def root(self):
if self._root is None:
from pymol.Qt import QtCore
tkinter_init()
# create Tk instance in this thread
self._root = tkinter.Tk()
self._root.tk = tkapp_proxy(self._root.tk, self)
self._root.withdraw()
# feed Tk event loop from this thread
timer = QtCore.QTimer()
@timer.timeout.connect
def _():
if not self._tk_update_paused:
self._root.update()
timer.start()
timer.setSingleShot(True)
timer.start(50)
# keep reference to timer
self._tk_update_timer = timer
import Pmw
Pmw.initialise(self._root)
return self._root
def __init__(self, parent):
self.gui = parent
self.fb_scale = 1.0
# OpenGL context setup
if USE_QOPENGLWIDGET:
f = QtGui.QSurfaceFormat()
else:
f = QtOpenGL.QGLFormat()
from pymol.invocation import options
# logic equivalent to layer5/main.cpp:launch
if options.multisample:
f.setSamples(4)
if options.force_stereo != -1:
# See layer1/Setting.h for stereo modes
if options.stereo_mode in (1, 12) or (
options.stereo_mode == 0 and AUTO_DETECT_STEREO):
f.setStereo(True)
if options.stereo_mode in (11, 12) and not USE_QOPENGLWIDGET:
f.setAccum(True)
if USE_QOPENGLWIDGET:
super(PyMOLGLWidget, self).__init__(parent=parent)
self.setFormat(f)
self.setUpdateBehavior(QtWidgets.QOpenGLWidget.PartialUpdate)
else:
super(PyMOLGLWidget, self).__init__(f, parent=parent)
# pymol instance
self.pymol = PyMOL()
self.pymol.start()
self.cmd = self.pymol.cmd
# capture python output for feedback
import pcatch
pcatch._install()
# for passive move drag
self.setMouseTracking(True)
# for accepting keyboard input (command line, shortcuts)
self.setFocusPolicy(Qt.ClickFocus)
# for idle rendering
self._timer = QtCore.QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self._pymolProcess)
# drag n drop
self.setAcceptDrops(True)
# pinch-zoom
self.grabGesture(Qt.PinchGesture)
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 dialog(_self=None):
if _self is None:
from pymol import cmd as _self
dialog = QtWidgets.QDialog()
uifile = os.path.join(os.path.dirname(__file__), 'apbs.ui')
form = loadUi(uifile, dialog)
form._dialog = dialog
form._proclist = []
def set_apbs_in(contents):
form.apbs_template.setPlainText(contents.strip())
# hide options widgets
form.optarea_prep.setVisible(False)
form.optarea_apbs.setVisible(False)
form.optarea_surf.setVisible(False)
form.optarea_other.setVisible(False)
# pre-fill form with likely data
names = _self.get_object_list()
names += ['(' + n + ')' for n in _self.get_names('public_selections')]
if names:
form.input_sele.clear()
form.input_sele.addItems([
('polymer & ' +
name) if _self.count_atoms('polymer & ' + name) > 0 else name
for name in names
])
form.surf_map.addItems(_self.get_names_of_type('object:map'))
set_apbs_in(electrostatics.template_apbs_in)
# executables
from distutils.spawn import find_executable
form.apbs_exe.setText(electrostatics.find_apbs_exe() or 'apbs')
form.pdb2pqr_exe.setText(
find_executable('pdb2pqr') or
# acellera::htmd-pdb2pqr provides pdb2pqr_cli
find_executable('pdb2pqr_cli') or find_executable(
'share/pdb2pqr/pdb2pqr.py', os.getenv('FREEMOL', '/usr'))
or 'pdb2pqr')
# for async panels
form._callInMainThread = MainThreadCaller()
run_impl_async = AsyncFunc(run_impl)
# "Run" button callback
def run():
form.tabWidget.setEnabled(False)
form.button_ok.clicked.disconnect()
form.button_ok.clicked.connect(abort)
form.button_ok.setText('Abort')
form._capture = StdOutCapture()
# detach from main thread
run_impl_async(form, _self)
# "Run" button "finally" actions (main thread)
@run_impl_async.finished.connect
def run_finally(args):
_, exception = args
form._proclist[:] = []
stdout = form._capture.release()
print(stdout)
form.button_ok.setText('Run')
form.button_ok.clicked.disconnect()
form.button_ok.clicked.connect(run)
form.button_ok.setEnabled(True)
form.tabWidget.setEnabled(True)
if exception is not None:
handle_exception(exception, stdout)
return
quit_msg = "Finished with Success. Close the APBS dialog?"
