Function in libSBML to return parameter/species names specified by an assignment rule from XML string?

[ver...@uw.edu]

Hello,

Are there functions within libSBML that return only the parameter or species names which are defined by an assignment rule from an XML string from the full parameter/species list? 

Thank you,

Veronica

[Herbert Sauro]

Use getRule (n) on the model instance, eg

ar = model.getRule (n)
print (ar.getId())

I think that should do it. I've not checked but I imagine there will be something to check if the selected rule is an assignment rule.

Herbert

[Lucian Smith]

On Fri, Jan 18, 2019 at 4:09 PM Herbert Sauro <hsa...@gmail.com> wrote:

Use getRule (n) on the model instance, eg

ar = model.getRule (n)
print (ar.getId())

I think that should do it. I've not checked but I imagine there will be something to check if the selected rule is an assignment rule.

If you know all your rules are assignment rules, that'll work; if there is or might be a mix, you can check first:

ar = model.getRule(n)

if (ar.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE):

  print(ar.getVariable())

-Lucian

[Herbert Sauro]

That's the bit I didn't know.

Herbert

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[ver...@uw.edu]

Thank you, Lucian and Herbert.

 

Taking your responses, I find this solves the problem and returns a list of all parameter names associated with assignment rules: 

import libsbml

doc = libsbml.readSBMLFromFile ('someSBMLmodel.xml')

model = doc.getModel();

lenListRules = len(model.getListOfRules())

ruleParams = []

for i in range(lenListRules):

    rule = model.getRule(i)

    if (rule.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE):

        ruleId = rule.getVariable()

        ruleParams.append(ruleId)

On Friday, January 18, 2019 at 4:20:39 PM UTC-8, Herbert Sauro wrote:

That's the bit I didn't know.

Herbert

On Fri, Jan 18, 2019 at 4:16 PM Lucian Smith <luciano...@gmail.com> wrote:

On Fri, Jan 18, 2019 at 4:09 PM Herbert Sauro <hsa...@gmail.com> wrote:

Use getRule (n) on the model instance, eg

ar = model.getRule (n)
print (ar.getId())

I think that should do it. I've not checked but I imagine there will be something to check if the selected rule is an assignment rule.

If you know all your rules are assignment rules, that'll work; if there is or might be a mix, you can check first:

ar = model.getRule(n)

if (ar.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE):

  print(ar.getVariable())

-Lucian

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