class Hmmscan_options_window_qt(PyMod_protocol_window_qt):
def build_protocol_middle_frame(self):
# Add the buttons to choose the database in which to search for domain profiles.
if self.protocol.father_protocol.domain_search_mode == 'remote':
self.hmmer_database_rds = PyMod_radioselect_qt(
label_text="Database Selection", buttons=("PFAM", "Gene3D"))
for button in self.hmmer_database_rds.get_buttons():
button.clicked.connect(self.database_opt_cmd)
elif self.protocol.father_protocol.domain_search_mode == 'local':
# Build the list of database names.
self.protocol.hmmscan_db_dict = {
} # This dictionary associates a database code (displayed in the GUI) to its filename.
db_list = []
for db_filename in self.protocol.hmmscan_db_list:
db_name = "".join(db_filename.split(".")[0:-2])
db_list.append(db_name)
self.protocol.hmmscan_db_dict[db_name] = db_filename
# Packs the PHMMER database selection widget.
self.hmmer_database_rds = PyMod_radioselect_qt(
label_text="Database Selection", buttons=db_list)
self.middle_formlayout.add_widget_to_align(self.hmmer_database_rds)
# E-value selection.
self.e_value_threshold_enf = PyMod_entryfield_qt(
label_text="E-value Threshold",
value="1.0",
validate={
'validator': 'real',
'min': 0.0,
'max': 1000.0
})
self.middle_formlayout.add_widget_to_align(self.e_value_threshold_enf)
# Note about the Gene3D and Evalues.
if self.protocol.father_protocol.domain_search_mode == 'remote':
info_note = ('Note: The Gene3D online database will\n'
'ignore custom cut-off parameters since\n'
'they use a post processing step that\n'
'involves preset thresholds.')
self.notelabel = QtWidgets.QLabel(info_note)
self.middle_formlayout.addRow(self.notelabel)
self.middle_formlayout.set_input_widgets_width(140)
def database_opt_cmd(self):
if self.hmmer_database_rds.getvalue() == 'Gene3D':
self.e_value_threshold_enf.entry.setStyleSheet(
inactive_entry_style)
self.e_value_threshold_enf.entry.setEnabled(False)
else:
self.e_value_threshold_enf.entry.setStyleSheet(active_entry_style)
self.e_value_threshold_enf.entry.setEnabled(True)
class Contact_map_options_window_qt(PyMod_protocol_window_qt):
"""
Window with options for the contact map analysis.
"""
feature_types_list = [
"Contacts", "Distances", "Distance Difference", "Distance Mean",
"Distance Std"
]
interaction_centers_list = ["Carbon alpha", "Carbon beta"]
default_contact_threshold = 8.0
default_distance_threshold = 18.0
default_distance_diff_threshold = 3.5
default_distance_mean_threshold = default_distance_threshold
default_distance_std_threshold = default_distance_diff_threshold
def build_protocol_middle_frame(self):
# Feature type selection.
if len(self.protocol.target_sequences) == 1: # Contact and distance.
sel_option_idx = 0
all_options_idx = (0, 1)
elif len(self.protocol.target_sequences
) == 2: # Distance difference, mean and std.
sel_option_idx = 2
all_options_idx = (2, 3, 4)
elif len(self.protocol.target_sequences) > 2: # Distance mean and std.
sel_option_idx = 3
all_options_idx = (3, 4)
features_buttons = [
self.feature_types_list[i] for i in all_options_idx
]
self.feature_type_rds = PyMod_radioselect_qt(label_text="Feature Type",
buttons=features_buttons)
for button, option_idx in zip(self.feature_type_rds.get_buttons(),
all_options_idx):
button.clicked.connect(
lambda e=None, o=option_idx: self.feature_type_state(o))
self.feature_type_rds.setvalue(self.feature_types_list[sel_option_idx])
self.middle_formlayout.add_widget_to_align(self.feature_type_rds)
# Distance threshold for contacts.
if len(self.protocol.target_sequences) == 1:
threshold = self.default_contact_threshold
elif len(self.protocol.target_sequences) == 2:
threshold = self.default_distance_diff_threshold
else:
threshold = self.default_distance_threshold
self.dist_threshold_enf = PyMod_entryfield_qt(
label_text="Contact Threshold (%s)" % ("\u212B"),
value=str(threshold),
validate={
'validator': 'real',
'min': 1.0,
'max': 100.0
})
self.middle_formlayout.add_widget_to_align(self.dist_threshold_enf)
# Interaction center selection.
self.interaction_center_rds = PyMod_radioselect_qt(
label_text="Interaction Center",
buttons=self.interaction_centers_list)
self.interaction_center_rds.setvalue(self.interaction_centers_list[0])
self.middle_formlayout.add_widget_to_align(self.interaction_center_rds)
# Reference structure combobox.
if len(self.protocol.target_sequences) > 1:
structures_list = [
element.my_header for element in self.protocol.target_sequences
]
self.reference_combobox = PyMod_combobox_qt(
label_text="Reference Structure", items=structures_list)
self.reference_combobox.combobox.setCurrentIndex(0)
self.middle_formlayout.add_widget_to_align(self.reference_combobox)
self.middle_formlayout.set_input_widgets_width("auto", padding=10)
def feature_type_state(self, state):
"""
Launched when the user changes the "Feature Type" in the Options window.
"""
# Change the status of the Tkinter checkbutton.
if state == 0:
self.feature_type_rds.setvalue(self.feature_types_list[0])
self.dist_threshold_enf.setvalue(
str(self.default_contact_threshold))
elif state == 1:
self.feature_type_rds.setvalue(self.feature_types_list[1])
self.dist_threshold_enf.setvalue(
str(self.default_distance_threshold))
elif state == 2:
self.feature_type_rds.setvalue(self.feature_types_list[2])
self.dist_threshold_enf.setvalue(
str(self.default_distance_diff_threshold))
elif state == 3:
self.feature_type_rds.setvalue(self.feature_types_list[3])
self.dist_threshold_enf.setvalue(
str(self.default_distance_mean_threshold))
elif state == 4:
self.feature_type_rds.setvalue(self.feature_types_list[4])
self.dist_threshold_enf.setvalue(
str(self.default_distance_std_threshold))
else:
KeyError(state)
def get_feature_type(self):
feature_type = self.feature_type_rds.getvalue()
if feature_type == self.feature_types_list[0]:
return "contact", feature_type
elif feature_type == self.feature_types_list[1]:
return "distance", feature_type
elif feature_type == self.feature_types_list[2]:
return "distances_difference", feature_type
elif feature_type == self.feature_types_list[3]:
return "distances_mean", feature_type
elif feature_type == self.feature_types_list[4]:
return "distances_std", feature_type
else:
raise KeyError(feature_type)
def get_interaction_center(self):
int_center_string = self.interaction_center_rds.getvalue()
if int_center_string == self.interaction_centers_list[0]:
return "ca"
elif int_center_string == self.interaction_centers_list[1]:
return "cb"
else:
raise KeyError(int_center_string)
def get_reference_id(self):
try:
return self.reference_combobox.get_index()
except:
print("- WARNING: could not obtain the reference structure id.")
return 0