def __init__(self): # noqa QtWidgets.QMainWindow.__init__(self) self.setDockOptions(QtWidgets.QMainWindow.AllowTabbedDocks | QtWidgets.QMainWindow.AllowNestedDocks) # resize Window before it is shown options = pymol.invocation.options self.resize(options.win_x + (220 if options.internal_gui else 0), options.win_y + (246 if options.external_gui else 18)) # for thread-safe viewport command self.viewportsignal.connect(self.pymolviewport) # reusable dialogs self.dialog_png = None self.advanced_settings_dialog = None self.props_dialog = None self.builder = None # setting index -> callable self.setting_callbacks = defaultdict(list) # "session_file" setting in window title self.setting_callbacks[440].append(lambda v: self.setWindowTitle( "PyMOL (" + os.path.basename(v) + ")")) # "External" Command Line and Loggin Widget self._setup_history() self.lineedit = CommandLineEdit() self.lineedit.setObjectName("command_line") self.browser = QtWidgets.QPlainTextEdit() self.browser.setObjectName("feedback_browser") self.browser.setReadOnly(True) # convenience: clicking into feedback browser gives focus to command # line. Drawback: Copying with CTRL+C doesn't work in feedback # browser -> clear focus proxy while text selected self.browser.setFocusProxy(self.lineedit) @self.browser.copyAvailable.connect def _(yes): self.browser.setFocusProxy(None if yes else self.lineedit) self.browser.setFocus() # Font self.browser.setFont(getMonospaceFont()) connectFontContextMenu(self.browser) lineeditlayout = QtWidgets.QHBoxLayout() command_label = QtWidgets.QLabel("PyMOL>") command_label.setObjectName("command_label") lineeditlayout.addWidget(command_label) lineeditlayout.addWidget(self.lineedit) self.lineedit.setToolTip('''Command Input Area Get the list of commands by hitting <TAB> Get the list of arguments for one command with a question mark: PyMOL> color ? Read the online help for a command with "help": PyMOL> help color Get autocompletion for many arguments by hitting <TAB> PyMOL> color ye<TAB> (will autocomplete "yellow") ''') layout = QtWidgets.QVBoxLayout() layout.addWidget(self.browser) layout.addLayout(lineeditlayout) quickbuttonslayout = QtWidgets.QVBoxLayout() quickbuttonslayout.setSpacing(2) extguilayout = QtWidgets.QBoxLayout(QtWidgets.QBoxLayout.LeftToRight) extguilayout.setContentsMargins(2, 2, 2, 2) extguilayout.addLayout(layout) extguilayout.addLayout(quickbuttonslayout) class ExtGuiFrame(QtWidgets.QFrame): def mouseDoubleClickEvent(_, event): self.toggle_ext_window_dockable(True) dockWidgetContents = ExtGuiFrame(self) dockWidgetContents.setLayout(extguilayout) dockWidgetContents.setObjectName("extgui") self.ext_window = \ dockWidget = QtWidgets.QDockWidget(self) dockWidget.setWindowTitle("External GUI") dockWidget.setWidget(dockWidgetContents) if options.external_gui: dockWidget.setTitleBarWidget(QtWidgets.QWidget()) else: dockWidget.hide() self.addDockWidget(Qt.TopDockWidgetArea, dockWidget) # rearrange vertically if docking left or right @dockWidget.dockLocationChanged.connect def _(area): if area == Qt.LeftDockWidgetArea or area == Qt.RightDockWidgetArea: extguilayout.setDirection(QtWidgets.QBoxLayout.BottomToTop) quickbuttonslayout.takeAt(quickbuttons_stretch_index) else: extguilayout.setDirection(QtWidgets.QBoxLayout.LeftToRight) if quickbuttons_stretch_index >= quickbuttonslayout.count(): quickbuttonslayout.addStretch() # OpenGL Widget self.pymolwidget = PyMOLGLWidget(self) self.setCentralWidget(self.pymolwidget) cmd = self.cmd = self.pymolwidget.cmd ''' # command completion completer = QtWidgets.QCompleter(cmd.kwhash.keywords, self) self.lineedit.setCompleter(completer) ''' # overload <Tab> action self.lineedit.installEventFilter(self) self.pymolwidget.installEventFilter(self) # Quick Buttons for row in [ [ ('Reset', cmd.reset), ('Zoom', lambda: cmd.zoom(animate=1.0)), ('Orient', lambda: cmd.orient(animate=1.0)), # render