def _init_fields(self):
fields = QFormLayout()
self.lhs = common_widgets.make_species_combo()
self.rhs = QLineEdit()
self.rhs.setValidator(helper.get_double_validator())
self.rhs.setPlaceholderText("Constraint value")
self.sign_combo = QComboBox()
self.sign_combo.addItems([">=", "<="])
constraint_box = QHBoxLayout()
constraint_box.addWidget(self.lhs)
constraint_box.addWidget(self.sign_combo)
constraint_box.addWidget(self.rhs)
fields.addRow("Constraint (e.g. X >= 20)", constraint_box)
self.time_lb = QLineEdit()
self.time_lb.setValidator(helper.get_double_validator())
self.time_lb.setPlaceholderText("Start")
self.time_ub = QLineEdit()
self.time_ub.setValidator(helper.get_double_validator())
self.time_ub.setPlaceholderText("End")
time_box = QHBoxLayout()
time_box.addWidget(self.time_lb)
time_box.addWidget(QLabel("-"))
time_box.addWidget(self.time_ub)
fields.addRow("Time period (e.g. 0 - 20)", time_box)
self.layout.addLayout(fields)
def __init__(self):
super().__init__()
layout = QVBoxLayout()
self.transcription_reactions_combo = self._make_transcription_reactions_combo()
self.regulators_list = self._make_regulators_list()
reg_type_box, self.activation_check, self.repression_check = self._make_reg_type_box()
k_box, self.lb_edit, self.ub_edit, self.step_edit = self._make_k_box()
self.add_button = self._make_add_button()
self.hill_edit = QLineEdit()
self.hill_edit.setValidator(helper.get_double_validator())
layout.addWidget(QLabel("This reaction can be regulated..."))
layout.addWidget(self.transcription_reactions_combo)
layout.addWidget(QLabel("By one of these species..."))
layout.addWidget(self.regulators_list)
layout.addWidget(QLabel("In these ways..."))
layout.addWidget(reg_type_box)
layout.addWidget(QLabel("And have a K value with the range..."))
layout.addWidget(k_box)
layout.addWidget(QLabel("Will have this immutable hill coefficient..."))
layout.addWidget(self.hill_edit)
layout.addWidget(self.add_button)
self.setLayout(layout)
def __init__(self):
super().__init__()
fields = QFormLayout()
self.regulations = list()
self.reaction_name = QLineEdit()
self.transcription_rate = QLineEdit()
self.transcription_rate.setValidator(helper.get_double_validator())
self.transcribed_species = common_widgets.make_species_combo()
self.transcribed_species.currentIndexChanged.connect(self._transcribed_species_current_index_changed)
self.is_regulated = QCheckBox("Is Regulated")
self.is_regulated.stateChanged.connect(self._is_regulated_state_changed)
self.regulation_settings_panel = self._make_regulation_settings_panel()
fields.addRow(QLabel("Reaction name"), self.reaction_name)
fields.addRow(QLabel("Transcription rate"), self.transcription_rate)
fields.addRow(QLabel("Transcribed species: "), self.transcribed_species)
fields.addRow(self.is_regulated)
fields.addRow(self.regulation_settings_panel)
self._is_regulated_state_changed()
self.setLayout(fields)
def _init_fields(self):
fields = QFormLayout()
self.mutables_combo, self.mutable_combo_values = self._make_mutables_combo(
)
fields.addRow(QLabel("Mutable: "), self.mutables_combo)
self.lb = QLineEdit()
self.lb.setValidator(helper.get_double_validator())
fields.addRow(QLabel("Lower bound"), self.lb)
self.ub = QLineEdit()
self.ub.setValidator(helper.get_double_validator())
fields.addRow(QLabel("Upper bound"), self.ub)
self.inc = QLineEdit()
self.inc.setValidator(helper.get_double_validator())
fields.addRow(QLabel("Increments"), self.inc)
self.layout.addLayout(fields)
def _make_k_box():
lb_edit = QLineEdit()
lb_edit.setValidator(helper.get_double_validator())
lb_edit.setFixedWidth(60)
ub_edit = QLineEdit()
ub_edit.setValidator(helper.get_double_validator())
ub_edit.setFixedWidth(60)
