def validate_equation(self):
ok = False
test_reaction = cobra.Reaction(
"xxxx_cnapy_test_reaction", name="cnapy test reaction")
with self.parent.appdata.project.cobra_py_model as model:
model.add_reaction(test_reaction)
try:
eqtxt = self.equation.text().rstrip()
if len(eqtxt) > 0 and eqtxt[-1] == '+':
turn_red(self.equation)
else:
test_reaction.build_reaction_from_string(eqtxt)
turn_white(self.equation)
ok = True
except ValueError:
turn_red(self.equation)
try:
test_reaction = self.parent.appdata.project.cobra_py_model.reactions.get_by_id(
"xxxx_cnapy_test_reaction")
self.parent.appdata.project.cobra_py_model.remove_reactions(
[test_reaction], remove_orphans=True)
except KeyError:
pass
return ok
def metabolite_selected(self, item, _column):
if item is None:
self.metabolite_mask.hide()
else:
self.metabolite_mask.show()
metabolite: cobra.Metabolite = item.data(2, 0)
self.metabolite_mask.metabolite = metabolite
self.metabolite_mask.id.setText(metabolite.id)
self.metabolite_mask.name.setText(metabolite.name)
self.metabolite_mask.formula.setText(metabolite.formula)
if metabolite.charge is None:
pass
else:
self.metabolite_mask.charge.setText(str(metabolite.charge))
self.metabolite_mask.compartment.setText(metabolite.compartment)
self.update_annotations(metabolite.annotation)
self.metabolite_mask.changed = False
turn_white(self.metabolite_mask.id)
turn_white(self.metabolite_mask.name)
turn_white(self.metabolite_mask.formula)
turn_white(self.metabolite_mask.charge)
turn_white(self.metabolite_mask.compartment)
self.metabolite_mask.is_valid = True
self.metabolite_mask.update_state()
def validate_gene_reaction_rule(self):
try:
_x = float(self.gene_reaction_rule.text())
except ValueError:
turn_red(self.gene_reaction_rule)
return False
else:
turn_white(self.gene_reaction_rule)
return True
def validate_coefficient(self):
try:
_x = float(self.coefficent.text())
except ValueError:
turn_red(self.coefficent)
return False
else:
turn_white(self.coefficent)
return True
def validate_upperbound(self):
try:
_x = float(self.upper_bound.text())
except ValueError:
turn_red(self.upper_bound)
return False
else:
turn_white(self.upper_bound)
return True
def validate_charge(self):
try:
if self.charge.text() != "":
_x = int(self.charge.text())
except ValueError:
turn_red(self.charge)
return False
else:
turn_white(self.charge)
return True
def validate_name(self):
with self.parent.appdata.project.cobra_py_model as model:
try:
r = cobra.Reaction(id="testid", name=self.name.text())
model.add_reaction(r)
except ValueError:
turn_red(self.name)
return False
else:
turn_white(self.name)
return True
def validate_name(self):
with self.appdata.project.cobra_py_model as model:
try:
m = cobra.Metabolite(id="test_id", name=self.name.text())
model.add_metabolites([m])
except ValueError:
turn_red(self.name)
return False
else:
turn_white(self.name)
return True
def validate_compartment(self):
try:
if ' ' in self.compartment.text():
turn_red(self.compartment)
return False
if '-' in self.compartment.text():
turn_red(self.compartment)
return False
_m = cobra.Metabolite(id="test_id", name=self.compartment.text())
except ValueError:
turn_red(self.compartment)
return False
else:
turn_white(self.compartment)
return True
def validate_id(self):
with self.appdata.project.cobra_py_model as model:
text = self.id.text()
if text == "":
turn_red(self.id)
return False
if ' ' in text:
turn_red(self.id)
return False
try:
m = cobra.Metabolite(id=self.id.text())
model.add_metabolites([m])
except ValueError:
turn_red(self.id)
return False
else:
turn_white(self.id)
return True
def reaction_selected(self, item: QTreeWidgetItem, _column):
if item is None:
self.reaction_mask.hide()
else:
item.setSelected(True)
self.reaction_mask.show()
reaction: cobra.Reaction = item.data(3, 0)
self.last_selected = reaction.id
self.reaction_mask.reaction = reaction
self.reaction_mask.id.setText(reaction.id)
self.reaction_mask.name.setText(reaction.name)
self.reaction_mask.equation.setText(
reaction.build_reaction_string())
self.reaction_mask.lower_bound.setText(str(reaction.lower_bound))
self.reaction_mask.upper_bound.setText(str(reaction.upper_bound))
self.reaction_mask.coefficent.setText(
str(reaction.objective_coefficient))
self.reaction_mask.gene_reaction_rule.setText(
str(reaction.gene_reaction_rule))
self.update_annotations(reaction.annotation)
self.reaction_mask.changed = False
turn_white(self.reaction_mask.id)
turn_white(self.reaction_mask.name)
turn_white(self.reaction_mask.name)
turn_white(self.reaction_mask.equation)
turn_white(self.reaction_mask.lower_bound)
turn_white(self.reaction_mask.upper_bound)
turn_white(self.reaction_mask.coefficent)
turn_white(self.reaction_mask.gene_reaction_rule)
self.reaction_mask.is_valid = True
(_, r) = self.splitter.getRange(1)
self.splitter.moveSplitter(r/2, 1)
self.reaction_mask.update_state()
