Skip to content

mm

Jump to bottom
Okerew edited this page Sep 13, 2025 · 1 revision

MolecularMachinery Class

Overview

The MolecularMachinery class simulates complex molecular machines such as ribosomes, ATP synthases, and DNA polymerases. It models their components, functions, efficiency, energy consumption, and interactions with proteins and cells. The class supports serialization to/from JSON, performance tracking, and maintenance operations.

Class Definition

class MolecularMachinery:
    def __init__(self, name: str, components: List[Union[Protein, Cell]], function: str):
        """
        Initialize a new MolecularMachinery object.
        :param name: Name of the molecular machinery
        :param components: List of Protein or Cell components
        :param function: Biological function of the machinery
        """
        ...

Attributes

Attribute Type Description
name str Name of the molecular machinery.
components List[Union[Protein, Cell]] List of Protein or Cell components.
function str Biological function of the machinery.
efficiency float Efficiency of the machinery (0.0 to 1.0).
energy_level float Current energy level (0.0 to 100.0).
energy_consumed float Total energy consumed.
performance_history List[bool] History of performance outcomes.
last_maintenance float Timestamp of the last maintenance.
age int Age of the machinery.
mutation_rate float Probability of mutation.

Methods

Initialization

  • __init__(self, name: str, components: List[Union[Protein, Cell]], function: str) Initializes a new MolecularMachinery instance with the specified name, components, and function.

Factory Methods

  • create_ribosome(cls) Creates a ribosome molecular machinery.

    • Returns: A MolecularMachinery instance representing a ribosome.

  • create_atp_synthase(cls) Creates an ATP synthase molecular machinery.

    • Returns: A MolecularMachinery instance representing an ATP synthase.

  • create_dna_polymerase(cls) Creates a DNA polymerase molecular machinery.

    • Returns: A MolecularMachinery instance representing a DNA polymerase.

  • create_custom(cls, name: str, components: List[Union[Protein, Cell]], function: str) Creates a custom molecular machinery.

    • Parameters:

      • name: Name of the molecular machinery.
      • components: List of Protein or Cell components.
      • function: Biological function of the machinery.

    • Returns: A MolecularMachinery instance with the specified parameters.

Interaction

  • interact(self, target: Union[Protein, Cell]) -> str Simulates an interaction between the machinery and a target (protein or cell).

    • Parameters:

      • target: The target to interact with (Protein or Cell).

    • Returns: A string describing the interaction.

Function Performance

  • perform_function(self) -> str Simulates the machinery performing its function.

    • Returns: A string describing the outcome of the function performance.

Energy Management

  • energy_consumption_report(self) -> str Reports the total energy consumed by the machinery.

    • Returns: A string describing the energy consumption.

  • recharge(self, amount: float) -> str Recharges the machinery's energy level.

    • Parameters:

      • amount: The amount of energy to recharge.

    • Returns: A string describing the new energy level.

  • consume_energy(self, amount: float) -> None Consumes energy from the machinery.

    • Parameters:
      • amount: The amount of energy to consume.

Component Management

  • component_details(self) -> str Provides details about the machinery's components.

    • Returns: A string listing the components and their details.

  • add_component(self, component: Union[Protein, Cell]) -> str Adds a component to the machinery.

    • Parameters:

      • component: The component to add (Protein or Cell).

    • Returns: A string confirming the addition or indicating an error.

  • remove_component(self, component_name: str) -> str Removes a component from the machinery.

    • Parameters:

      • component_name: The name of the component to remove.

    • Returns: A string confirming the removal or indicating an error.

Aging and Mutation

  • age_machinery(self, time_units: int) -> str Simulates the aging of the machinery.

    • Parameters:

      • time_units: The number of time units to age the machinery.

    • Returns: A string describing the new efficiency.

  • mutate(self) -> str Simulates a mutation in the machinery.

    • Returns: A string describing the mutation outcome.

Maintenance

  • perform_maintenance(self) -> str Performs maintenance on the machinery.

    • Returns: A string describing the maintenance outcome.

  • emergency_shutdown(self) -> str Performs an emergency shutdown of the machinery.

    • Returns: A string confirming the shutdown.

Performance Analysis

  • analyze_performance(self) -> str Analyzes the performance history of the machinery.

    • Returns: A string describing the performance analysis.

  • optimize(self) -> str Optimizes the machinery's efficiency.

    • Returns: A string describing the optimization outcome.

Internal Interaction

  • internal_interaction(self) -> str Simulates an interaction between the machinery's components.

    • Returns: A string describing the interaction.

Serialization

  • to_json(self) -> str Converts the machinery to a JSON string representation.

    • Returns: A JSON string representing the machinery.

  • from_json(cls, json_str: str) -> 'MolecularMachinery' Creates a MolecularMachinery instance from a JSON string.

    • Parameters:

      • json_str: A JSON string representing the machinery.

    • Returns: A MolecularMachinery instance.

String Representation

  • __str__(self) -> str Returns a string representation of the machinery.

    • Returns: A string describing the machinery.

Example Usage

# Create a ribosome
ribosome = MolecularMachinery.create_ribosome()
print(ribosome)

# Create an ATP synthase
atp_synthase = MolecularMachinery.create_atp_synthase()
print(atp_synthase)

# Create a DNA polymerase
dna_polymerase = MolecularMachinery.create_dna_polymerase()
print(dna_polymerase)

# Create a custom molecular machinery
protein1 = Protein("Custom Protein 1", "ATGCGATCG")
protein2 = Protein("Custom Protein 2", "TACGTAGCT")
custom_machinery = MolecularMachinery.create_custom("Custom Machinery", [protein1, protein2], "Custom Function")
print(custom_machinery)

# Perform a function
print(ribosome.perform_function())

# Interact with a protein
protein = Protein("Target Protein", "GATCGATCG")
print(ribosome.interact(protein))

# Recharge energy
print(ribosome.recharge(50))

# Add a component
print(ribosome.add_component(protein))

# Remove a component
print(ribosome.remove_component("Small subunit"))

# Age the machinery
print(ribosome.age_machinery(10))

# Mutate the machinery
print(ribosome.mutate())

# Perform maintenance
print(ribosome.perform_maintenance())

# Analyze performance
print(ribosome.analyze_performance())

# Optimize the machinery
print(ribosome.optimize())

# Emergency shutdown
print(ribosome.emergency_shutdown())

# Serialize to JSON
json_str = ribosome.to_json()
print(json_str)

# Deserialize from JSON
new_ribosome = MolecularMachinery.from_json(json_str)
print(new_ribosome)

Dependencies

  • random: For simulating random events such as mutations and interactions.
  • json: For JSON serialization and deserialization.
  • time: For tracking the last maintenance time.
  • biobridge.blocks.protein.Protein: For protein components.
  • biobridge.blocks.cell.Cell: For cell components.

Error Handling

  • The class includes basic checks for valid component types and handles potential errors during component addition and removal.

Notes

  • The MolecularMachinery class is designed to simulate complex molecular machines.
  • It supports common molecular machines such as ribosomes, ATP synthases, and DNA polymerases.
  • The class models energy consumption, efficiency, and performance history.
  • Serialization methods allow for saving and loading the machinery's state.

Clone this wiki locally