Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)
Here's the SBML model:
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
Here's the same model encoded as SBML level 2, which works on atomizer without error:
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
Both models were exported from Python LibSBML.
Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
Here's the SBML model:
Here's the same model encoded as SBML level 2, which works on atomizer without error:
Both models were exported from Python LibSBML.