dialog will be constructed when the menu is shown # for the first time. This way it's populated with the current # viewport and settings. Also defers parsing of the ui file. ('Draw/Ray', WidgetMenu(self).setSetupUi(self.render_dialog)), ], [ ('Unpick', cmd.unpick), ('Deselect', cmd.deselect), ('Rock', cmd.rock), ('Get View', self.get_view), ], [ ('|<', cmd.rewind), ('<', cmd.backward), ('Stop', cmd.mstop), ('Play', cmd.mplay), ('>', cmd.forward), ('>|', cmd.ending), ('MClear', cmd.mclear), ], [ ('Builder', self.open_builder_panel), ('Properties', self.open_props_dialog), ('Rebuild', cmd.rebuild), ], ]: hbox = QtWidgets.QHBoxLayout() hbox.setSpacing(2) for name, callback in row: btn = QtWidgets.QPushButton(name) btn.setProperty("quickbutton", True) btn.setAttribute(Qt.WA_LayoutUsesWidgetRect) # OS X workaround hbox.addWidget(btn) if callback is None: btn.setEnabled(False) elif isinstance(callback, QtWidgets.QMenu): btn.setMenu(callback) else: btn.released.connect(callback) quickbuttonslayout.addLayout(hbox) quickbuttonslayout.addStretch() quickbuttons_stretch_index = quickbuttonslayout.count() - 1 # menu top level self.menubar = menubar = self.menuBar() # action groups actiongroups = {} def _addmenu(data, menu): '''Fill a menu from "data"''' menu.setTearOffEnabled(True) menu.setWindowTitle(menu.title()) # needed for Windows for item in data: if item[0] == 'separator': menu.addSeparator() elif item[0] == 'menu': _addmenu(item[2], menu.addMenu(item[1].replace('&', '&&'))) elif item[0] == 'command': command = item[2] if command is None: print('warning: skipping', item) else: if isinstance(command, str): command = lambda c=command: cmd.do(c) menu.addAction(item[1], command) elif item[0] == 'check': if len(item) > 4: menu.addAction( SettingAction(self, cmd, item[2], item[1], item[3], item[4])) else: menu.addAction( SettingAction(self, cmd, item[2], item[1])) elif item[0] == 'radio': label, name, value = item[1:4] try: group, type_, values = actiongroups[item[2]] except KeyError: group = QtWidgets.QActionGroup(self) type_, values = cmd.get_setting_tuple(name) actiongroups[item[2]] = group, type_, values action = QtWidgets.QAction(label, self) action.triggered.connect(lambda _=0, args=(name, value): cmd.set(*args, log=1, quiet=0)) self.setting_callbacks[cmd.setting._get_index( name)].append( lambda v, V=value, a=action: a.setChecked(v == V)) group.addAction(action) menu.addAction(action) action.setCheckable(True) if values[0] == value: action.setChecked(True) elif item[0] == 'open_recent_menu': self.open_recent_menu = menu.addMenu('Open Recent...') else: print('error:', item) # recent files menu self.open_recent_menu = None # for plugins self.menudict = {'': menubar} # menu for _, label, data in self.get_menudata(cmd): assert _ == 'menu' menu = menubar.addMenu(label) self.menudict[label] = menu _addmenu(data, menu) # hack for macOS to hide "Edit > Start Dictation" # https://bugreports.qt.io/browse/QTBUG-43217 if pymol.IS_MACOS: self.menudict['Edit'].setTitle('Edit_') QtCore.QTimer.singleShot( 10, lambda: self.menudict['Edit'].setTitle('Edit')) # recent files menu if self.open_recent_menu: @self.open_recent_menu.aboutToShow.connect def _(): self.open_recent_menu.clear() for fname in self.recent_filenames: self.open_recent_menu.addAction( fname if len(fname) < 128 else '...' + fname[-120:], lambda fname=fname: self.load_dialog(fname)) # some experimental window control menu = self.menudict['Display'].addSeparator() menu = self.menudict['Display'].addMenu('External GUI') menu.addAction('Toggle floating', self.toggle_ext_window_dockable, QtGui.QKeySequence('Ctrl+E')) ext_vis_action = self.ext_window.toggleViewAction() ext_vis_action.setText('Visible') menu.addAction(ext_vis_action) # extra key mappings (MacPyMOL