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@dweindl
dweindl committed Jul 2, 2024
1 parent f0d634b commit c74bab4
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24 changes: 22 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0005/0005.py
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import pandas as pd
from petab.v1.C import *

from petabtests import PetabTestCase, analytical_a
from petabtests import PetabTestCase, analytical_a, antimony_to_sbml_str

DESCRIPTION = cleandoc("""
## Objective
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""")

# problem --------------------------------------------------------------------
ant_model = """
model *petab_test_0011()
compartment compartment_ = 1;
species A in compartment_, B in compartment_;
fwd: A => B; compartment_ * k1 * A;
rev: B => A; compartment_ * k2 * B;
A = a0;
B = b0;
B = 1;
a0 = 1;
b0 = 1;
k1 = 0;
k2 = 0;
offset_A = 0;
end
"""
model_file = sbml_file = Path(__file__).parent / "_model.xml"
model_file.write_text(antimony_to_sbml_str(ant_model))

condition_df = pd.DataFrame(
data={
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brief="Simulation. Condition-specific parameters only defined in "
"parameter table.",
description=DESCRIPTION,
model=Path("conversion_modified.xml"),
model=model_file,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df],
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69 changes: 19 additions & 50 deletions petabtests/cases/v1.0.0/sbml/0005/_model.xml
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@@ -1,96 +1,65 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="conversion_reaction_0" name="Conversion Reaction 0">

<listOfUnitDefinitions>
<unitDefinition id="volume" name="volume">
<listOfUnits>
<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="substance" name="substance">
<listOfUnits>
<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>

<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="petab_test_0011" id="petab_test_0011">
<listOfCompartments>
<compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
</compartment>
<compartment id="compartment_" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>

<listOfSpecies>
<species id="A" name="A" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
</species>
<species id="B" name="B" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
</species>
<species id="A" compartment="compartment_" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="B" compartment="compartment_" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>

<listOfParameters>
<parameter id="a0" name="a0" value="1" constant="true">
</parameter>
<parameter id="b0" name="b0" value="1" constant="true">
</parameter>
<parameter id="k1" name="k1" value="0" constant="true">
</parameter>
<parameter id="k2" name="k2" value="0" constant="true">
</parameter>
<parameter id="offset_A" name="offset_A" value="0" constant="true">
</parameter>
<parameter id="k1" value="0" constant="true"/>
<parameter id="k2" value="0" constant="true"/>
<parameter id="a0" value="1" constant="true"/>
<parameter id="b0" value="1" constant="true"/>
<parameter id="offset_A" value="0" constant="true"/>
</listOfParameters>

<listOfInitialAssignments>
<initialAssignment symbol="A">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> a0 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="B">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> b0 </ci>
</math>
</initialAssignment>
</listOfInitialAssignments>

<listOfReactions>
<reaction id="fwd" name="fwd" reversible="false">
<reaction id="fwd" reversible="false">
<listOfReactants>
<speciesReference species="A" stoichiometry="1"/>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="B" stoichiometry="1"/>
<speciesReference species="B" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<ci> compartment_ </ci>
<ci> k1 </ci>
<ci> A </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="rev" name="rev" reversible="false">
<reaction id="rev" reversible="false">
<listOfReactants>
<speciesReference species="B" stoichiometry="1"/>
<speciesReference species="B" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="A" stoichiometry="1"/>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<ci> compartment_ </ci>
<ci> k2 </ci>
<ci> B </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>

</model>
</sbml>

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