def initUI(self):
self.setWindowTitle(self.title)
vertical_layout = QtWidgets.QVBoxLayout()
self.thread_progressbar = QtWidgets.QProgressBar(self)
if self.progress:
self.thread_progressbar.setMinimum(0)
self.thread_progressbar.setMaximum(0)
progressbar_label = "Computing..." # "Wait for the protocol to complete."
self.thread_progressbar.setFormat(progressbar_label)
self.thread_progressbar.setValue(0)
vertical_layout.addWidget(self.thread_progressbar)
self.thread_progress_label = QtWidgets.QLabel(self.label_text, self)
self.thread_progress_label.setWordWrap(True)
vertical_layout.addWidget(self.thread_progress_label)
# Button for canceling the execution of the thread.
horizontal_layout = QtWidgets.QHBoxLayout()
self.cancel_button = QtWidgets.QPushButton('Cancel', self)
self.cancel_button.clicked.connect(self.on_cancel_button_click)
self.cancel_button.setEnabled(not self.lock)
horizontal_layout.addWidget(self.cancel_button)
vertical_layout.addLayout(horizontal_layout)
self.setLayout(vertical_layout)
def __init__(self, parent, cmd):
QtWidgets.QWidget.__init__(self, parent, Qt.Window)
self.setMinimumSize(400, 500)
self.cmd = cmd
self.model = QtGui.QStandardItemModel(self)
self.proxy_model = QtCoreModels.QSortFilterProxyModel(self)
self.proxy_model.setSourceModel(self.model)
self.setWindowTitle('PyMOL Advanced Settings')
layout = QtWidgets.QVBoxLayout(self)
self.setLayout(layout)
self.filter_le = QtWidgets.QLineEdit(self)
layout.addWidget(self.filter_le)
self.filter_le.setPlaceholderText("Filter")
self.filter_le.textChanged.connect(self.proxy_model.setFilterRegExp)
self.populateData()
self.table = QtWidgets.QTableView(self)
self.table.setModel(self.proxy_model)
layout.addWidget(self.table)
self.formatTable()
self.model.itemChanged.connect(self.itemChanged)
def initUI(self):
self.setWindowTitle('PyMod Directory Selection')
self.vertical_layout = QtWidgets.QVBoxLayout()
# Main label.
self.label = QtWidgets.QLabel(
"Select a folder inside which to build the 'PyMod Directory'",
self)
self.vertical_layout.addWidget(self.label)
# Entry and "Browse" button.
self.horizontal_layout = QtWidgets.QHBoxLayout()
self.main_entry = QtWidgets.QLineEdit(self.pymod.home_directory, self)
self.main_entry.setStyleSheet("background-color: white; color: black")
self.horizontal_layout.addWidget(self.main_entry)
self.browse_button = QtWidgets.QPushButton("BROWSE", self)
self.browse_button.clicked.connect(self.pymod_directory_browse_state)
self.horizontal_layout.addWidget(self.browse_button)
self.vertical_layout.addLayout(self.horizontal_layout)
# "Submit" button.
self.submit_button = QtWidgets.QPushButton("SUBMIT", self)
self.submit_button.setFixedWidth(self.submit_button.sizeHint().width())
self.submit_button.clicked.connect(self.on_submit_button_press)
self.vertical_layout.addWidget(self.submit_button)
self.vertical_layout.setAlignment(self.submit_button,
QtCore.Qt.AlignCenter)
# Set the layouts.
self.setLayout(self.vertical_layout)
def __init__(self, label_text="Input", buttons=[]):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Buttons.
self.input = QtWidgets.QVBoxLayout()
if not buttons:
raise ValueError("Please provide a list of button names")
if len(buttons) != len(set(buttons)):
raise ValueError("Please provide a non redundant list of buttons")
self.button_group = QtWidgets.QButtonGroup()
self.buttons_names = []
self.buttons_dict = {}
for button_name in buttons:
button = QtWidgets.QPushButton(button_name)
button.setCheckable(True)
self.input.addWidget(button)
self.buttons_names.append(button_name)
self.buttons_dict[button_name] = button
self.button_group.addButton(button)
def build_alignment_mode_frame(self):
"""
Builds a frame with some options to choose the alignment mode.