compatible) QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+O'), self).activated.connect(self.file_open) QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+S'), self).activated.connect(self.session_save) # feedback self.feedback_timer = QtCore.QTimer() self.feedback_timer.setSingleShot(True) self.feedback_timer.timeout.connect(self.update_feedback) self.feedback_timer.start(100) # legacy plugin system self.menudict['Plugin'].addAction('Initialize Plugin System', self.initializePlugins) # focus in command line if options.external_gui: self.lineedit.setFocus() else: self.pymolwidget.setFocus() # Apply PyMOL stylesheet try: with open( cmd.exp_path('$PYMOL_DATA/pmg_qt/styles/pymol.sty')) as f: style = f.read() except IOError: print('Could not read PyMOL stylesheet.') print('DEBUG: PYMOL_DATA=' + repr(os.getenv('PYMOL_DATA'))) style = "" if style: self.setStyleSheet(style)
def __init__(self, parent, protocol): super(Similarity_searches_results_window_qt, self).__init__(parent) self.protocol = protocol ######################### # Configure the window. # ######################### self.setWindowTitle(self._get_window_title()) # 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() ################ # Upper frame. # ################ title_text = self._get_upper_frame_title() self.upper_frame_title = QtWidgets.QLabel(title_text) self.main_vbox.addWidget(self.upper_frame_title) ################# # 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) #----------------- # Buttons frame. - #----------------- # Set the frame and its layout. self.buttons_frame = QtWidgets.QFrame() self.middle_formlayout.addRow(self.buttons_frame) self.buttons_hbox = QtWidgets.QHBoxLayout() self.buttons_frame.setLayout(self.buttons_hbox) # Build the control buttons. self.blast_select_all_button = QtWidgets.QPushButton(text="Select All") self.blast_select_all_button.clicked.connect(self.blast_select_all) self.blast_select_none_button = QtWidgets.QPushButton(text="Select None") self.blast_select_none_button.clicked.connect(self.blast_select_none) self.blast_select_n_button = QtWidgets.QPushButton(text="Select Top:") self.blast_select_n_button.clicked.connect(self.blast_select_n) for button in [self.blast_select_all_button, self.blast_select_none_button, self.blast_select_n_button]: self.buttons_hbox.addWidget(button) # Build the line-edit for selecting only top entries. self.blast_select_n_enf = PyMod_entryfield_qt(label_text="", value="10", validate={'validator': 'integer', 'min': 1, 'max': 5000}) self.blast_select_n_enf.entry.setFixedWidth(70) self.buttons_hbox.addWidget(self.blast_select_n_enf.entry) # Align to the left all these widgets. self.buttons_hbox.setAlignment(QtCore.Qt.AlignLeft) for button in [self.blast_select_all_button, self.blast_select_none_button, self.blast_select_n_button]: button.setFixedWidth(button.sizeHint().width()+30) #----------------- # 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_blast_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.blast_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)
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 create_dialog(): dialog = QtWidgets.QDialog() dialog.setWindowTitle('Lighting Settings') setting = plugins.get_pmgapp().skin.setting sliders = [ "Diffuse Reflection", ('ambient', 0, 1, None), ('reflect', -1, 1, None), "Direct Light from Front", ('direct (+reflect)', -1, 1, None), # diffuse, coupled with "reflect" ('spec_direct', 0, 1, None), ('spec_direct_power', 0, 100, 1), "Free placeable directed Lights", ('light_count', 1, 8, 1), ('edit_light', 1, 7, 1), "Specular Reflection", ('spec_count', -1, 8, 1), # ('spec_power', -1, 200, 1), # deprecated since v1.5 ('shininess', 0, 100, None), # same as spec_power ('spec_reflect', -0.01, 1, None), ('specular', 0, 1, None), ('specular_intensity (=specular)', 0, 1, None), # same as specular "Ambient Occlusion (Surface only)", ('ambient_occlusion_mode', 0, 2, 1), ('ambient_occlusion_scale', 1.0, 