Included Files¶

Here are the files that are used in the examples as well as the interactive notebook versions of the documentation.

Models¶

The models used in this documentation are included below (together with other additional files). These files must be downloaded to the psc directory to be used in the example notebooks unless otherwise specified.

example_model.psc¶

model

layout file

The text of example_model.psc is included below:

# example_model.psc
# -----------------------------------------------------------------------------
# Fixed Species

FIX: X0 X2 X3

# -----------------------------------------------------------------------------
# Reaction definitions

R1:
    X0 = S1
    ((Vf1 / Km1_X0) * (X0 - S1 / Keq1)) / (1 + X0/Km1_X0 + S1/Km1_S1)

R2:
    S1 = X2
    ((Vf2 / Km2_S1) * (S1 - X2 / Keq2)) / (1 + S1/Km2_S1 + X2/Km2_X2)

R3:
    S1 = X3
    ((Vf3 / Km3_S1) * (S1 - X3 / Keq3)) / (1 + S1/Km3_S1 + X3/Km3_X3)

# -----------------------------------------------------------------------------
# Variable species initial concentrations

S1 = 1

# -----------------------------------------------------------------------------
# Fixed species concentrations

X0 = 100
X2 = 10
X3 = 1

# -----------------------------------------------------------------------------
# Parameters

Vf1 = 100.0
Keq1 = 10.0
Km1_X0 = 1.0
Km1_S1 = 1.0

Vf2 = 50.0
Keq2 = 10.0
Km2_S1 = 1.0
Km2_X2 = 1.0

Vf3 = 10.0
Keq3 = 10.0
Km3_S1 = 1.0
Km3_X3 = 1.0
# -----------------------------------------------------------------------------

lin4_fb.psc¶

model

layout file

separated rate equations file

The text of lin4_fb.psc is included below:

# lin4_fb.psc
# -----------------------------------------------------------------------------
# Fixed Species

FIX: X0 X4

# -----------------------------------------------------------------------------
# Reaction definitions

R1:
    X0 = S1
    (Vf_1 * (X0 / X0_05_1) * (1 - ((S1/X0)/Keq_1)) *
    (X0/X0_05_1 + S1/S1_05_1)**(h_1-1)) /
    ((X0/X0_05_1 + S1/S1_05_1)**(h_1) +
    (1 + (S3/S3_05_1)**(h_1))/(1 + a_1 * (S3/S3_05_1)**(h_1)))

R2:
    S1 = S2
    (Vf_2 * (S1 / S1_05_2) *
    (1 - ((S2/S1)/Keq_2))) / (1 + S1/S1_05_2 + S2/S2_05_2)

R3:
    S2 = S3
    (Vf_3 * (S2 / S2_05_3) *
    (1 - ((S3/S2)/Keq_3))) / (1 + S2/S2_05_3 + S3/S3_05_3)

R4:
    S3 = X4
    (Vf_4*S3)/(S3 + S3_05_4)

# -----------------------------------------------------------------------------
# Variable species initial concentrations

S1 = 1
S2 = 1
S3 = 1

# -----------------------------------------------------------------------------
# Fixed species concentrations

X0 = 1
X4 = 1

# -----------------------------------------------------------------------------
# Parameters

Vf_1 = 400.0
Keq_1 = 100.0
X0_05_1 = 1.0
S1_05_1 = 10000.0
h_1 = 4
S3_05_1 = 5.0
a_1 = 0.01

Vf_2 = 10000.0
Keq_2 = 10.0
S1_05_2 = 1.0
S2_05_2 = 1.0

Vf_3 = 1000.0
Keq_3 = 10.0
S2_05_3 = 0.01
S3_05_3 = 1.0

Vf_4 = 50.0
S3_05_4 = 1.0

# -----------------------------------------------------------------------------

Example Notebooks¶

The example Jupyter notebooks are runnable versions of the pages Basic Usage, RateChar, Symca and Thermokin found in this documentation.