"""
# Vbox which will store all the widgets for the alignment mode options.
self.alignment_mode_vbox = QtWidgets.QVBoxLayout()
self.alignment_mode_label = QtWidgets.QLabel("Alignment Mode")
self.alignment_mode_vbox.addWidget(self.alignment_mode_label)
self.alignment_mode_button_group = QtWidgets.QButtonGroup()
self.build_strategy_specific_modes_frames() # Defined in child classes.
self.middle_formlayout.addRow(self.alignment_mode_vbox)
def create_dialog():
dialog = QtWidgets.QDialog()
dialog.setWindowTitle('AlignIt Pymol plugin')
layout = QtWidgets.QVBoxLayout(dialog)
alignit = AlignItPlugin()
actions = {
'Read pharmacophore...': lambda: alignit.readAlignIt(dialog),
}
for name, action in actions.items():
btn = QtWidgets.QPushButton(name, dialog)
btn.pressed.connect(action)
layout.addWidget(btn)
return dialog
def _build_table_elements(self, parent):
'''
Create the various elements in the table and add them to the
proper layout.
'''
self.setWindowTitle('Scene Panel')
layout = QtWidgets.QVBoxLayout(self)
self.setLayout(layout)
top_layout = QtWidgets.QGridLayout()
layout.addLayout(top_layout)
mid_layout = QtWidgets.QGridLayout()
layout.addLayout(mid_layout)
low_layout = QtWidgets.QGridLayout()
layout.addLayout(low_layout)
# Top Elements
self.instructionLabel = QtWidgets.QLabel(self)
self.instructionLabel.setText(
'Double click selected thumbnail to \nload into Workspace.')
top_layout.addWidget(self.instructionLabel, 0, 0)
self.addSceneButton = QtWidgets.QPushButton(self)
self.addSceneButton.setText('Add Scene')
top_layout.addWidget(self.addSceneButton, 0, 1)
# Mid Elements
self.sceneTableWidget = QtWidgets.QTableWidget(self)
mid_layout.addWidget(self.sceneTableWidget, 0, 0)
self.sceneTableWidget.viewport().installEventFilter(self)
self.sceneTableWidget.itemChanged.connect(self._item_changed)
self.sceneTableWidget.selectionModel().selectionChanged.connect(
self._selection_changed)
self.sceneTableWidget.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.sceneTableWidget.verticalHeader().setSectionsMovable(True)
# Lower Buttom Elements
self.deleteButton = QtWidgets.QPushButton(self)
self.deleteButton.setText("Delete Scene")
low_layout.addWidget(self.deleteButton, 0, 1)
self.deleteButton.setEnabled(False)
self.updateButton = QtWidgets.QPushButton(self)
self.updateButton.setText("Update Scene")
low_layout.addWidget(self.updateButton, 0, 0)
self.updateButton.setEnabled(False)
def initUI(self):
self.setWindowTitle('Import PDB Options')
vertical_layout = QtWidgets.QVBoxLayout()
# Installation options label.
info_text = "Please select the 3D structure import mode:"
self.fetch_info_label = QtWidgets.QLabel(info_text, self)
# self.fetch_info_label.setStyleSheet(label_style_1)
vertical_layout.addWidget(self.fetch_info_label)
vertical_layout.addStretch(1)
# Import options radiobuttons.
horizontal_layout = QtWidgets.QHBoxLayout()
self.import_all_radiobutton = QtWidgets.QRadioButton(
"Import in PyMod the structure of every chain of the PDB files.")
# self.import_all_radiobutton.setChecked(True)
# self.import_all_radiobutton.setStyleSheet(label_font_1)
vertical_layout.addWidget(self.import_all_radiobutton)
self.import_fragment_radiobutton = QtWidgets.QRadioButton(
"Import in PyMod only the structure of the hit sequences fragments."