50., None), ('ambient_occlusion_smooth', 1, 20, 1), "Ray trace only", ('power', 1, 10, None), ('reflect_power', 1, 10, None), ] layout = QtWidgets.QVBoxLayout(dialog) button_layout = QtWidgets.QHBoxLayout() layout.addLayout(button_layout) layout.setContentsMargins(5, 0, 5, 0) button_layout.addWidget( QtWidgets.QLabel("<font color=red>Presets:</font>")) presets = [ ("Default", preset_default), ("Metal", preset_metal), ("Plastic", preset_plastic), ("Rubber", preset_rubber), ("X-Ray", preset_xray), ] for name, fun in presets: btn = QtWidgets.QPushButton(name, dialog) btn.pressed.connect(fun) btn.setAutoDefault(False) button_layout.addWidget(btn) form_layout = QtWidgets.QFormLayout() form_layout.setContentsMargins(0, 0, 0, 0) form_layout.setVerticalSpacing(0) form_layout.setLabelAlignment(Qt.AlignLeft) layout.addLayout(form_layout) for i, item in enumerate(sliders, 1): if isinstance(item, str): label = QtWidgets.QLabel("<font color=blue>" + item + "</font>") form_layout.addRow(label) continue name, min, max, res = item if res is None: res = 0.01 if (max - min < 100) else 0.1 line_edit = QtWidgets.QLineEdit(dialog) slider = SettingSlider(dialog, name.split()[0], min, max, res, line_edit) h_layout = QtWidgets.QHBoxLayout() h_layout.addWidget(slider, 3) h_layout.addWidget(line_edit, 1) form_layout.addRow(name, h_layout) return dialog
def __init__(self, parent=None, app=None): super(_BuilderPanel, self).__init__(parent) self.setWindowTitle("Builder") self.setObjectName("builder") self.cmd = app.pymol.cmd self.layout = QtWidgets.QVBoxLayout() self.setLayout(self.layout) self.buttons_layout = QtWidgets.QVBoxLayout() self.tabs = QtWidgets.QTabWidget(self) self.layout.setContentsMargins(5, 5, 5, 5); self.layout.setSpacing(5); self.layout.addWidget(self.tabs) self.layout.addLayout(self.buttons_layout) self.layout.addStretch() self.fragments_layout = QtWidgets.QGridLayout() self.fragments_layout.setContentsMargins(5, 5, 5, 5); self.fragments_layout.setSpacing(5); self.fragments_tab = QtWidgets.QWidget() self.fragments_tab.setLayout(self.fragments_layout) self.protein_layout = QtWidgets.QGridLayout() self.protein_layout.setContentsMargins(5, 5, 5, 5); self.protein_layout.setSpacing(5); self.protein_tab = QtWidgets.QWidget() self.protein_tab.setLayout(self.protein_layout) self.tabs.addTab(self.fragments_tab, "Chemical") self.tabs.addTab(self.protein_tab, "Protein") self.getIcons() buttons = [ [ ("H", "Hydrogen", lambda: self.replace("H", 1, 1, "Hydrogen")), ("C", "Carbon", lambda: self.replace("C", 4, 4, "Carbon")), ("N", "Nitrogen", lambda: self.replace("N", 4, 3, "Nitrogen")), ("O", "Oxygen", lambda: self.replace("O", 4, 2, "Oxygen")), ("P", "Phosphorus", lambda: self.replace("P",4,3, "Phosphorous")), ("S", "Sulfur", lambda: self.replace("S",2,2, "Sulfur")), ("F", "Fluorine", lambda: self.replace("F",1,1, "Fluorine")), ("Cl", "Chlorrine", lambda: self.replace("Cl",1,1, "Chlorine")), ("Br", "Bromine", lambda: self.replace("Br",1,1, "Bromine")), ("I", "Iodine", lambda: self.replace("I",1,1, "Iodine")), ("-CF3", "Trifluoromethane", lambda: self.replace("trifluoromethane",4,0, "trifluoro")), ("-OMe", "Methanol", lambda: self.replace("methanol",5,0, "methoxy")), ], [ ("CH4", "Methyl", lambda: self.grow("methane",1,0,"methyl")), ("C=C", "Ethylene", lambda: self.grow("ethylene",4,0,"vinyl")), ("C#C", "Acetylene", lambda: self.grow("acetylene",2,0,"alkynl")), ("C#N", "Cyanide", lambda: self.grow("cyanide",2,0,"cyano")), ("C=O", "Aldehyde", lambda: self.grow("formaldehyde",2,0,"carbonyl",)), ("C=OO", "Formic Acid", lambda: self.grow("formic",4,0,"carboxyl")), ("C=ON", "C->N amide", lambda: self.grow("formamide",5,0,"C->N amide")), ("NC=O", "N->C amide", lambda: self.grow("formamide",3,1,"N->C amide")), ("S=O2", "Sulfone", lambda: self.grow("sulfone",3,1,"sulfonyl")), ("P=O3", "Phosphite", lambda: self.grow("phosphite",4,0,"phosphoryl")), ("N=O2", "Nitro", lambda: