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State

Snapshot of molecule concentrations (single-compartment, legacy).

Overview

State represents a snapshot of all molecule concentrations at a point in time for single-compartment simulations. For multi-compartment simulations, use WorldState instead.

Property Type Description
timestamp float Simulation time of this snapshot
concentrations Dict[str, float] Molecule name to concentration
Method Returns Description
get(molecule, compartment) float Get concentration of molecule
copy() State Create a deep copy of this state

Discussion

Usage Example

from alienbio import StateImpl

state = StateImpl(
    chemistry=chem,
    initial={"glucose": 10.0, "atp": 5.0}
)

# Access concentration
glucose_conc = state.get("glucose")

# Copy for simulation
new_state = state.copy()

Relationship to WorldState

  • State: Single-compartment, uses molecule names as strings
  • WorldState: Multi-compartment, uses integer IDs for efficiency

Protocol

from typing import Protocol, Dict

class State(Protocol):
    """Snapshot of system concentrations (single-compartment)."""

    timestamp: float
    concentrations: Dict[str, float]

    def get(self, molecule: str) -> float:
        """Get concentration of molecule."""
        ...

    def copy(self) -> "State":
        """Create a deep copy of this state."""
        ...

See Also