step_edit = QLineEdit()
step_edit.setValidator(helper.get_double_validator())
step_edit.setFixedWidth(60)
fields = QHBoxLayout()
fields.addWidget(lb_edit)
fields.addWidget(QLabel(" - "))
fields.addWidget(ub_edit)
fields.addWidget(QLabel(" Step: "))
fields.addWidget(step_edit)
k_box = QGroupBox()
k_box.setLayout(fields)
return k_box, lb_edit, ub_edit, step_edit
def _init_degradation_fields(self):
fields = QFormLayout()
self.reaction_name3 = QLineEdit()
fields.addRow(QLabel("Reaction name"), self.reaction_name3)
self.decay_rate = QLineEdit()
self.decay_rate.setValidator(helper.get_double_validator())
fields.addRow(QLabel("Decay rate: "), self.decay_rate)
self.decaying_species = common_widgets.make_species_combo()
fields.addRow(QLabel("Decaying species: "), self.decaying_species)
self.degradation_fields = QWidget()
self.degradation_fields.setLayout(fields)
self.properties_layout.addWidget(self.degradation_fields)
self.degradation_fields.hide()
def _init_translation_fields(self):
fields = QFormLayout()
self.reaction_name2 = QLineEdit()
fields.addRow(QLabel("Reaction name"), self.reaction_name2)
self.translation_rate = QLineEdit()
self.translation_rate.setValidator(helper.get_double_validator())
fields.addRow(QLabel("Translation rate: "), self.translation_rate)
self.translated_mrna = common_widgets.make_species_combo()
fields.addRow(QLabel("Translated mRNA: "), self.translated_mrna)
self.produced_protein = common_widgets.make_species_combo()
fields.addRow(QLabel("Produced protein: "), self.produced_protein)
self.translation_fields = QWidget()
self.translation_fields.setLayout(fields)
self.properties_layout.addWidget(self.translation_fields)
self.translation_fields.hide()
def _make_add_regulation_box(self):
self.activation_radio = QRadioButton("Activation")
self.repression_radio = QRadioButton("Repression")
self.regulator = common_widgets.make_species_combo()
self.k = QLineEdit()
self.k.setValidator(helper.get_double_validator())
self.add_button = QPushButton("Add regulation")
self.add_button.clicked.connect(self._add_regulation_clicked)
fields = QFormLayout()
fields.addRow(self.activation_radio, self.repression_radio)
fields.addRow(QLabel("Regulating species:"), self.regulator)
fields.addRow(QLabel("K:"), self.k)
fields.addRow(self.add_button)
add_regulation_box = QGroupBox()
add_regulation_box.setLayout(fields)
return add_regulation_box
def _make_regulation_settings_panel(self):
fields = QFormLayout()
self.hill = QLineEdit()
self.hill.setValidator(helper.get_double_validator())
self.input_gate = QComboBox()
self.input_gate.addItems(["NONE", "AND", "OR"])
self.add_regulation_box = self._make_add_regulation_box()
self.regulations_list = QListWidget()
self.regulations_list.setFixedHeight(100)
fields.addRow(QLabel("Hill coefficient: "), self.hill)
fields.addRow(QLabel("Input gate: "), self.input_gate)
fields.addRow(QLabel("Regulations"))
fields.addRow(self.regulations_list)
fields.addRow(self.add_regulation_box)
self.activation_radio.setChecked(True)
return fields
def __init__(self):
super().__init__()
main = QVBoxLayout()
fields = QFormLayout()
self.time_field = QLineEdit()
self.time_field.setValidator(helper.get_double_validator())
fields.addRow(QLabel("Simulation time"), self.time_field)
self.species_checkboxes = common_widgets.make_species_checkboxes_layout(
)
self.ok_button = QPushButton("Ok")
self.ok_button.clicked.connect(self._ok_button_clicked)
main.addLayout(fields)
main.addWidget(QLabel("Which species to show: "))
main.addLayout(self.species_checkboxes)
main.addWidget(self.ok_button)
self.setLayout(main)
self.setMinimumWidth(200)
self.setWindowTitle("Simulation settings")
self.exec_()