self.grow("nitro",3,0,"nitro")), ], [ ("#cyc3", "Cyclopropane", lambda: self.grow("cyclopropane",4,0,"cyclopropyl")), ("#cyc4", "Cyclobutane", lambda: self.grow("cyclobutane",4,0,"cyclobutyl")), ("#cyc5", "Cyclopentane", lambda: self.grow("cyclopentane",5,0,"cyclopentyl")), ("#cyc6", "Cyclohexane", lambda: self.grow("cyclohexane",7,0,"cyclohexyl")), ("#cyc7", "Cycloheptane", lambda: self.grow("cycloheptane",8,0,"cycloheptyl")), ("#aro5", "Cyclopentadiene", lambda: self.grow("cyclopentadiene",5,0,"cyclopentadienyl")), ("#aro6", "Benzene", lambda: self.grow("benzene",6,0,"phenyl")), ("#aro65", "Indane", lambda: self.grow("indane",12,0,"indanyl")), ("#aro66", "Napthylene", lambda: self.grow("napthylene",13,0,"napthyl")), ("#aro67", "Benzocycloheptane", lambda: self.grow("benzocycloheptane",13,0, "benzocycloheptyl")), ] ] self.btn_icons = {} requestsize = QtCore.QSize(48, 48) for row, btn_row in enumerate(buttons): for col, bb in enumerate(btn_row): btn_label, btn_tooltip, btn_command = bb btn = makeFragmentButton() if btn_label.startswith('#'): icons = self.icons[btn_label[1:]] btn.setIcon(icons[0]) btn.setIconSize(icons[1].actualSize(requestsize)) self.btn_icons[btn] = icons else: btn.setText(btn_label) btn.setToolTip(btn_tooltip) btn.clicked.connect(btn_command) self.fragments_layout.addWidget(btn, row, col) buttons = [ [ 'Ace', 'Ala', 'Arg', 'Asn', 'Asp', 'Cys', 'Gln', 'Glu', 'Gly', 'His', 'Ile', 'Leu' ], [ 'Lys', 'Met', 'Phe', 'Pro', 'Ser', 'Thr', 'Trp', 'Tyr', 'Val', 'NMe', 'NHH' ] ] for row, btn_row in enumerate(buttons): for col, btn_label in enumerate(btn_row): btn = makeFragmentButton() btn.setText(btn_label) btn.setToolTip("Build %s residue" % btn_label) res = btn_label.lower() slot = lambda val=None, s=self,r=res: s.attach(r) btn.clicked.connect(slot) self.protein_layout.addWidget(btn, row, col) lab = QtWidgets.QLabel('Secondary Structure:') lab_cols = 3 self.ss_cbox = QtWidgets.QComboBox() self.ss_cbox.addItem("Alpha Helix") self.ss_cbox.addItem("Beta Sheet (Anti-Parallel)") self.ss_cbox.addItem("Beta Sheet (Parallel)") self.protein_layout.addWidget(lab, 2, 0, 1, lab_cols) self.protein_layout.addWidget(self.ss_cbox, 2, lab_cols, 1, 4) self.ss_cbox.currentIndexChanged[int].connect(self.ssIndexChanged) buttons = [ [ ( "@Atoms:", None, None), ( "Fix H", "Fix hydrogens on picked atoms", self.fixH), ( "Add H", "Add hydrogens to entire molecule", self.addH), ( "Invert", "Invert stereochemistry around pk1 (pk2 and pk3 will remain fixed)", self.invert), ( "Delete", "Remove atoms", self.removeAtom), ( "Clear", "Delete everything", self.clear), ( "@ Charge:", None, None), ( " +1 ", "Positive Charge", lambda: self.setCharge(1,"+1")), ( " 0 ", "Neutral Charge", lambda: self.setCharge(0,"neutral")), ( " -1 ", "Negative Charge", lambda: self.setCharge(-1,"-1")), ], [ ( "@Bonds:", None, None), ( "Create", "Create bond between pk1 and pk2", self.createBond), ( "Delete", "Delete bond between pk1 and pk2", self.deleteBond), ( "Cycle", "Cycle bond valence", self.cycleBond), ( " | ", "Create single bond", lambda: self.setOrder("1", "single")), ( " || ", "Create double bond", lambda: self.setOrder("2", "double")), ( " ||| ", "Create triple bond", lambda: self.setOrder("3", "triple")), ( "Arom", "Create aromatic bond", lambda: self.setOrder("4", "aromatic")), ( "@ Model:", None, None), ( "Clean", "Cleanup structure", self.clean), ( "Sculpt", "Molecular sculpting", self.sculpt), ( "Fix", "Fix atom positions", self.fix), ( "Rest", "Restrain atom positions", self.rest), ], [ ( "$El-stat", "Electrostatics term for 'Clean' action", "clean_electro_mode"), ( "@ ", None, None), ( "$Bumps", "Show VDW contacts during sculpting", "sculpt_vdw_vis_mode"), ( "@ ", None, None), ( "#Undo Enabled", "", "suspend_undo"), ( "Undo", "Undo last change", self.undo), ( "Redo", "Redo last change", self.redo), ] ] for