fbc: GeneProductAssociations not written to SBML

[Matthias König]

Not sure what is going on, but it seems that GeneProductAssociations are not written to SBML.

import libsbml

sbmlns: libsbml.SBMLNamespaces = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPkgNamespace("fbc", 3)

doc: libsbml.SBMLDocument = libsbml.SBMLDocument(sbmlns)
doc_fbc: libsbml.FbcSBMLDocumentPlugin = doc.getPlugin("fbc")
doc_fbc.setRequired(False)

model: libsbml.Model = doc.createModel()
model_fbc: libsbml.FbcModelPlugin = model.getPlugin("fbc")
model_fbc.setStrict(True)


c: libsbml.Compartment = model.createCompartment()
c.setId("c1")
c.setSize(1.0)
c.setConstant(True)

s1: libsbml.Species = model.createSpecies()
s1.setId("s1")
s1.setCompartment("c1")
s1.setInitialConcentration(1.0)
s1.setConstant(False)
s1.setHasOnlySubstanceUnits(False)
s1.setBoundaryCondition(False)

p1: libsbml.Parameter = model.createParameter()
p1.setId("lb")
p1.setValue(-100)
p1.setConstant(True)

p2: libsbml.Parameter = model.createParameter()
p2.setId("ub")
p2.setValue(100)
p2.setConstant(True)

# Support exists for user constraints
r: libsbml.Reaction = model.createReaction()
r.setId("r1")
r.setReversible(True)
r.setFast(False)
r_fbc: libsbml.FbcReactionPlugin = r.getPlugin("fbc")
r_fbc.setUpperFluxBound("ub")
r_fbc.setLowerFluxBound("lb")

reactant: libsbml.SpeciesReference = r.createReactant()
reactant.setSpecies("s1")
reactant.setConstant(True)
reactant.setStoichiometry(1.0)

gp1 = model_fbc.createGeneProduct()
gp1.setId("g1")
gp1.setLabel("g1")

gp2 = model_fbc.createGeneProduct()
gp2.setId("g2")
gp2.setLabel("g2")

gpa: libsbml.GeneProductAssociation = r_fbc.createGeneProductAssociation()
gpa.setId("r_gpa")
gpa.setName("r_gpa")

gpa.setAssociation("g1 and g2", True, False)
print("required attributes:", gpa.hasRequiredAttributes())
print(gpa.toSBML())

sbml_str: str = libsbml.writeSBMLToString(doc)
print("-" * 80)
print(sbml_str)
print("-" * 80)

Results in

required attributes: True
<fbc:geneProductAssociation fbc:id="r_gpa" fbc:name="r_gpa">
  <fbc:and>
    <fbc:geneProductRef fbc:geneProduct="g1"/>
    <fbc:geneProductRef fbc:geneProduct="g2"/>
  </fbc:and>
</fbc:geneProductAssociation>
--------------------------------------------------------------------------------
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version3" level="3" version="1" fbc:required="false">
  <model fbc:strict="true">
    <listOfCompartments>
      <compartment id="c1" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="s1" compartment="c1" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="lb" value="-100" constant="true"/>
      <parameter id="ub" value="100" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" reversible="true" fast="false" fbc:lowerFluxBound="lb" fbc:upperFluxBound="ub">
        <listOfReactants>
          <speciesReference species="s1" stoichiometry="1" constant="true"/>
        </listOfReactants>
      </reaction>
    </listOfReactions>
    <fbc:listOfGeneProducts>
      <fbc:geneProduct fbc:id="g1" fbc:label="g1"/>
      <fbc:geneProduct fbc:id="g2" fbc:label="g2"/>
    </fbc:listOfGeneProducts>
  </model>
</sbml>

The GeneProductAssociation just does not appear in the SBML despite added ?!

This probably also solves #253, because the association is set successfully but just not written to SBML.