if QMessageBox.Yes == QMessageBox.question(form._dialog, 'Finished',
quit_msg, QMessageBox.Yes,
QMessageBox.No):
form._dialog.close()
def handle_exception(e, stdout):
if isinstance(e, SilentAbort):
return
msg = str(e) or 'unknown error'
msgbox = QMessageBox(QMessageBox.Critical, 'Error', msg,
QMessageBox.Close, form._dialog)
if stdout.strip():
msgbox.setDetailedText(stdout)
msgbox.exec_()
# "Abort" button callback
def abort():
form.button_ok.setEnabled(False)
while form._proclist:
p = form._proclist.pop()
try:
p.terminate()
p.returncode = -15 # SIGTERM
except OSError as e:
print(e)
# selection checker
check_sele_timer = QtCore.QTimer()
check_sele_timer.setSingleShot(True)
# grid auto-value
form.apbs_grid_userchanged = False
form.apbs_grid.setStyleSheet('background: #ff6')
@form.apbs_grid.editingFinished.connect
def _():
form.apbs_grid_userchanged = True
form.apbs_grid.setStyleSheet('')
@check_sele_timer.timeout.connect
def _():
has_props = ['no', 'no']
def callback(partial_charge, elec_radius):
if partial_charge: has_props[0] = 'YES'
if elec_radius > 0: has_props[1] = 'YES'
n = _self.iterate(form.input_sele.currentText(),
'callback(partial_charge, elec_radius)',
space={'callback': callback})
# grid auto-value (keep map size in the order of 200x200x200)
if n > 1 and not form.apbs_grid_userchanged:
e = _self.get_extent(form.input_sele.currentText())
volume = (e[1][0] - e[0][0]) * (e[1][1] - e[0][1]) * (e[1][2] -
e[0][2])
grid = max(0.5, volume**0.333 / 200.0)
form.apbs_grid.setValue(grid)
if n < 1:
label = 'Selection is invalid'
color = '#f66'
elif has_props == ['YES', 'YES']:
label = 'No preparation necessary, selection has charges and radii'
form.do_prepare.setChecked(False)
color = '#6f6'
else:
label = 'Selection needs preparation (partial_charge: %s, elec_radius: %s)' % tuple(
has_props)
form.do_prepare.setChecked(True)
color = '#fc6'
form.label_sele_has.setText(label)
form.label_sele_has.setStyleSheet('background: %s; padding: 5' % color)
check_sele_timer.start(0)
@form.apbs_exe_browse.clicked.connect
def _():
fnames = getOpenFileNames(None,
filter='apbs (apbs*);;All Files (*)')[0]
if fnames:
form.apbs_exe.setText(fnames[0])
@form.pdb2pqr_exe_browse.clicked.connect
def _():
fnames = getOpenFileNames(
None, filter='pdb2pqr (pdb2pqr*);;All Files (*)')[0]
if fnames:
form.pdb2pqr_exe.setText(fnames[0])
# hook up events
form.input_sele.currentIndexChanged.connect(
lambda: check_sele_timer.start(0))
form.input_sele.editTextChanged.connect(
lambda: check_sele_timer.start(1000))
form.button_ok.clicked.connect(run)
# "Register" opens a web browser
@form.button_register.clicked.connect
def _():
import webbrowser
webbrowser.open("http://www.poissonboltzmann.org/")
@form.button_load.clicked.connect
def _():
fnames = getOpenFileNames(None,
filter='APBS Input (*.in);;All Files (*)')[0]
if fnames:
contents = load_apbs_in(form, fnames[0])
set_apbs_in(contents)
@form.button_reset.clicked.connect
def _():
set_apbs_in(electrostatics.template_apbs_in)
form._dialog.show()
form._dialog.resize(500, 600)
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 __init__(self, parent):
self.gui = parent
# OpenGL context setup
f = QtOpenGL.QGLFormat()
f.setRgba(True)
f.setDepth(True)
f.setDoubleBuffer(True)
from pymol.invocation import options
# logic equivalent to layer5/main.cpp:launch
if options.multisample:
f.setSampleBuffers(True)
if options.force_stereo != -1:
# See layer1/Setting.h for stereo modes
if options.stereo_mode in (0, 1, 12):
# this effectively disables stereo detection
# on Linux that is faulty in QGLWidget / PyQt5
if not (options.stereo_mode == 0
and sys.platform.startswith("linux")):
f.setStereo(True)
if options.stereo_mode in (11, 12):
f.setAccum(True)
if options.stereo_mode in (0, 6, 7, 8, 9):
f.setStencil(True)
QtOpenGL.QGLWidget.__init__(self, f, parent=parent)
if not self.isValid():
raise RuntimeError('OpenGL initialization failed')
f_actual = self.format()
# report if quad buffer available
options.stereo_capable = int(f_actual.stereo()
or (options.force_stereo == 1))
# feedback if stereo request failed
if options.stereo_mode and (
# QTBUG-59636 f.stereo() and not f_actual.stereo() or
f.accum() and not f_actual.accum()
or f.stencil() and not f_actual.stencil()):
# cPyMOLGlobals_LaunchStatus_StereoFailed
options.launch_status |= 0x1
# feedback if multisample request failed
if options.multisample and not f_actual.sampleBuffers():
# cPyMOLGlobals_LaunchStatus_MultisampleFailed
options.launch_status |= 0x2
# pymol instance
self.pymol = PyMOL()
self.pymol.start()
self.cmd = self.pymol.cmd
# capture python output for feedback
import pcatch
pcatch._install()
# for passive move drag
self.setMouseTracking(True)
# for accepting keyboard input (command line, shortcuts)
self.setFocusPolicy(Qt.ClickFocus)
# for idle rendering
self._timer = QtCore.QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self._pymolProcess)
# drag n drop
self.setAcceptDrops(True)
# pinch-zoom
self.grabGesture(Qt.PinchGesture)