)
# label_font_1
self.import_fragment_radiobutton.setStyleSheet("margin-bottom: 10px")
vertical_layout.addWidget(self.import_fragment_radiobutton)
# Import fragments button.
self.import_button = QtWidgets.QPushButton("Import 3D Structures",
self)
# self.import_button.setStyleSheet(label_style_2)
self.import_button.clicked.connect(self.on_import_button_click)
horizontal_layout.addWidget(self.import_button)
horizontal_layout.addStretch(1)
# Cancel button.
self.cancel_button = QtWidgets.QPushButton('Cancel', self)
# self.cancel_button.setStyleSheet(label_style_2)
self.cancel_button.clicked.connect(self.on_cancel_button_click)
horizontal_layout.addWidget(self.cancel_button)
vertical_layout.addLayout(horizontal_layout)
self.setLayout(vertical_layout)
def show_plugin_info_dialog(self, info):
dialog = QtWidgets.QDialog(None)
dialog.setWindowTitle('Plugin Information')
layout = QtWidgets.QVBoxLayout()
table = QtWidgets.QTableWidget(0, 2)
table.verticalHeader().hide()
table.horizontalHeader().hide()
table.horizontalHeader().setStretchLastSection(True)
layout.addWidget(table)
dialog.setLayout(layout)
def add_line(label, text):
row = table.rowCount()
table.insertRow(table.rowCount())
table_item = QtWidgets.QTableWidgetItem(label)
table_item.setFlags(table_item.flags() &
~(Qt.ItemIsEditable))
table.setItem(row, 0, table_item)
table_item = QtWidgets.QTableWidgetItem(text)
table_item.setFlags(table_item.flags() &
~(Qt.ItemIsEditable))
table.setItem(row, 1, table_item)
add_line('Name', info.name)
if not info.is_temporary:
add_line('Python Module Name', info.mod_name)
add_line('Filename', info.filename)
metadata = info.get_metadata()
for label, value in metadata.items():
add_line(label, value)
if not info.is_temporary:
if info.loaded:
add_line('commands', ', '.join(info.commands))
docstring = info.get_docstring() or 'No documentation available.'
browser = QtWidgets.QTextBrowser()
browser.setPlainText(docstring)
layout.addWidget(browser)
table.resizeColumnsToContents()
dialog.resize(600, dialog.height())
dialog.exec_()
def __init__(self, widget, window=None, name='', _self=None):
if window:
window.setWindowTitle(name + ' - Volume Color Map Editor')
cmd = _self
layout = QtWidgets.QVBoxLayout()
widget.setLayout(layout)
widget.editor = VolumeEditorWidget(widget, name, _self)
layout.addWidget(widget.editor)
layout.setContentsMargins(5, 5, 5, 5)
get_colors_btn = QtWidgets.QPushButton("Get colors as script")
get_colors_btn.setAutoDefault(False)
get_colors_btn.clicked.connect(widget.editor.displayScript)
help_btn = QtWidgets.QPushButton("Help")
help_btn.setAutoDefault(False)
help_btn.clicked.connect(widget.editor.displayHelp)
reset_btn = QtWidgets.QPushButton("Reset Data Range")
reset_btn.setAutoDefault(False)
reset_btn.clicked.connect(widget.editor.reset)
widget.editor.update_cb = QtWidgets.QCheckBox(
"Update volume colors in real-time")
widget.editor.update_cb.setObjectName("volume_checkbox")
widget.editor.update_cb.setChecked(True)
widget.editor.update_cb.setMinimumWidth(30)
widget.editor.update_cb.toggled.connect(
widget.editor.toggleRealTimeUpdates)
button_layout = QtWidgets.QHBoxLayout()
button_layout.addWidget(get_colors_btn)
button_layout.addWidget(reset_btn)
button_layout.addWidget(help_btn)
button_layout.addStretch()
button_layout.addWidget(widget.editor.update_cb)
layout.addLayout(button_layout)
histogram = cmd.get_volume_histogram(name)
widget.editor.setHistogram(histogram)
colors = cmd.volume_color(name)
widget.editor.setColors(colors)
def displayTextDialog(self, text):
"""
Opens a generic text dialog and displays provided text.
