def create_little_canvas(self, hit, domain_hit, default_width=300, default_height=11): # Builds the graphics view and scene. canvas_plot_scene = QtWidgets.QGraphicsScene() canvas_plot_view = QtWidgets.QGraphicsView(canvas_plot_scene) canvas_plot_view.setFixedHeight(default_height) canvas_plot_view.setFixedWidth(default_width) canvas_plot_view.setSizePolicy(self.preferred_size_policy) canvas_plot_view.setHorizontalScrollBarPolicy( QtCore.Qt.ScrollBarAlwaysOff) canvas_plot_view.setVerticalScrollBarPolicy( QtCore.Qt.ScrollBarAlwaysOff) canvas_plot_view.setFrameShape(QtWidgets.QFrame.NoFrame) canvas_plot_view.setStyleSheet("border: 0px; background: %s" % self.view_bg_color) # Get the coordinates of the various graphics elements. one_res_span = default_width / float( self.query_len ) # proporzione tra la lunghezza della seq e lo spazio grafico queryspan_start = int(domain_hit['start']) queryspan_end = int(domain_hit['end']) queryspan_start_graphic = int(queryspan_start * one_res_span) queryspan_end_graphic = int(queryspan_end * one_res_span) # canvas_true_width = int(queryspan_end_graphic-queryspan_start_graphic) # space_at_end = int(int(default_width)-(canvas_true_width+queryspan_start_graphic)) # Draws a gray rectangle representing the full protein sequence. canvas_plot_scene.addRect(0, 3, default_width, 5, self.full_seq_pen, self.full_seq_brush) # Draws a colored rectangle representing the domain. line_pen = QtGui.QPen(QtGui.QColor(0, 0, 0, 255), 1) qcolor = QtGui.QColor(0, 0, 0) qcolor.setNamedColor(hit['dom_color_hex']) brush = QtGui.QBrush(qcolor) canvas_plot_scene.addRect( queryspan_start_graphic, 0, queryspan_end_graphic - queryspan_start_graphic, default_height, line_pen, brush) return canvas_plot_view
def initialize_map(self, pymod, data_array, pymod_elements, ref_residues, ref_selectors, title=None, pixel_size=5, feature_type="contact", threshold=8.0, interaction_center="ca"): # Sets the attributes. self.data_array = data_array self.pixel_size = pixel_size self.feature_type = feature_type self.threshold = threshold self.interaction_center = interaction_center if self.feature_type in ("contact", "distance"): self.pymod_elements = pymod_elements self.pymod_element = self.pymod_elements[0] else: self.pymod_elements = pymod_elements # Get the PyMod residues for each residue having an interaction center and the PyMOL selectors # for each residue. self.ref_residues = ref_residues self.ref_selectors = ref_selectors # Assign the methods to get the labels. if self.feature_type == "contact": self.get_value_label = self._get_value_label_contact elif self.feature_type == "distance": self.get_value_label = self._get_value_label_distance elif self.feature_type == "distances_difference": self.get_value_label = self._get_value_label_distance_diff elif self.feature_type == "distances_mean": self.get_value_label = self._get_value_label_distance_mean elif self.feature_type == "distances_std": self.get_value_label = self._get_value_label_distance_std else: raise KeyError(self.feature_type) # Set the canvas size. min_size = 150 h = self.pixel_size * len(self.data_array) win_size = min((910, h)) win_size = max((min_size, win_size)) if title: self.setWindowTitle(title) # Set some appearance parameters. self.controls_padding = 4 if self.feature_type in ("contact", "distance"): self.controls_font = "helvetica 11 bold" else: self.controls_font = "helvetica 10 bold" self.controls_config = { "fg": "black", "font": self.controls_font, "padx": self.controls_padding, "pady": self.controls_padding } self.labels_pack_config = { "side": "left", "pady": (0, 5), "padx": (5, 0) } self.buttons_pack_config = { "side": "left", "pady": (0, 5), "padx": (1, 0) } # Frame of the window containing a row for some control buttons, a row for # the plot and a row for a messagebar. self.plot_frame = QtWidgets.QWidget() self.plot_frame_layout = QtWidgets.QGridLayout() self.plot_frame.setLayout(self.plot_frame_layout) self.setCentralWidget(self.plot_frame) # Control frame. self.controls_frame = QtWidgets.QWidget() self.controls_frame_layout = QtWidgets.QGridLayout() self.controls_frame.setLayout(self.controls_frame_layout) self.plot_frame_layout.addWidget(self.controls_frame) self.delete_distances_button = QtWidgets.QPushButton( "Delete all distances in PyMOL") self.delete_distances_button.setEnabled(False) self.delete_distances_button.clicked.connect( lambda a=None: self.clear_plot()) self.controls_frame_layout.addWidget(self.delete_distances_button, 0, 0) self.scale_factor = 0 self.scale_down_button = QtWidgets.QPushButton("Zoom out") try: self.scale_down_button.setIcon(QtGui.QIcon.fromTheme("go-down")) except: pass self.scale_down_button.clicked.connect( lambda a=None: self.scale_plot_down()) self.controls_frame_layout.addWidget(self.scale_down_button, 0, 1) self.scale_up_button = QtWidgets.QPushButton("Zoom in") try: self.scale_up_button.setIcon(QtGui.QIcon.fromTheme("go-up")) except: pass self.scale_up_button.clicked.connect( lambda a=None: self.scale_plot_up()) self.controls_frame_layout.addWidget(self.scale_up_button, 0, 2) self.controls_frame_layout.setAlignment(QtCore.Qt.AlignLeft) # Frame containing the plot (with a scrollbar). self.canvas_plot_frame = QtWidgets.QWidget() self.canvas_plot_frame.setStyleSheet("background-color: white") self.canvas_plot_frame_layout = QtWidgets.QGridLayout() self.canvas_plot_frame.setLayout(self.canvas_plot_frame_layout) self.canvas_plot_scrollarea = QtWidgets.QScrollArea() self.canvas_plot_scrollarea.setWidgetResizable(True) self.canvas_plot_scrollarea.setWidget(self.canvas_plot_frame) self.plot_frame_layout.addWidget(self.canvas_plot_scrollarea) # Builds the scene where to draw the contact map. self.canvas_plot_scene = QtWidgets.QGraphicsScene() # Builds the graphics view containing the scene above. self.canvas_plot_view = Contact_map_graphics_view( self.canvas_plot_scene) self.canvas_plot_frame_layout.addWidget(self.canvas_plot_view) # A bottom frame fo the window, containing some buttons to interact with the graph. self.message_frame = QtWidgets.QFrame() self.message_frame_layout = QtWidgets.QHBoxLayout() self.message_frame.setLayout(self.message_frame_layout) self.plot_frame_layout.addWidget(self.message_frame) # Label to show which residue/position pair is currently being hovered by the mouse pointer. if self.feature_type in ("contact", "distance"): view_label_text = "Couple:" else: view_label_text = "Alignment positions:" self.view_label = QtWidgets.QLabel(view_label_text) # self.view_label.setStyleSheet(self.controls_config) self.message_frame_layout.addWidget(self.view_label) # Actually draws the contact map. self.draw_map()
def initialize_plot(self, pymod, target_element, residues_tags, plot_title, aa_list): self.pymod = pymod self.target_element = target_element self.residues_tags = residues_tags self.plot_title = plot_title self.setWindowTitle("%s Ramachandran Plot" % self.target_element.my_header) self.aa_list = aa_list # Frame of the window containing a row for some control buttons, a row for # the plot and a row for a messagebar. self.plot_frame = QtWidgets.QWidget() self.plot_frame_layout = QtWidgets.QGridLayout() self.plot_frame.setLayout(self.plot_frame_layout) self.setCentralWidget(self.plot_frame) # Control frame. self.controls_frame = QtWidgets.QWidget() self.controls_frame_layout = QtWidgets.QGridLayout() self.controls_frame.setLayout(self.controls_frame_layout) self.plot_frame_layout.addWidget(self.controls_frame, 0, 0) self.scale_factor = 0 self.scale_down_button = QtWidgets.QPushButton("Zoom out") try: self.scale_down_button.setIcon(QtGui.QIcon.fromTheme("go-down")) except: pass self.scale_down_button.clicked.connect( lambda a=None: self.scale_plot_down()) self.controls_frame_layout.addWidget(self.scale_down_button, 0, 0) self.scale_up_button = QtWidgets.QPushButton("Zoom in") try: self.scale_up_button.setIcon(QtGui.QIcon.fromTheme("go-up")) except: pass self.scale_up_button.clicked.connect( lambda a=None: self.scale_plot_up()) self.controls_frame_layout.addWidget(self.scale_up_button, 0, 1) self.controls_frame_layout.setAlignment(QtCore.Qt.AlignLeft) # Frame