*edited 6/17/10 I’m trying to understand how to improve my code (make it more

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Asked: May 20, 20262026-05-20T10:12:48+00:00 2026-05-20T10:12:48+00:00

*edited 6/17/10 I’m trying to understand how to improve my code (make it more

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*edited 6/17/10

I’m trying to understand how to improve my code (make it more pythonic). Also, I’m interested in writing more intuitive ‘conditionals’ that would describe scenarios that are commonplace in biochemistry. The conditional criteria in the below program I’ve explained in Answer #2, but I am not satisfied with the code- it works fine, but isn’t obvious and isn’t easy to implement for more complicated conditional scenarios. Ideas welcome. Comments/criticisms welcome. First posting experience @ stackoverflow- please comment on etiquette if needed.

The code generates a list of values that are the solution to the following exercise:

“In a programming language of your choice, implement Gillespie’s First Reaction Algorithm to study the temporal behaviour of the reaction A—>B in which the transition from A to B can only take place if another compound, C, is present, and where C dynamically interconverts with D, as modelled in the Petri-net below. Assume that there are 100 molecules of A, 1 of C, and no B or D present at the start of the reaction. Set kAB to 0.1 s-1 and both kCD and kDC to 1.0 s-1. Simulate the behaviour of the system over 100 s.”

def sim():
    # Set the rate constants for all transitions
    kAB = 0.1
    kCD = 1.0
    kDC = 1.0

    # Set up the initial state
    A = 100
    B = 0
    C = 1
    D = 0

    # Set the start and end times
    t = 0.0
    tEnd = 100.0

    print "Time\t", "Transition\t", "A\t", "B\t", "C\t", "D"

    # Compute the first interval
    transition, interval = transitionData(A, B, C, D, kAB, kCD, kDC)
    # Loop until the end time is exceded or no transition can fire any more
    while t <= tEnd and transition >= 0:
        print t, '\t', transition, '\t', A, '\t', B, '\t', C, '\t', D
        t += interval
        if transition == 0:
            A -= 1
            B += 1
        if transition == 1:
            C -= 1
            D += 1
        if transition == 2:
            C += 1
            D -= 1
        transition, interval = transitionData(A, B, C, D, kAB, kCD, kDC)


def transitionData(A, B, C, D, kAB, kCD, kDC):
    """ Returns nTransition, the number of the firing transition (0: A->B,
    1: C->D, 2: D->C), and interval, the interval between the time of
    the previous transition and that of the current one. """
    RAB = kAB * A * C
    RCD = kCD * C
    RDC = kDC * D
    dt = [-1.0, -1.0, -1.0]
    if RAB > 0.0:
        dt[0] = -math.log(1.0 - random.random())/RAB
    if RCD > 0.0:
        dt[1] = -math.log(1.0 - random.random())/RCD
    if RDC > 0.0:
        dt[2] = -math.log(1.0 - random.random())/RDC
    interval = 1e36
    transition = -1
    for n in range(len(dt)):
        if dt[n] > 0.0 and dt[n] < interval:
            interval = dt[n]
            transition = n
    return transition, interval       


if __name__ == '__main__':
    sim()