"""
if not self.text_dialog:
self.text_dialog = QtWidgets.QDialog()
layout = QtWidgets.QVBoxLayout()
self.text_dialog.setLayout(layout)
self.text_dialog.text_display = QtWidgets.QPlainTextEdit()
self.text_dialog.text_display.setReadOnly(True)
self.text_dialog.text_display.setStyleSheet(
"font-family: monospace, courier")
size = self.text_dialog.size()
size.setWidth(DEFAULT_TEXT_DIALOG_WIDTH)
self.text_dialog.resize(size)
layout.addWidget(self.text_dialog.text_display)
self.text_dialog.text_display.setPlainText(text)
self.text_dialog.show()
self.text_dialog.raise_()
def __init__(self, parent=None):
super(SurfStampFrame, self).__init__(parent)
self.layout = QtWidgets.QVBoxLayout()
self.setLayout(self.layout)
glayout1 = QtWidgets.QGridLayout()
self.label_message = QtWidgets.QLabel(self)
self.label_message.setText("SurfStamp PyMOL plugin")
self.layout.addWidget(self.label_message)
self.combo_model = QtWidgets.QComboBox()
self.combo_model.addItems([])
self.layout.addWidget(self.combo_model)
self.label_reso = QtWidgets.QLabel(self)
self.label_reso.setText("Surface Resolution")
glayout1.addWidget(self.label_reso, 1, 0)
self.spin_reso = QtWidgets.QDoubleSpinBox(self)
self.spin_reso.setRange(0.1, 1.0)
self.spin_reso.setSingleStep(0.05)
self.spin_reso.setValue(0.7)
glayout1.addWidget(self.spin_reso, 1, 1)
self.label_imagesize = QtWidgets.QLabel(self)
self.label_imagesize.setText("Image Size")
glayout1.addWidget(self.label_imagesize, 2, 0)
self.spin_imagesize = QtWidgets.QSpinBox(self)
self.spin_imagesize.setRange(1000, 10000)
#PILLOW？は 13000 くらいが Max っぽい
self.spin_imagesize.setSingleStep(100)
self.spin_imagesize.setValue(4000)
glayout1.addWidget(self.spin_imagesize, 2, 1)
self.label_fontsize = QtWidgets.QLabel(self)
self.label_fontsize.setText("Font Size")
glayout1.addWidget(self.label_fontsize, 3, 0)
self.spin_fontsize = QtWidgets.QSpinBox(self)
self.spin_fontsize.setRange(3, 100)
self.spin_fontsize.setSingleStep(1)
self.spin_fontsize.setValue(20)
glayout1.addWidget(self.spin_fontsize, 3, 1)
glayout2 = QtWidgets.QGridLayout()
self.check_outline = QtWidgets.QCheckBox('Outline')
self.check_outline.setChecked(True)
glayout2.addWidget(self.check_outline, 0, 0)
self.check_nowater = QtWidgets.QCheckBox('Remove Waters')
self.check_nowater.setChecked(True)
glayout2.addWidget(self.check_nowater, 0, 1)
self.check_colorall = QtWidgets.QCheckBox('Color All')
self.check_colorall.setChecked(False)
glayout2.addWidget(self.check_colorall, 1, 0)
self.check_tile = QtWidgets.QCheckBox('Repeating Tile')
self.check_tile.clicked.connect(self.checkTileOn)
self.check_tile.setChecked(False)
glayout2.addWidget(self.check_tile, 1, 1)
self.check_oneletter = QtWidgets.QCheckBox('One Letter')
glayout2.addWidget(self.check_oneletter, 2, 0)
self.check_nochainname = QtWidgets.QCheckBox('No Chain Name')
glayout2.addWidget(self.check_nochainname, 2, 1)
self.check_ignore_occupancy = QtWidgets.QCheckBox('Ignore Occupancy')
glayout2.addWidget(self.check_ignore_occupancy, 3, 0)
self.check_cartoon = QtWidgets.QCheckBox('Cartoon')
self.check_cartoon.clicked.connect(self.checkCartoonOn)
glayout2.addWidget(self.check_cartoon, 3, 1)
self.check_mmcif = QtWidgets.QCheckBox('Use MMCIF')
glayout2.addWidget(self.check_mmcif, 4, 0)
self.check_builtin = QtWidgets.QCheckBox('Built-in Surface Generator')
glayout2.addWidget(self.check_builtin, 4, 1)
self.check_builtin.clicked.connect(self.checkBuiltinOn)
#MMCIF は AUTH が不完全だ！
#self.check_label = QtWidgets.QCheckBox('ID Label');
#self.layout.addWidget(self.check_label);
# Text field for output file
glayout4 = QtWidgets.QVBoxLayout()
self.label_outprefix = QtWidgets.QLabel(
'Output Prefix (Prefix+<something> will be overwritten.)')