row, btn_row in enumerate(buttons): btn_row_layout = QtWidgets.QHBoxLayout() self.buttons_layout.addLayout(btn_row_layout) for col, bb in enumerate(btn_row): btn_label, btn_tooltip, btn_command = bb if btn_label[0] == '@': btn = QtWidgets.QLabel(btn_label[1:]) elif btn_label[0] in ('#', '$'): btn = QtWidgets.QCheckBox(btn_label[1:]) setting = btn_command value = self.cmd.get_setting_int(setting) if btn_label[0] == '$': btn.setChecked(bool(value)) @btn.toggled.connect def _(checked, n=setting): self.cmd.set(n, checked, quiet=0) else: btn.setChecked(not value) @btn.toggled.connect def _(checked, n=setting): self.cmd.set(n, not checked, quiet=0) else: btn = makeFragmentButton() btn.setText(btn_label) btn.clicked.connect(btn_command) if btn_tooltip: btn.setToolTip(btn_tooltip) btn_row_layout.addWidget(btn) btn_row_layout.addStretch()
def setupUi(self, UpdateDialog): UpdateDialog.setObjectName("UpdateDialog") UpdateDialog.resize(950, 470) self.verticalLayout = QtWidgets.QVBoxLayout(UpdateDialog) self.verticalLayout.setObjectName("verticalLayout") self.select_comp_label = QtWidgets.QLabel(UpdateDialog) self.select_comp_label.setObjectName("select_comp_label") self.verticalLayout.addWidget(self.select_comp_label) self.components_tableWidget = QtWidgets.QTableWidget(UpdateDialog) default_font = QtGui.QFont() default_font.setPointSize(default_font.pointSize()-1) self.components_tableWidget.setFont(default_font) self.components_tableWidget.setProperty("showDropIndicator", False) self.components_tableWidget.setDragDropOverwriteMode(False) self.components_tableWidget.setAlternatingRowColors(True) self.components_tableWidget.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) self.components_tableWidget.setGridStyle(QtCore.Qt.NoPen) self.components_tableWidget.setColumnCount(self.n_cols) self.components_tableWidget.setObjectName("components_tableWidget") self.components_tableWidget.setRowCount(1) vertical_header_item = QtWidgets.QTableWidgetItem() self.components_tableWidget.setVerticalHeaderItem(0, vertical_header_item) for i in range(self.n_cols): item = QtWidgets.QTableWidgetItem() self.components_tableWidget.setHorizontalHeaderItem(i, item) item = QtWidgets.QTableWidgetItem() self.components_tableWidget.setItem(0, self.component_col_idx, item) item = QtWidgets.QTableWidgetItem() self.components_tableWidget.setItem(0, self.databases_col_idx, item) self.components_tableWidget.horizontalHeader().setVisible(True) self.components_tableWidget.horizontalHeader().setCascadingSectionResizes(False) self.components_tableWidget.setColumnWidth(self.component_col_idx, 210) self.components_tableWidget.setColumnWidth(self.databases_col_idx, 180) self.components_tableWidget.setColumnWidth(self.status_col_idx, 190) # self.components_tableWidget.setColumnWidth(self.source_col_idx, 390) # self.components_tableWidget.setColumnWidth(self.last_download_col_idx, 250) self.components_tableWidget.horizontalHeader().setStretchLastSection(True) self.components_tableWidget.verticalHeader().setVisible(False) self.components_tableWidget.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) self.verticalLayout.addWidget(self.components_tableWidget) self.statusLabel = QtWidgets.QLabel(UpdateDialog) self.statusLabel.setObjectName("statusLabel") self.verticalLayout.addWidget(self.statusLabel) self.installation_progressBar = QtWidgets.QProgressBar(UpdateDialog) self.installation_progressBar.setEnabled(True) self.installation_progressBar.setProperty("value", 10) self.installation_progressBar.setObjectName("installation_progressBar") self.verticalLayout.addWidget(self.installation_progressBar) self.buttonsHorizontalLayout = QtWidgets.QHBoxLayout() self.buttonsHorizontalLayout.setObjectName("buttonsHorizontalLayout") self.installSel_button = QtWidgets.QPushButton(UpdateDialog) self.installSel_button.setObjectName("installSel_button") self.buttonsHorizontalLayout.addWidget(self.installSel_button) spacerItem = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum) self.buttonsHorizontalLayout.addItem(spacerItem) self.cancel_button = QtWidgets.QPushButton(UpdateDialog) self.cancel_button.setObjectName("cancel_button") self.buttonsHorizontalLayout.addWidget(self.cancel_button) self.verticalLayout.addLayout(self.buttonsHorizontalLayout) UpdateDialog.setWindowTitle("Install and update databases") self.select_comp_label.setText("Select components to install or update") self.components_tableWidget.setSortingEnabled(True) self.components_tableWidget.horizontalHeaderItem(self.component_col_idx).setText("Component") self.components_tableWidget.horizontalHeaderItem(self.databases_col_idx).setText("Databases Names") self.components_tableWidget.horizontalHeaderItem(self.status_col_idx).setText("Status") self.components_tableWidget.horizontalHeaderItem(self.source_col_idx).setText("Source") self.components_tableWidget.horizontalHeaderItem(self.last_download_col_idx).setText("Last Downloaded") __sortingEnabled = self.components_tableWidget.isSortingEnabled() self.components_tableWidget.setSortingEnabled(False) self.components_tableWidget.setSortingEnabled(__sortingEnabled) self.statusLabel.setText("") self.cancel_button.setText("Cancel") self.installSel_button.setText("Install Selected") QtCore.QMetaObject.connectSlotsByName(UpdateDialog)
def initUI(self): #---------------------------- # Left frame (for headers). - #---------------------------- self.sequence_ID_groupbox = QtWidgets.QGroupBox('SEQUENCE ID') # self.sequence_ID_groupbox.setStyleSheet("QLabel {font: 14pt COURIER NEW font-weight: bold} ") id_frame_stylesheet = "QLabel {font: %spt %s; font-weight: %s; color: white}" % ( self.main_window.font_size, self.main_window.font, self.main_window.font_weight) self.sequence_ID_groupbox.setStyleSheet(id_frame_stylesheet) self.id_form_layout = QtWidgets.QFormLayout() #self.left_scroll self.left_scroll = QtWidgets.QScrollArea() self.left_scroll.setHorizontalScrollBarPolicy( QtCore.Qt.ScrollBarAlwaysOn) self.left_scroll.setVerticalScrollBarPolicy( QtCore.Qt.ScrollBarAsNeeded) self.left_scroll.resize(200, 400) self.left_scroll.setWidget( self.sequence_ID_groupbox ) # sequence_ID_groupbox dentro left_scroll area self.left_scroll.setWidgetResizable(True) #self.left_frame self.left_frame = QtWidgets.QFrame(self) self.left_frame.setFrameShape(QtWidgets.QFrame.StyledPanel) self.left_frame.resize(200, 400) self.left_frame.setStyleSheet(self.style) self.left_frame.setFrameShadow(QtWidgets.QFrame.Sunken) #self.left_frame_layout self.left_frame_layout = QtWidgets.QVBoxLayout(self) self.left_frame_layout.addWidget(self.left_scroll) self.left_frame.setLayout( self.left_frame_layout) # left_frame_layout dentro left_frame #------------------------------- # Right frame (for sequences). - #------------------------------- # This groupbox self.sequence_SEQ_groupbox = QtWidgets.QGroupBox('SEQUENCES') seq_frame_stylesheet = "QLabel {font: %spt %s; font-weight: %s; color: white}" % ( self.main_window.font_size, self.main_window.font, self.main_window.font_weight) self.sequence_SEQ_groupbox.setStyleSheet(seq_frame_stylesheet) self.seq_form_layout = QtWidgets.QFormLayout() #self.right_scroll self.right_scroll = QtWidgets.QScrollArea() self.right_scroll.setHorizontalScrollBarPolicy( QtCore.Qt.ScrollBarAlwaysOn) self.right_scroll.setVerticalScrollBarPolicy( QtCore.Qt.ScrollBarAsNeeded) self.right_scroll.resize(900, 400) self.right_scroll.setWidget( self.sequence_SEQ_groupbox ) # sequence_ID_groupbox dentro left_scroll area self.right_scroll.setWidgetResizable(True) #self.right_frame self.right_frame = QtWidgets.QFrame(self) self.right_frame.setFrameShape(QtWidgets.QFrame.StyledPanel) self.right_frame.resize(900, 400) self.right_frame.setStyleSheet(self.style) self.right_frame.setFrameShadow(QtWidgets.QFrame.Sunken) #self.right_frame_layout