def selected_part(self):
from tellurium.visualization import SBMLDiagram
from tellurium.analysis import _annotations, make_submodel
import tellurium as te
self.set_visible(5)
r = self.widgets['reactionResults'].value
biomodel_id = _annotations.get_biomodel_id(r.model.getSBMLDocument())
self.sbml = self.matched_sbml_lookup[biomodel_id]
self.submodel = make_submodel(r)
antimony = te.sbmlToAntimony(self.submodel.toSBML())
self.widgets['selectedReaction'].children[1].value = antimony
# Draw diagram
diagram = SBMLDiagram(self.submodel, reactions={
'shape': 'box'
})
img = diagram.draw(layout='dot')
self.widgets['selectedReaction'].children[0].value = img.data
# Modular import code snippet
self.widgets['selectedReaction'].children[2].value = '''!pip install git+https://github.com/biomodels/%s.git > /dev/null
# Modular Import of Biomodel reaction
import %s as m
import tellurium as te
from tellurium.analysis import make_submodel
r = m.sbml.model.getReaction('%s')
submodel = make_submodel(r)
antimony = te.sbmlToAntimony(submodel.toSBML())
print antimony
''' % (biomodel_id, biomodel_id, r.getId())
def create_parts(self):
import libsbml
from tellurium.analysis import _annotations
self.set_visible(3)
uri_id = self.widgets['ontologyResults'].value
if self.widgets['ontologySelect'].value == 'ChEBI':
matched_ids = self.bm.getModelsIdByChEBIId(uri_id)
elif self.widgets['ontologySelect'].value == 'GO':
matched_ids = self.bm.getModelsIdByGO(uri_id)
else:
raise Exception('No ontology selected')
if not matched_ids:
print 'No biomodels containing %s' % uri_id
return
self.matched_sbml = [libsbml.readSBMLFromString(
self.bm.getModelSBMLById(id).encode('utf-8'))
for id in matched_ids]
self.matched_sbml_lookup = dict(zip(matched_ids, self.matched_sbml))
self.matched_reactions = [_annotations.matching_reactions(sbml, uri_id)
for sbml in self.matched_sbml]
values = {}
for r in sum(self.matched_reactions, []):
msg = '%s: %s' % (
_annotations.get_biomodel_id(r.model.getSBMLDocument()),
r.__str__())
values[msg] = r
self.widgets['reactionResults'].values = values