glayout4.addWidget(self.label_outprefix)
glayout4b = QtWidgets.QGridLayout()
self.text_outprefix = QtWidgets.QLineEdit(self)
self.text_outprefix.setReadOnly(True)
glayout4b.addWidget(self.text_outprefix, 0, 0)
self.button_outprefix = QtWidgets.QPushButton(self)
self.button_outprefix.setText("Save As")
self.button_outprefix.clicked.connect(self.getFile)
self.text_outprefix.setStyleSheet("background-color: lightgray;")
glayout4b.addWidget(self.button_outprefix, 0, 1)
glayout4.addLayout(glayout4b)
glayout3 = QtWidgets.QGridLayout()
self.button_ok = QtWidgets.QPushButton('Create')
self.button_ok.clicked.connect(self.runSurfStamp)
glayout3.addWidget(self.button_ok, 0, 0)
self.button_close = QtWidgets.QPushButton('Close')
self.button_close.clicked.connect(self.hide)
glayout3.addWidget(self.button_close, 0, 1)
self.layout.addLayout(glayout1)
self.layout.addLayout(glayout2)
self.layout.addLayout(glayout4)
self.layout.addLayout(glayout3)
screengeom = QtWidgets.qApp.desktop().screenGeometry()
wwidth = 300
hheight = 200
self.setGeometry(screengeom.width() / 2 - wwidth / 2,
screengeom.height() / 2 - hheight / 2, wwidth,
hheight)
self.setWindowTitle('SurfStamp')
self.checkTileOn()
self.checkBuiltinOn()
self.checkCartoonOn()
self.show()
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)
_size_hint = QtCore.QSize(options.win_x, options.ext_y)
def sizeHint(self):
return self._size_hint
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)
# progress bar
hbox = QtWidgets.QHBoxLayout()
self.progressbar = QtWidgets.QProgressBar()
self.progressbar.setSizePolicy(QtWidgets.QSizePolicy.Minimum,
QtWidgets.QSizePolicy.Minimum)
hbox.addWidget(self.progressbar)
self.abortbutton = QtWidgets.QPushButton('Abort')
self.abortbutton.setStyleSheet("background: #FF0000; color: #FFFFFF")
self.abortbutton.released.connect(cmd.interrupt)
hbox.addWidget(self.abortbutton)
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):
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
def create_dialog():
dialog = QtWidgets.QDialog()
dialog.setWindowTitle('Lighting Settings')
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, 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 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 new_manager_widget(manager, title):
dockWidget = QtWidgets.QDockWidget()
dockWidget.setWindowTitle(title)
widget = QtWidgets.QWidget()
layout = QtWidgets.QVBoxLayout(widget)
dockWidget.setWidget(widget)
widget.setLayout(layout)
model = QtGui.QStandardItemModel(0, 1, widget)
tree = QtWidgets.QTreeView(widget)
tree.setModel(model)
tree.setHeaderHidden(True)
current_key = None
def update_treeview():
model.clear()
for key in manager.get_keys():
item = QtGui.QStandardItem()
item.setText(key)
model.blockSignals(True)
model.appendRow(item)
model.blockSignals(False)
@model.rowsInserted.connect
def onRowsInserted(index):
key = model.itemFromIndex(index).text()
store_view(key)
update_treeview()
@model.dataChanged.connect
def onDataChanged(index):
new_key = model.itemFromIndex(index).text()
if new_key == "":
manager.clear(current_key)
else:
manager.rename(current_key, new_key)
update_treeview()
@dockWidget.visibilityChanged.connect
def onVisibilityChanged(visible):
if not visible:
return
update_treeview()
@tree.clicked.connect
def onClicked(index):
nonlocal current_key
key = model.itemFromIndex(index).text()
current_key = key
manager.recall(key)
storeBtn = QtWidgets.QPushButton("Store", widget)
@storeBtn.clicked.connect
def onClicked():
count = len(manager.get_keys())
manager.store(f"view{count}")
update_treeview()
layout.addWidget(tree)
layout.addWidget(storeBtn)
return dockWidget
def build_protocol_middle_frame(self):
#------------------
# Simple options. -
#------------------
# Let users decide how to import new sequences when the query is a child element (that
# is, it is already present in a cluster).
if self.protocol.blast_query_element.is_child():
self.import_mode_vbox = QtWidgets.QVBoxLayout()
self.import_mode_label = QtWidgets.QLabel("Hit Import Mode")
self.import_mode_vbox.addWidget(self.import_mode_label)
self.import_mode_button_group = QtWidgets.QButtonGroup()
self.middle_formlayout.addRow(self.import_mode_vbox)
