libsbml set fbc model / reaction / species extension

[Michiel Karrenbelt]

So I can parse FBC plugin related features, now I want the opposite: write a new model and add them

How do I add extension plugin to the model, reactions and species?

[Keating, Sarah M.]

The extension plugins will exist if you have declared the fbc namespace
when creating the document/model/species etc. You can access them in the
same way as when parsing.

See

http://sbml.org/Software/libSBML/5.17.0/docs//cpp-api/fbc_example1_8cpp-example.html

Sarah

[Matthias König]

Hi Michiel,

You have to enable the package on the SBMLDocument instance.

In addition you have to set the required and strict tags for fbc.

Depending on if you have a strict or non-strict model you set the strict tag (see the fbc specification for definition).

doc.enablePackage("http://www.sbml.org/sbml/level3/version1/fbc/version2", "fbc", True)
doc.setPackageRequired("fbc", False)
fmodel = model.getPlugin("fbc")  # type: libsbml.FbcModelPlugin
fmodel.setStrict(False)

Afterwards you can just get the extension plugins and set the information on them (similar to reading them from a file with the package)

Hope this helps.

Code example is based on the python bindings, but should easily transfer to the other libsbml language bindings.

Best Matthias