How to read attributes for a sbml file with libsbml

Question

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()

score 2 · Accepted Answer · answered Jan 22 '21 at 05:25

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())

Thank you! This is exactly what I was looking for. – kikyo91 Feb 10 '21 at 03:19 — kikyo91, Feb 10 '21 at 03:19

How to read attributes for a sbml file with libsbml

1 Answers1