# Build new alignment.
new_alignment_radiobutton = QtWidgets.QRadioButton("Build a new alignment with the query and the new hit sequences")
new_alignment_radiobutton._value = "build-new"
new_alignment_radiobutton.setChecked(True)
self.import_mode_vbox.addWidget(new_alignment_radiobutton)
self.import_mode_button_group.addButton(new_alignment_radiobutton)
# Expand alignment.
expand_alignment_radiobutton = QtWidgets.QRadioButton("Expand the existing alignment by appending the new hit sequences")
# "Expand the already existing cluster by appending to it the new hit sequences"
expand_alignment_radiobutton._value = "expand"
self.import_mode_vbox.addWidget(expand_alignment_radiobutton)
self.import_mode_button_group.addButton(expand_alignment_radiobutton)
# Each algorithm will have its own standard widgets.
self.build_algorithm_standard_options_widgets()
# E-value selection.
if self.protocol.protocol_name in hmmer_protocols_names:
e_value_threshold_enf_text = "c-Evalue Threshold"
else:
e_value_threshold_enf_text = "E-value Threshold"
self.e_value_threshold_enf = PyMod_entryfield_qt(label_text=e_value_threshold_enf_text,
value=str(self.protocol.e_value_threshold_default),
validate={'validator': 'real',
'min': 0.0, 'max': 1000.0})
self.middle_formlayout.add_widget_to_align(self.e_value_threshold_enf, validate=True)
# Max hit number selection.
self.max_hits_enf = PyMod_entryfield_qt(label_text="Max Number of Hits",
value=str(self.protocol.default_max_number_of_hits),
validate={'validator': 'integer',
'min': 1, 'max': 5000})
self.middle_formlayout.add_widget_to_align(self.max_hits_enf, validate=True)
# -------------------
# Advanced options. -
# -------------------
self.show_advanced_button()
# Minimum id% on with query.
self.min_id_enf = PyMod_entryfield_qt(label_text="Min Id% Threshold",
value="0",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.min_id_enf, advanced_option=True, validate=True)
# Maximum id% on with query.
self.max_id_enf = PyMod_entryfield_qt(label_text="Max Id% Threshold",
value="100",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.max_id_enf, advanced_option=True, validate=True)
# Minimum coverage on the query.
self.min_coverage_enf = PyMod_entryfield_qt(label_text="Min Coverage% Threshold",
value="0",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.min_coverage_enf, advanced_option=True, validate=True)
# Advanced options for a specific algorithm.
self.build_algorithm_advanced_options_widgets()
self.middle_formlayout.set_input_widgets_width("auto")
def __init__(
self,
parent,
title="New PyMod Window",
upper_frame_title="New PyMod Window Sub-title",
submit_command=None,
submit_button_text="Submit",
with_scroll=True,
# geometry=None
):
super(PyMod_tool_window_qt, self).__init__(parent)
#------------------------
# Configure the window. -
#------------------------
# Command executed when pressing on the main button of the window.
self.submit_command = submit_command
# Configure the window.
self.setWindowTitle(title)
# if geometry is not None:
# self.setGeometry(*geometry)
# 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. -
#---------------
self.upper_frame_title = QtWidgets.QLabel(upper_frame_title)
self.main_vbox.addWidget(self.upper_frame_title)
#----------------
# Middle frame. -
#----------------
# Widget that contains the collection of Vertical Box.
self.middle_widget = QtWidgets.QWidget()
# The Vertical Box that contains other widgets to be displayed in the window.
self.middle_vbox = QtWidgets.QVBoxLayout()
self.middle_widget.setLayout(self.middle_vbox)
# Scroll area which contains the widgets, set as the centralWidget.
self.middle_scroll = QtWidgets.QScrollArea()
