[SOLVED] How to read attributes for a sbml file with libsbml

How to read attributes for a sbml file with libsbml

I have a sbml model from Reactome, you can download it from https://reactome.org/content/detail/R-HSA-156581 and clicking sbml. For the <reaction>, some of it have attribute of <listOfModifiers>, and I'm trying to use libsbml or cobrapy for doing that.

My code read the sbml file, but how to get the attribute for <listOfModifiers>?

sbml_test_file = "./R-HSA-156581.sbml"

# Using the libSBML python API
# http://model.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/libsbml-python-reading-files.html
reader = libsbml.SBMLReader()
document = reader.readSBML(sbml_test_file)
model = document.getModel()

Solution

The libsbml API is designed to directly mimic the structure of SBML itself. So, once you have the model, you get the reactions from the model, and once you have a reaction, you get the reaction's modifiers:

    import libsbml
    
    sbml_test_file = "R-HSA-156581.sbml"
    reader = libsbml.SBMLReader()
    document = reader.readSBML(sbml_test_file)
    model = document.getModel()
    for r in range(model.getNumReactions()):
        rxn = model.getReaction(r)
        for m in range(rxn.getNumModifiers()):
            mod = rxn.getModifier(m)
            print(mod.getId(), "in reaction", rxn.getId())