def add_button_clicked(self):
reaction_name = self.transcription_reactions_combo.currentText()
regulators = []
for i in range(0, self.regulators_list.count()):
item = self.regulators_list.item(i)
if item.checkState() == Qt.Checked:
regulators.append(item.text())
reg_types = []
if self.activation_check.isChecked():
reg_types.append(RegType.ACTIVATION)
if self.repression_check.isChecked():
reg_types.append(RegType.REPRESSION)
k_lb = float(self.lb_edit.text())
k_ub = float(self.ub_edit.text())
k_step = float(self.step_edit.text())
hill_coeff = float(self.hill_edit.text())
reg_mut = RegulationMutable(reaction_name, regulators,
VariableMutable("k", k_lb, k_ub, k_step),
reg_types, False, hill_coeff)
GenePresenter.get_instance().mutables.append(reg_mut)
# Climb up the hierarchy to find the window and close that.
self.parent().parent().parent().close()
def _ok_button_clicked_handler(self):
index = self.reaction_types_list.currentRow()
if index == 0: # Transcription
GenePresenter.get_instance().add_reaction(self.transcription_fields.get_transcription_reaction())
elif index == 1: # Translation
name = str(self.reaction_name2.text())
rate = float(self.translation_rate.text())
translated_mrna = str(self.translated_mrna.currentText())
produced_protein = str(self.produced_protein.currentText())
formula = TranslationFormula(rate, translated_mrna)
GenePresenter.get_instance().add_reaction(Reaction(name, [translated_mrna], [produced_protein], formula))
elif index == 2: # Degradation
name = str(self.reaction_name3.text())
rate = float(self.decay_rate.text())
decaying_species = str(self.decaying_species.currentText())
formula = DegradationFormula(rate, decaying_species)
GenePresenter.get_instance().add_reaction(Reaction(name, [decaying_species], [], formula))
else: # Custom
name = str(self.reaction_name4.text())
reactant = str(self.reactant.currentText())
product = str(self.product.currentText())
equation = str(self.equation.text())
formula = CustomFormula(equation, {}, {})
GenePresenter.get_instance().add_reaction(Reaction(name, [reactant], [product], formula))
self.close()
def _add_species_click_handler(self):
(text, ok) = QInputDialog.getText(
self, "Add Species", "Write species and initial "
"concentration in this format: \n"
"species1: 20.0, species2: 30.0")
if ok:
for pair in text.split(','):
split = pair.strip().split(':')
species_name = split[0].strip()
species_concent = float(split[1].strip())
GenePresenter.get_instance().add_species(
species_name, species_concent)
self.update_ui()
self.parent.reactions_tab.update_ui()
def _save_file_as_sbml_clicked(self):
net = GenePresenter.get_instance().network
d = QFileDialog()
filename = d.getSaveFileName(self, "Save file", ".",
"XML Files (*.xml)")
if filename:
SbmlSaver.save_network_to_file(net, filename[0] + ".xml")
def _make_transcription_reactions_combo():
c = QComboBox()
for r in GenePresenter.get_instance().network.reactions:
if isinstance(r.rate_function, TranscriptionFormula):
c.addItem(r.name)
return c
def _constraint_satisfaction_handler(self, s):
g = GenePresenter.get_instance()
if self.method_combo.currentIndex() == 0:
give_up_time = int(self.give_up_edit.text())
t = ConstraintSatisfaction.find_network(g.network, s,
g.get_mutables(),
g.get_constraints(),
give_up_time)
else:
temperature = int(self.temperature_edit.text())
schedule = ConstraintSatisfaction.generate_schedule(temperature)
t = ConstraintSatisfaction.find_closest_network(
g.network, s, g.get_mutables(), g.get_constraints(), schedule)
if t:
variables_dialog = QDialog()
scroll = QScrollArea()
scroll.setWidget(QLabel(t.str_variables()))
layout = QVBoxLayout()
layout.addWidget(scroll)
ok_button = QPushButton("OK")
ok_button.clicked.connect(lambda _: variables_dialog.close())
layout.addWidget(ok_button)
variables_dialog.setLayout(layout)
variables_dialog.setMinimumWidth(300)
variables_dialog.exec_()
def draw_simulation():
results = OdeSimulator.simulate(t, s)
values = StructuredResults.label_results(results, t.species)
for species in s.plotted_species:
plt.plot(s.generate_time_space(),
values[species],
label=species)
plt.xlabel("Time (s)")
plt.ylabel("Concentration")
plt.legend(loc=0)
plt.title("Results")
plt.draw()
plt.figure()
plt.subplot(2, 1, 1)
draw_simulation()
plt.subplot(2, 1, 2)
im = NetworkVisualiser.visualise_as_image(t, "gene")
plt.imshow(im)
plt.show()
else:
helper.show_error_message(
"No matching network found within the given parameters.")
