Custom Reactions

It’s not possible to pre-define every rate equation anyone would ever need. However many of the most common rate equations are already set up (see section on Reactions).

There are two options for custom rate equations.

1. Use the Generic Reaction Class

This is a reaction class which lets you specify your own rate equation.

class kinetics.Generic(params=[], species=[], rate_equation='', substrates=[], products=[])

This Reaction class allows you to specify your own rate equation. Enter the parameter names in params, and the substrate names used in the reaction in species. Type the rate equation as a string in rate_equation, using these same names. Enter the substrates used up, and the products made in the reaction as normal.

An example which models a UniUni enzyme

import kinetics
import kinetics.Uncertainty as ua
import matplotlib.pyplot as plt
from scipy.stats import norm

step1 = kinetics.Generic(params=['k1', 'k_1'], species=['a','e','ea'],
                         rate_equation='(k1*a*e)-(k_1*ea)',
                         substrates=['a', 'e'], products=['ea'])

step2 = kinetics.Generic(params=['k2','k_2'], species=['ea','e','p'],
                         rate_equation='(k2*ea)-(k_2*ea*p)',
                         substrates=['ea'], products=['e', 'p'])

step1.parameters = {'k1' : 0.1,
                    'k_1' : 0.001}

step2.parameters = {'k2' : 100,
                    'k_2': 0.1}

step1.parameter_distributions = {'k1' : norm(0.1, 0.01),
                                 'k_1' : norm(0.001, 0.0001)}

step2.parameter_distributions = {'k2' : norm(100, 10),
                                 'k_2' : norm(0.1, 0.01)}

model = kinetics.Model()

model.append(step1)
model.append(step2)
model.species = {'e' : 1,
                 'a' : 100}

model.setup_model()

model.run_model()
model.plot_substrate('a')
model.plot_substrate('e')
model.plot_substrate('ea')
model.plot_substrate('p')
plt.show()

samples = ua.make_samples_from_distributions(model, num_samples=1000)
outputs = ua.run_all_models(model, samples, logging=True)
all_runs_dataframes = ua.dataframes_all_runs(model, outputs)
ua.plot_substrate('a', all_runs_dataframes, colour='blue', alpha=0.01, linewidth=5)
ua.plot_substrate('e', all_runs_dataframes, colour='darkorange', alpha=0.01, linewidth=5)
ua.plot_substrate('ea', all_runs_dataframes, colour='green', alpha=0.01, linewidth=5)
ua.plot_substrate('p', all_runs_dataframes, colour='purple', alpha=0.01, linewidth=5)
plt.show()

2. Make your own reaction class.

This might be useful if its going to be re-used alot

To make a reaction class for a custom rate equation we need to define a new class which inherits from kinetics.Reaction

The new class needs two funcions. an __init__() function and a calculate_rate() function.

The following code example provides an example for doing this:

class My_New_Reaction(kinetics.Reaction):

    def __init__(self,
                 param1='', param2='', species1='', species2='',
                 substrates=[], products=[]):

    # This is required to inherit from kinetics.Reaction
    super().__init__()

    # Set parameter and substrates names from the arguments passed in.  The order is important here.
    self.parameter_names=[param1, param2]
    self.reaction_substrate_names = [species1, species2]

    # Set the substrates and products from the arguments passed in.
    # Substrates are used up in the reaction, while produces are generated.
    self.substrates = substrates
    self.products = products

    def calculate_rate(self, substrates, parameters):

        # This function is used to calculate the rate at each time step in the model
        # It takes substrates and parameters as arguments, which are lists with the same order as we defined in __init__.

        # Substrates
        species1 = substrates[0]
        species2 = substrates[1]

        # Parameters
        param1 = parameters[0]
        param2 = parameters[1]

        # This is where the rate equation goes.  An example is shown.
        rate = param1*species1 + param2*species2

        return rate