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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

included_files_files/example_model.png

:download:`model <included_files/example_model.psc>`

:download:`layout file <included_files/example_model_layout.dict>`

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

included_files_files/lin4_fb.png

:download:`model <included_files/lin4_fb.psc>`

:download:`layout file <included_files/lin4_fb.dict>`

:download:`separated rate equations file <included_files/lin4_fb.reqn>`

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.

:download:`basic_usage.ipynb <example_notebooks/basic_usage.ipynb>`

:download:`RateChar.ipynb <example_notebooks/RateChar.ipynb>`

:download:`Symca.ipynb <example_notebooks/Symca.ipynb>`

:download:`Thermokin.ipynb <example_notebooks/Thermokin.ipynb>`