Issue: Implement Activation States and Cascades in Enzyme Class

Summary

Enhance the Enzyme class by adding the ability to model activation states and cascading effects. These changes will allow enzymes to be activated or deactivated and to regulate the activity of other enzymes, creating a more dynamic and realistic simulation of signal transduction pathways.

Proposed Changes

Activation State

Attribute: Introduce an active attribute to represent the activation state of the enzyme (e.g., True for active, False for inactive).

Purpose: This attribute will determine whether an enzyme can catalyze reactions.

Activation Methods

Methods: Add activate() and deactivate() methods to control the enzyme's state.

activate(): Sets the active attribute to True.

deactivate(): Sets the active attribute to False.

Purpose: These methods provide a simple interface for managing enzyme activity.

Cascades

Regulation Method: Add a regulate_enzyme() method to activate or deactivate other enzymes.

regulate_enzyme(target_enzyme: 'Enzyme', action: str): Takes another enzyme and an action ('activate' or 'deactivate') and modifies the target enzyme's state.

Purpose: Allows the creation of cascading effects where the activation of one enzyme can trigger the activation or deactivation of others.

Downstream Enzymes

Attribute: Add a downstream_enzymes list to the Enzyme class.

Purpose: Store references to other enzymes that should be regulated when this enzyme is activated, allowing the simulation of enzyme cascades.

Acceptance Criteria

Activation State Management

The active attribute should default to True when an enzyme is created without specifying its activation state.

activate() should set the active attribute to True.

deactivate() should set the active attribute to False.

The calculate_rate() method should return 0.0 when the enzyme is inactive.

Regulation of Other Enzymes

The regulate_enzyme() method should accept a target enzyme and either 'activate' or 'deactivate' as parameters.

When called with 'activate', the target enzyme's active attribute should be set to True.

When called with 'deactivate', the target enzyme's active attribute should be set to False.

If the regulate_enzyme() method is called with an invalid action, it should raise a ValueError.

Downstream Enzyme Activation

When an enzyme is activated, it should trigger the activation of all enzymes in its downstream_enzymes list.

If an enzyme is deactivated, it should not affect the downstream_enzymes.

Unit Tests

Here are the unit tests needed to verify the functionality:

Test Activation State Management

import unittest from enzyme import Enzyme from metabolite import Metabolite

class TestEnzymeActivation(unittest.TestCase):

def test_default_activation_state(self):
    enzyme = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0})
    self.assertTrue(enzyme.active)

def test_activate_method(self):
    enzyme = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0}, active=False)
    enzyme.activate()
    self.assertTrue(enzyme.active)

def test_deactivate_method(self):
    enzyme = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0})
    enzyme.deactivate()
    self.assertFalse(enzyme.active)

def test_inactive_enzyme_calculate_rate(self):
    enzyme = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0}, active=False)
    rate = enzyme.calculate_rate({'A': Metabolite(name='A', quantity=50.0)})
    self.assertEqual(rate, 0.0)

Test Regulation of Other Enzymes

class TestEnzymeRegulation(unittest.TestCase):

def test_regulate_enzyme_activate(self):
    enzyme1 = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0})
    enzyme2 = Enzyme(name='Enzyme2', k_cat=1.0, k_m={'B': 10.0}, active=False)
    enzyme1.regulate_enzyme(enzyme2, 'activate')
    self.assertTrue(enzyme2.active)

def test_regulate_enzyme_deactivate(self):
    enzyme1 = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0})
    enzyme2 = Enzyme(name='Enzyme2', k_cat=1.0, k_m={'B': 10.0})
    enzyme1.regulate_enzyme(enzyme2, 'deactivate')
    self.assertFalse(enzyme2.active)

def test_regulate_enzyme_invalid_action(self):
    enzyme1 = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0})
    enzyme2 = Enzyme(name='Enzyme2', k_cat=1.0, k_m={'B': 10.0})
    with self.assertRaises(ValueError):
        enzyme1.regulate_enzyme(enzyme2, 'invalid_action')

Test Downstream Enzyme Activation

class TestEnzymeCascades(unittest.TestCase):

def test_downstream_enzyme_activation(self):
    enzyme1 = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0})
    enzyme2 = Enzyme(name='Enzyme2', k_cat=1.0, k_m={'B': 10.0}, active=False)
    enzyme1.downstream_enzymes.append(enzyme2)

    # Activate enzyme1 and ensure it activates enzyme2
    enzyme1.activate()
    for downstream in enzyme1.downstream_enzymes:
        enzyme1.regulate_enzyme(downstream, 'activate')

    self.assertTrue(enzyme2.active)

def test_downstream_enzyme_no_deactivation(self):
    enzyme1 = Enzyme(name='Enzyme1', k_cat=1.0, k_m={'A': 10.0})
    enzyme2 = Enzyme(name='Enzyme2', k_cat=1.0, k_m={'B': 10.0}, active=True)
    enzyme1.downstream_enzymes.append(enzyme2)

    # Deactivate enzyme1 and ensure it does not deactivate enzyme2
    enzyme1.deactivate()
    self.assertTrue(enzyme2.active)

Tasks

[ ] Add an active attribute to the Enzyme class.

[ ] Implement activate() and deactivate() methods.

[ ] Add a regulate_enzyme() method for controlling other enzymes.

[ ] Add a downstream_enzymes list to store enzymes that should be activated or deactivated.

[ ] Write unit tests to cover activation, deactivation, and cascade behaviors.

[ ] Update documentation for the Enzyme class to reflect new methods and attributes.

Rationale

Implementing these changes will provide more flexibility in simulating complex biochemical pathways where enzymes can dynamically regulate each other. This improvement is essential for modeling realistic signal transduction cascades in cellular processes.

Note: Please adjust the code snippets and the implementation as needed based on the specific context of your project.

Dooders / Pyology

Issue: Implement Activation States and Cascades in Enzyme Class #33