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‎petabtests/cases/v1.0.0/sbml/0005/0005.py

Lines changed: 22 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
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import pandas as pd
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from petab.v1.C import *
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7-
from petabtests import PetabTestCase, analytical_a
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from petabtests import PetabTestCase, analytical_a, antimony_to_sbml_str
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DESCRIPTION = cleandoc("""
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## Objective
@@ -23,6 +23,26 @@
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""")
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# problem --------------------------------------------------------------------
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ant_model = """
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model *petab_test_0011()
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compartment compartment_ = 1;
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species A in compartment_, B in compartment_;
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fwd: A => B; compartment_ * k1 * A;
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rev: B => A; compartment_ * k2 * B;
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A = a0;
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B = b0;
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B = 1;
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a0 = 1;
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b0 = 1;
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k1 = 0;
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k2 = 0;
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offset_A = 0;
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end
43+
"""
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model_file = sbml_file = Path(__file__).parent / "_model.xml"
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model_file.write_text(antimony_to_sbml_str(ant_model))
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condition_df = pd.DataFrame(
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data={
@@ -73,7 +93,7 @@
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brief="Simulation. Condition-specific parameters only defined in "
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"parameter table.",
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description=DESCRIPTION,
76-
model=Path("conversion_modified.xml"),
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model=model_file,
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condition_dfs=[condition_df],
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observable_dfs=[observable_df],
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measurement_dfs=[measurement_df],

‎petabtests/cases/v1.0.0/sbml/0005/_model.xml

Lines changed: 19 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -1,96 +1,65 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
3-
<model id="conversion_reaction_0" name="Conversion Reaction 0">
4-
5-
<listOfUnitDefinitions>
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<unitDefinition id="volume" name="volume">
7-
<listOfUnits>
8-
<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="substance" name="substance">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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</listOfUnitDefinitions>
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2+
<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
3+
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
4+
<model metaid="petab_test_0011" id="petab_test_0011">
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<listOfCompartments>
19-
<compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
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</compartment>
6+
<compartment id="compartment_" spatialDimensions="3" size="1" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species id="A" name="A" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
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</species>
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<species id="B" name="B" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
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</species>
9+
<species id="A" compartment="compartment_" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="B" compartment="compartment_" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="a0" name="a0" value="1" constant="true">
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</parameter>
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<parameter id="b0" name="b0" value="1" constant="true">
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</parameter>
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<parameter id="k1" name="k1" value="0" constant="true">
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</parameter>
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<parameter id="k2" name="k2" value="0" constant="true">
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</parameter>
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<parameter id="offset_A" name="offset_A" value="0" constant="true">
40-
</parameter>
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<parameter id="k1" value="0" constant="true"/>
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<parameter id="k2" value="0" constant="true"/>
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<parameter id="a0" value="1" constant="true"/>
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<parameter id="b0" value="1" constant="true"/>
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<parameter id="offset_A" value="0" constant="true"/>
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</listOfParameters>
42-
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<listOfInitialAssignments>
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<initialAssignment symbol="A">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> a0 </ci>
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</math>
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</initialAssignment>
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<initialAssignment symbol="B">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
51-
<ci> b0 </ci>
52-
</math>
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</initialAssignment>
5425
</listOfInitialAssignments>
55-
5626
<listOfReactions>
57-
<reaction id="fwd" name="fwd" reversible="false">
27+
<reaction id="fwd" reversible="false">
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<listOfReactants>
59-
<speciesReference species="A" stoichiometry="1"/>
29+
<speciesReference species="A" stoichiometry="1" constant="true"/>
6030
</listOfReactants>
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<listOfProducts>
62-
<speciesReference species="B" stoichiometry="1"/>
32+
<speciesReference species="B" stoichiometry="1" constant="true"/>
6333
</listOfProducts>
6434
<kineticLaw>
6535
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
6737
<times/>
68-
<ci> compartment </ci>
38+
<ci> compartment_ </ci>
6939
<ci> k1 </ci>
7040
<ci> A </ci>
7141
</apply>
7242
</math>
7343
</kineticLaw>
7444
</reaction>
75-
<reaction id="rev" name="rev" reversible="false">
45+
<reaction id="rev" reversible="false">
7646
<listOfReactants>
77-
<speciesReference species="B" stoichiometry="1"/>
47+
<speciesReference species="B" stoichiometry="1" constant="true"/>
7848
</listOfReactants>
7949
<listOfProducts>
80-
<speciesReference species="A" stoichiometry="1"/>
50+
<speciesReference species="A" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
8555
<times/>
86-
<ci> compartment </ci>
56+
<ci> compartment_ </ci>
8757
<ci> k2 </ci>
8858
<ci> B </ci>
8959
</apply>
9060
</math>
9161
</kineticLaw>
9262
</reaction>
9363
</listOfReactions>
94-
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</model>
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</sbml>

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