
- remove_change(self, sid)[source]¶
Remove change for given id.
- Parameters
sid (str) –
- Return type
None
- add_model_change(self, sid, change)[source]¶
Add model change.
- Parameters
sid (str) –
- Return type
None
- add_model_changes(self, model_changes)[source]¶
Add model changes.
- Parameters
model_changes (Dict[str, str]) –
- Return type
None
- remove_model_change(self, sid)[source]¶
Remove model change for id.
- Parameters
sid (str) –
- Return type
None
- normalize(self, uinfo)[source]¶
Normalize values to model units for all changes.
- Parameters
uinfo (sbmlsim.units.UnitsInformation) –
- Return type
None
- class sbmlsim.simulation.timecourse.TimecourseSim(timecourses, selections=None, reset=True, time_offset=0.0)[source]¶
Bases:
sbmlsim.simulation.AbstractSim
Timecourse simulation consisting of multiple concatenated timecourses.
In case of a single timecourse, only the single timecourse is executed.
- Parameters
timecourses (Union[Timecourse, List[Timecourse]]) –
selections (Optional[List[str]]) –
reset (bool) –
time_offset (float) –
- add_model_changes(self, model_changes)[source]¶
Add model changes to given simulation.
- Parameters
model_changes (Dict) –
- Return type
None
- normalize(self, uinfo)[source]¶
Normalize timecourse simulation.
- Parameters
uinfo (sbmlsim.units.UnitsInformation) –
- Return type
None
- to_json(self, path=None)[source]¶
Convert definition to JSON.
- Parameters
path (pathlib.Path) –
- Return type
str