reconstruction.ecoli.dataclasses.state.external_state
Simulation data for external state
This base class includes all data associated with states external to the cells. Initializes the environment using conditions and time series from raw_data.
saved_timelines: a dictionary of all timelines.
- current_timeline_id: a string specifying the timelines
used for the current simulation.
- current_media: a dictionary of molecules (keys) and
their concentrations (values).
- saved_media: a dictionary of all media, each entry
itself a dictionary molecules (keys) and their concentrations (values).
- class reconstruction.ecoli.dataclasses.state.external_state.ExternalState(raw_data, sim_data)[source]
Bases:
object
External State
- exchange_data_from_concentrations(molecules)[source]
Update importExchangeMolecules for FBA based on current nutrient concentrations. This provides a simple type of transport to accommodate changing nutrient concentrations in the environment. Transport is modeled as a binary switch: When there is a high concentrations of environment nutrients, transporters are unconstrained and nutrients are transported as needed by metabolism. When concentrations fall below the threshold, that nutrient’s transport is constrained to max flux of 0.
- Parameters:
molecules (dict[str, float]) – external molecules (no location tag) with external concentration, concentration can be inf
- Return type:
- Returns dict with the following keys:
- externalExchangeMolecules (set[str]): all exchange molecules (with
location tag), includes both import and secretion exchanged molecules
- importExchangeMolecules (set[str]): molecules (with location tag) that
can be imported from the environment into the cell
- importConstrainedExchangeMolecules (dict[str, float with mol/mass/time units]):
constrained molecules (with location tag) with upper bound flux constraints
- importUnconstrainedExchangeMolecules (set[str]): exchange molecules
(with location tag) that do not have an upper bound on their flux
- secretionExchangeMolecules (set[str]): molecules (with location tag)
that can be secreted by the cell into the environment
- exchange_data_from_media(media_label)[source]
- Returns:
exchange_data for a media_label saved in exchange_data_dict.
- Return type:
- get_import_constraints(unconstrained, constrained, units)[source]
- Returns:
- the indices of all
importUnconstrainedExchangeMolecules in self.all_external_exchange_molecules are true, the rest as false
- constrained_molecules (list[bool]): the indices of all
importConstrainedExchangeMolecules in self.all_external_exchange_molecules are true, the rest as false
- constraints (list[float]): uptake constraints for each molecule
that is constrained, nan for no constraint
- Return type: