reconstruction.ecoli.dataclasses.state.internal_state

SimulationData state associated data

class reconstruction.ecoli.dataclasses.state.internal_state.InternalState(raw_data, sim_data)

Bases: object

Internal State

_build_bulk_molecule_specs(sim_data, molecule_ids)

Builds a list of molecule IDs with compartment tags and a corresponding array of molecular masses to add to the bulk state. :param molecule_ids: List of molecule IDs w/o compartment tags :type molecule_ids: List[str]

Returns:

List of molecule IDs

with compartment tags

masses (np.ndarray): Array of molecular masses divided into

submasses

Return type:

molecule_ids_with_compartments (List[str])

_build_bulk_molecules(sim_data)

Add data (IDs and mass) for all classes of bulk molecules.

_build_compartments(raw_data, sim_data)

_build_unique_molecules(sim_data)

Add data (name, mass, and attribute data structure) for all classes of unique molecules.