self.right_frame_layout = QtWidgets.QVBoxLayout(self) self.right_frame_layout.addWidget(self.right_scroll) self.right_frame.setLayout( self.right_frame_layout) # left_frame_layout dentro left_frame #connect the two Vertical Bars to move them togheter self.left_scroll.verticalScrollBar().valueChanged.connect( self.right_scroll.verticalScrollBar().setValue) self.right_scroll.verticalScrollBar().valueChanged.connect( self.left_scroll.verticalScrollBar().setValue) #---------------------------------- # Bottom part of the main window. - #---------------------------------- self.splitter1 = QtWidgets.QSplitter(QtCore.Qt.Horizontal) self.splitter1.addWidget(self.left_frame) self.splitter1.addWidget(self.right_frame) # creating sequence and position labels self.label_sequence = QtWidgets.QLabel(self) self.label_sequence.setText('Sequence:') self.label_sequence.setStyleSheet(small_font_style) self.textbox_sequence = QtWidgets.QLineEdit(self) self.textbox_sequence.setStyleSheet(self.style + "; " + small_font_style) self.textbox_sequence.setReadOnly(True) self.label_position = QtWidgets.QLabel(self) self.label_position.setText('Position:') self.label_position.setStyleSheet(small_font_style) self.textbox_position = QtWidgets.QLineEdit(self) self.textbox_position.setReadOnly(True) self.textbox_position.setStyleSheet(self.style + "; " + small_font_style) self.textbox_position.setMinimumWidth( 675) # Width of the residues message bar width. # creating an horizontal layout with sequence and position labels self.text_layout = QtWidgets.QHBoxLayout() self.text_layout.addWidget(self.label_sequence) self.text_layout.addWidget(self.textbox_sequence) self.text_layout.addWidget(self.label_position) self.text_layout.addWidget(self.textbox_position) # creating a layout with sequence window and labels self.grid = QtWidgets.QVBoxLayout() self.grid.addWidget(self.splitter1) self.grid.addLayout(self.text_layout) self.setLayout(self.grid)
def __init__(self): QtWidgets.QWidget.__init__(self, parent, Qt.Window) self.setMinimumSize(400, 500) self.setWindowTitle('Register File Extensions') self.model = QtGui.QStandardItemModel(self) layout = QtWidgets.QVBoxLayout(self) self.setLayout(layout) label = QtWidgets.QLabel( "Select file types to register them with PyMOL", self) layout.addWidget(label) alluserslayout = QtWidgets.QHBoxLayout() alluserslayout.setObjectName("alluserslayout") layout.addLayout(alluserslayout) buttonlayout = QtWidgets.QHBoxLayout() buttonlayout.setObjectName("buttonlayout") layout.addLayout(buttonlayout) self.table = QtWidgets.QTableView(self) self.table.setModel(self.model) layout.addWidget(self.table) button = QtWidgets.QPushButton("Register Recommended (*)", self) buttonlayout.addWidget(button) button.pressed.connect(self.setRecommended) button = QtWidgets.QPushButton("Register All", self) buttonlayout.addWidget(button) button.pressed.connect(self.setAll) button = QtWidgets.QPushButton("Clear", self) button.setToolTip("Clean up Registry") buttonlayout.addWidget(button) button.pressed.connect(self.clear) if isAdmin(): r0 = QtWidgets.QRadioButton("Only for me") r0.setToolTip("HKEY_CURRENT_USER registry branch") r0.setChecked(True) r1 = QtWidgets.QRadioButton("For all users") r1.setToolTip("HKEY_LOCAL_MACHINE registry branch") allusersgroup = QtWidgets.QButtonGroup(self) allusersgroup.addButton(r0) allusersgroup.addButton(r1) allusersgroup.buttonClicked.connect(self.populateData) alluserslayout.addWidget(r0) alluserslayout.addWidget(r1) alluserslayout.addStretch() self.allusersbutton = r1 else: self.allusersbutton = None self.finalize_timer = QtCore.QTimer() self.finalize_timer.setSingleShot(True) self.finalize_timer.setInterval(500) self.finalize_timer.timeout.connect(finalize) self.populateData() # keep reference to window, otherwise Qt will auto-close it self._self_ref = self