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