# Scroll area properties.
# self.middle_scroll.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)
# self.middle_scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
self.middle_scroll.setWidgetResizable(True)
self.middle_scroll.setWidget(self.middle_widget)
# QFormLayout in the middle frame.
if self.middle_layout_type == "qform":
self.middle_formlayout = PyMod_QFormLayout()
self.middle_vbox.addLayout(self.middle_formlayout)
elif self.middle_layout_type == "qgrid":
self.middle_formlayout = QtWidgets.QGridLayout()
self.middle_vbox.addLayout(self.middle_formlayout)
else:
raise KeyError("Unknown 'middle_layout_type': %s" %
middle_layout_type)
self.add_middle_frame_widgets()
self.main_vbox.addWidget(self.middle_scroll)
#----------------
# Bottom frame. -
#----------------
self.submit_command = submit_command
if self.submit_command is not None:
self.main_button = QtWidgets.QPushButton(submit_button_text)
self.main_button.clicked.connect(
lambda a=None: self.submit_command())
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 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 build_panel_elements(self, parent):
'''
Responsible for creating all panel elements in order and adding them to the layout.
'''
self.create_new_form = parent.load_form("create_shortcut", None)
self.help_form = parent.load_form("help_shortcut", None)
self.confirm_change = parent.load_form("change_confirm", None)
self.model = QtGui.QStandardItemModel(self)
self.proxy_model = QtCoreModels.QSortFilterProxyModel(self)
self.proxy_model.setSourceModel(self.model)
self.proxy_model.setFilterCaseSensitivity(Qt.CaseInsensitive)
self.proxy_model.setFilterKeyColumn(-1)
self.setWindowTitle('Keyboard Shortcut Menu')
layout = QtWidgets.QVBoxLayout(self)
self.setLayout(layout)
# Create layout for filter bar and refresh button
top_layout = QtWidgets.QGridLayout()
layout.addLayout(top_layout)
# Filter
self.filter_le = QtWidgets.QLineEdit(self)
top_layout.addWidget(self.filter_le)
self.filter_le.setPlaceholderText("Filter")
self.filter_le.textChanged.connect(self.proxy_model.setFilterRegExp)
self.refresh_button = QtWidgets.QPushButton(self)
self.refresh_button.resize(26, 26)
top_layout.addWidget(self.refresh_button, 0, 1)
# themed icons only available by default on X11
if self.refresh_button.icon().isNull():
self.refresh_button.setIcon(QtGui.QIcon(
os.path.expandvars('$PYMOL_DATA/pmg_qt/icons/refresh.svg')))
self.refresh_button.setToolTip(
"Refresh the table to reflect any external changes")
self.refresh_button.clicked.connect(self.refresh_populate)
# Table
self.table = QtWidgets.QTableView(self)
self.table.setModel(self.proxy_model)
layout.addWidget(self.table)
self.intial_populate()
self.formatTable()
# Add layout for buttons
button_layout = QtWidgets.QGridLayout()
layout.addLayout(button_layout)
# Buttons
self.create_new_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.create_new_button, 0, 0)
self.create_new_button.setText("Create New")
self.create_new_button.setToolTip(
"Add a key binding that does not currently appear on the table")
self.create_new_button.clicked.connect(
lambda: self.create_new_form._dialog.show())
self.delete_selected_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.delete_selected_button, 0, 1)
self.delete_selected_button.setText("Delete Selected")
self.delete_selected_button.setToolTip(
"Unbind selected key bindings and remove any that have been created")
self.delete_selected_button.clicked.connect(self.delete_selected)
self.delete_selected_button.setEnabled(False)
self.reset_selected_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.reset_selected_button, 0, 2)
self.reset_selected_button.setText("Reset Selected")
self.reset_selected_button.setToolTip(
"Restore selected key bindings to their default values")
self.reset_selected_button.clicked.connect(self.reset_selected)
self.reset_selected_button.setEnabled(False)
self.reset_all_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.reset_all_button, 0, 3)
self.reset_all_button.setText("Reset All")
self.reset_all_button.setToolTip(
"Restore all key bindings to their default values and remove any that have been created")
self.reset_all_button.clicked.connect(self.reset_all_default)
self.save_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.save_button, 0, 4)
self.save_button.setText("Save")
self.save_button.setToolTip(
"Save the current key bindings to be loaded automatically when opening PyMOL")
self.save_button.clicked.connect(self.shortcut_manager.save_shortcuts)
# Ensuring that confirmed key and binding remain in scope
self.confirm_new_key = ''
self.confirm_new_binding = ''
# Connect create new and confirm menus
self.create_new_shortcut_menu_connect()
self.confirm_menu_connect()
self.model.itemChanged.connect(self.itemChanged)
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 __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)