containing the plot (with a scrollbar). self.canvas_plot_frame = QtWidgets.QWidget() self.canvas_plot_frame.setStyleSheet("background-color: white") self.canvas_plot_frame_layout = QtWidgets.QGridLayout() self.canvas_plot_frame.setLayout(self.canvas_plot_frame_layout) self.canvas_plot_scrollarea = QtWidgets.QScrollArea() self.canvas_plot_scrollarea.setWidgetResizable(True) self.canvas_plot_scrollarea.setWidget(self.canvas_plot_frame) self.plot_frame_layout.addWidget(self.canvas_plot_scrollarea, 1, 0) self.default_pen = QtGui.QPen(QtGui.QColor(0, 0, 0, 255), 1) self.default_brush = QtGui.QBrush(QtGui.QColor(0, 0, 0, 230)) self.highlight_brush = QtGui.QBrush(QtGui.QColor(255, 0, 255)) self.highlight_region_brush = QtGui.QBrush(QtGui.QColor(0, 255, 255)) # Builds the scene where to draw the Ramachandran plot. self.canvas_plot_scene = QtWidgets.QGraphicsScene() # Builds the graphics view containing the scene above. self.canvas_plot_view = QtWidgets.QGraphicsView(self.canvas_plot_scene) self.canvas_plot_frame_layout.addWidget(self.canvas_plot_view) # A bottom frame fo the window, containing some buttons to interact with the graph. self.message_frame = QtWidgets.QFrame() self.message_frame_layout = QtWidgets.QFormLayout() self.message_frame.setLayout(self.message_frame_layout) self.plot_frame_layout.addWidget(self.message_frame, 1, 1) # Label to show which residue/position pair is currently being hovered by the mouse pointer. self.view_label_prefix = "Showing: " self.default_message = "Hover dots to color residues of the same type" # Hover over title. self.message_label = QtWidgets.QLabel(self.default_message) self.message_label.setStyleSheet(small_font_style) self.message_frame_layout.addRow(self.message_label) # Actually draws the plot. self.draw_plot() # Shows some data about the type of residues and their dihedral angles. self.regions_labels_dict = {} tot_regular_res = float(self.residues_count["T"]) label_params = [ ("F", "Residues in the most favoured regions", "residues in most favoured regions", True, True), ("A", "Residues in additional allowed regions", "residues in additional allowed regions", True, True), ("G", "Residues in generously allowed regions", "residues in generously allowed regions", True, True), ("D", "Residues in disallowed regions", "residues in disallowed regions", True, True), ("T", "Non-gly and non-pro residues (circles)", "non-glycine and non-proline residues", True, True), ("end_res", "End-residues", "end residues", False, False), ("gly", "Gly residues (triangles)", "glycine residues", True, False), ("pro", "Pro residues (squares)", "proline residues", True, False), ("total", "Total number of residues", "all residues", True, False) ] for region, label, message, active, use_ratio in label_params: region_label = Ramachandran_plot_info_labels( label, message, region, active, self) region_label.setStyleSheet(small_font_style) if use_ratio: text = "%s (%s%%)" % (self.residues_count[region], round( self.residues_count[region] / tot_regular_res * 100, 1)) else: text = str(self.residues_count[region]) region_label_count = QtWidgets.QLabel(text) region_label_count.setStyleSheet(small_font_style) self.message_frame_layout.addRow(region_label, region_label_count) self.regions_labels_dict[region] = { "info": region_label, "data": region_label_count }
def __init__(self, parent, protocol): super(Hmmscan_results_window_qt, self).__init__(parent) self.protocol = protocol self.query_len = len( self.protocol.query_element.my_sequence.replace('-', '')) ######################### # Configure the window. # ######################### self.setWindowTitle("HMMSCAN Results") # Sets the central widget. self.central_widget = QtWidgets.QWidget() self.setCentralWidget(self.central_widget) # The window has a main vbox layout. self.main_vbox = QtWidgets.QVBoxLayout() # Parameters used to draw the 'QGraphicsView' widgets for showing domains. self.preferred_size_policy = QtWidgets.QSizePolicy( QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred) self.view_bg_color = "transparent" self.full_seq_pen = QtGui.QPen(QtGui.QColor(0, 0, 0, 0), 2) self.full_seq_color = "#7f7f7f" qcolor = QtGui.QColor(0, 0, 0) qcolor.setNamedColor(self.full_seq_color) self.full_seq_brush = QtGui.QBrush(qcolor) self.font_qcolor = QtGui.QColor(220, 220, 220, 255) self.font_size = 7 ################ # Upper frame. # ################ self.upper_frame = QtWidgets.QFrame() self.upper_frame_layout = QtWidgets.QGridLayout() self.upper_frame.setLayout(self.upper_frame_layout) self.main_vbox.addWidget(self.upper_frame) if 'query_descr' in self.protocol.parsed_res[ 0] and self.protocol.parsed_res[0]['query_descr']: labelseq = self.protocol.query_element.my_header # + '\n' + querydescr else: try: if len(self.protocol.query_element.description) > 79: labelseq = self.protocol.query_element.description[:78] + '...' else: labelseq = self.protocol.query_element.description except TypeError: labelseq = self.protocol.query_element.my_header self.upper_frame_title = QtWidgets.QLabel( "HMMSCAN search results for " + labelseq) self.upper_frame_layout.addWidget(self.upper_frame_title) #------------------------- # Domain graphics frame. - #------------------------- # Builds the scene where to draw the domain representations. self.canvas_plot_scene = QtWidgets.QGraphicsScene() self.canvas_plot_view = QtWidgets.QGraphicsView(self.canvas_plot_scene) self.canvas_plot_view.setFixedHeight(120) self.canvas_plot_view.setSizePolicy(self.preferred_size_policy) self.canvas_plot_view.setStyleSheet("background: %s" % self.view_bg_color) self.upper_frame_layout.addWidget(self.canvas_plot_view) # Draw a rectangle with the full sequence. self.x_init = 10 y_init = 95 # 95 self.domain_y_init = y_init - 7 self.full_seq_rect_w = 800 full_seq_rect_h = 10 self.canvas_plot_scene.addRect(self.x_init, y_init, self.full_seq_rect_w, full_seq_rect_h, self.full_seq_pen, self.full_seq_brush) # Draw the labels for the N- and C-terminal residues. text_offset_y = 15 text_offset_x = 10 text_n = self.canvas_plot_scene.addText("1") text_n.setPos(self.x_init - text_offset_x, y_init + text_offset_y) text_n.setDefaultTextColor(self.font_qcolor) text_n.setFont(QtGui.QFont(text_n.font().family(), self.font_size)) c_label = str(self.query_len) text_c = self.canvas_plot_scene.addText(c_label) text_offset_x_add = 5 if len(c_label) > 2: text_offset_x_add = 10 text_c.setPos( self.x_init + self.full_seq_rect_w - text_offset_x - text_offset_x_add, y_init + text_offset_y) text_c.setDefaultTextColor(self.font_qcolor) text_c.setFont(QtGui.QFont(text_c.font().family(), self.font_size)) ################# # Middle frame. # ################# # Scroll area which contains the widgets, set as the centralWidget. self.middle_scroll = QtWidgets.QScrollArea() self.main_vbox.addWidget(self.middle_scroll) # Widget that contains the collection of Vertical Box. self.middle_widget = QtWidgets.QWidget() # Scroll area properties. self.middle_scroll.setWidgetResizable(True) self.middle_scroll.setWidget(self.middle_widget) # QFormLayout in the middle frame. self.middle_formlayout = QtWidgets.QFormLayout() self.middle_widget.setLayout(self.middle_formlayout) #----------------- # Results frame. - #----------------- # Set the frame and its layout. self.results_frame = QtWidgets.QFrame() self.middle_formlayout.addRow(self.results_frame) self.results_grid = QtWidgets.QGridLayout() self.results_frame.setLayout(self.results_grid) # Calls a method which actually displays the similarity searches results. self.display_hmmscan_hits() # Align the gridded widgets to the left. self.results_grid.setAlignment(QtCore.Qt.AlignLeft) self.results_grid.setHorizontalSpacing(30) ################# # Bottom frame. # ################# self.main_button = QtWidgets.QPushButton("Submit") self.main_button.clicked.connect( lambda a=None: self.protocol.hmmer_results_state()) self.main_vbox.addWidget(self.main_button) self.main_button.setFixedWidth(self.main_button.sizeHint().width()) # Sets the main vertical layout. self.central_widget.setLayout(self.main_vbox) self.main_vbox.setAlignment(self.main_button, QtCore.Qt.AlignCenter)