def _make_regulators_list():
t = QListWidget()
for s in GenePresenter.get_instance().network.species:
i = QListWidgetItem()
i.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
i.setCheckState(Qt.Unchecked)
i.setText(s)
t.addItem(i)
return t
def _add_clicked_handler(self):
combo_index = self.mutables_combo.currentIndex()
mutable_title = self.mutable_combo_values[combo_index][0]
mutable_reaction = self.mutable_combo_values[combo_index][1]
is_custom = self.mutable_combo_values[combo_index][2]
lo = self.lb.text().strip()
lo = float(lo) if lo != "" else 0.0
u = self.ub.text().strip()
u = float(u) if u != "" else 0.0
i = self.inc.text().strip()
i = float(i) if i != "" else 0.0
if mutable_reaction == "":
if is_custom:
GenePresenter.get_instance().mutables.append(
GlobalParameterMutable(mutable_title, lo, u, i))
else:
GenePresenter.get_instance().mutables.append(
VariableMutable(mutable_title, lo, u, i))
else:
GenePresenter.get_instance().mutables.append(
ReactionMutable(mutable_title, lo, u, i, mutable_reaction))
# Climb up the hierarchy to find the window and close that.
self.parent().parent().parent().close()
def _make_mutables_combo():
combo_items = []
item_values = []
for s in GenePresenter.get_instance().get_species():
combo_items.append("Species ⟹ {}".format(s))
item_values.append((s, "", False))
for r in GenePresenter.get_instance().get_reactions():
for p in r.rate_function.get_params():
combo_items.append("{} ⟹ {}".format(r.name, p))
item_values.append((p, r.name, False))
net = GenePresenter.get_instance().network
for symbol in net.symbols:
combo_items.append("Global parameter ⟹ {}".format(symbol))
item_values.append((symbol, "", True))
combo = QComboBox()
combo.addItems(combo_items)
return combo, item_values
def _button_clicked(self):
sign = self.sign_combo.currentText()
species = self.lhs.currentText()
value = float(self.rhs.text())
t0 = float(self.time_lb.text())
t1 = float(self.time_ub.text())
if sign == "<=":
cons = lambda v: v - value
elif sign == ">=":
cons = lambda v: value - v
else:
helper.show_error_message(
"Constraint syntax error: Unrecognised sign")
self.close()
return
c = Constraint(species, cons, (t0, t1))
c.pretty_print = species + sign + str(value) + " for time: " + str(
t0) + "s - " + str(t1) + "s"
GenePresenter.get_instance().add_constraint(c)
self.close()
def make_species_checkboxes_layout():
row = 0 # Row number to place the next species
left = True # Indicates that the next species must be placed to the left
g = QGridLayout()
for x in GenePresenter.get_instance().get_species():
col = 1 if left else 2 # Column number depending on variable "left"
g.addWidget(QCheckBox(x), row, col)
# Switch to next row after adding species to right
if not left:
row += 1
# Switch sides each time
left = not left
return g
def __init__(self, parent):
super().__init__()
self.setFileMode(QFileDialog.AnyFile)
filename = self.getOpenFileName(self, "Open file", ".",
"XML Files (*.xml);; All Files (*.*)")
if filename:
net = SbmlParser.parse(filename[0])
if not net:
helper.show_error_message(
"An error occurred while opening the SBML file.")
GenePresenter.get_instance().network = net
message = QMessageBox()
message.setText("SBML file has been opened")
message.exec_()
parent.species_tab.update_ui()
parent.reactions_tab.update_ui()
def _ok_button_clicked(self):
time_text = self.time_field.text().strip()
end_time = int(time_text) if time_text else 1
species = list()
for x in range(0, self.species_checkboxes.count()):
checkbox = self.species_checkboxes.itemAt(x).widget()
if checkbox.isChecked():
species.append(checkbox.text())
self.close()
# Precision field does not apply to stochastic simulation!
s = SimulationSettings(0, end_time, 0, [s.strip() for s in species])
sim_net = copy.deepcopy(GenePresenter.get_instance().network)
def do_simulation():
GillespieSimulator.visualise(
GillespieSimulator.simulate(sim_net, s), s)
# t = threading.Thread(target=do_simulation)
# t.start()
do_simulation()
def handler(s):
net = GenePresenter.get_instance().network
OdeSimulator.visualise(net, s, OdeSimulator.simulate(net, s))
def make_species_combo():
combo = QComboBox()
for x in GenePresenter.get_instance().get_species():
combo.addItem(x)
return combo
def _remove_species_click_handler(self):
text = self.species_list.item(self.species_list.currentRow()).text()
species = text.split(':')[0]
GenePresenter.get_instance().remove_species(species)
self.update_ui()
self.parent.reactions_tab.update_ui()
def update_ui(self):
self.species_list.clear()
for s in GenePresenter.get_instance().get_species():
self.species_list.addItem(
s + ": " + str(GenePresenter.get_instance().get_species()[s]))
def _remove_constraint_clicked(self):
i = self.constraints_list.currentRow()
GenePresenter.get_instance().remove_constraint(i)
self._update_constraints_list()
def _update_constraints_list(self):
self.constraints_list.clear()
for c in GenePresenter.get_instance().get_constraints():
self.constraints_list.addItem(str(c))
def _remove_mutable_clicked(self):
i = self.mutables_list.currentRow()
GenePresenter.get_instance().remove_mutable(i)
self._update_mutables_list()
def _update_mutables_list(self):
self.mutables_list.clear()
for m in GenePresenter.get_instance().get_mutables():
self.mutables_list.addItem(str(m))
