def parse_metabolites(metabolites_node,
model=None,
progress=None,
use_fbc=True):
species_node = metabolites_node.find(sbml3_listOfSpecies)
if species_node is None:
return
elif progress is None:
pass
elif not progress.wasCanceled():
progress.setLabelText("Reading metabolites...")
progress.setRange(0, len(species_node))
else:
return
metabolites = []
for i, xml_element in enumerate(species_node.iterfind(sbml3_species)):
if progress is None:
pass
elif not progress.wasCanceled():
progress.setValue(i)
QApplication.processEvents()
else:
return
new_metabolite = Metabolite(id=clip(xml_element.get("id"), "M_"),
name=xml_element.get("name"),
compartment=xml_element.get("compartment"))
if use_fbc:
formula = xml_element.get(fbc_chemicalFormula)
if formula:
if re.match(formula_validator, formula):
new_metabolite.formula = formula
else:
# Todo: Implement logging of errors
print("Formula '{}' for {} is invalid!".format(
formula, new_metabolite.id))
charge = xml_element.get(fbc_charge)
if charge is not None:
new_metabolite.charge = int(charge)
# Defaults to the standard value of 0 if charge not set in file
annotate_element_from_xml(xml_element, new_metabolite)
metabolites.append(new_metabolite)
if model is not None:
model.add_metabolites(metabolites)
return metabolites
def test_updating(self):
model = Model()
met1 = Metabolite(id="met1", formula="H2O", name="Water", charge=0., compartment="c")
react1 = Reaction(id="react1", name="test2", subsystem="test2", lower_bound=0., upper_bound=1000.)
react1.add_metabolites({met1: -1})
model.add_metabolites([met1])
model.add_reactions([react1])
model.setup_tables()
assert model.QtReactionTable.rowCount() == 1
assert model.QtMetaboliteTable.rowCount() == 1
# Check that content is right
for i, element in enumerate(model.QtMetaboliteTable.header):
assert str(getattr(met1, element.lower())) == model.QtMetaboliteTable.item(0, i).text()
# Check that metabolite id is in table
assert met1.id in model.QtReactionTable.item(0, 2).text()
# Change metabolite
met1.id = "new_id"
met1.name = "new_name"
met1.formula = "H2O2"
met1.name = "None"
met1.charge = 1.
met1.compartment = "e"
# Tables are out of sync
for i, element in enumerate(model.QtMetaboliteTable.header):
assert str(getattr(met1, element.lower())) != model.QtMetaboliteTable.item(0, i).text()
# Check reaction table out of sync
assert react1.id not in model.QtReactionTable.item(0, 2).text()
model.gem_update_metabolites([met1])
# Metabolite table updated
for i, element in enumerate(model.QtMetaboliteTable.header):
assert str(getattr(met1, element.lower())) == model.QtMetaboliteTable.item(0, i).text()
# Reaction table updated
assert met1.id in model.QtReactionTable.item(0, 2).text()
