def _build_ui(self):
fields = self._entity.fields()
fields = [
x for x in fields if x.name not in ('id', 'timestamp', 'username')
]
lyt_buttons = QHBoxLayout()
lyt_buttons.addWidget(self._btn_create)
lyt_buttons.addWidget(self._btn_cancel)
r = 0
lyt_grid = QGridLayout()
for field in fields:
editor = QLineEdit()
if field.type == int:
editor = QSpinBox()
editor.setRange(-1000000, 1000000)
self._wdg_map[field] = editor
lyt_grid.addWidget(QLabel(field.name), r, 0)
lyt_grid.addWidget(editor, r, 1)
r += 1
lyt_main = QVBoxLayout()
lyt_main.addLayout(lyt_grid)
lyt_main.addLayout(lyt_buttons)
self.setLayout(lyt_main)
def _build_ui(self):
layout = QGridLayout()
layout.setContentsMargins(0,0,0,0)
layout.setSpacing(0)
#TODO: make buttons disabled/enabled if items are selected that don't have the info
self.tree = QTreeWidget()
self.tree.setSelectionMode(QTreeWidget.ExtendedSelection)
self.tree.setHeaderLabels(["Name", "ID", "movie", "energy", "frequencies"])
self.tree.setUniformRowHeights(True)
self.tree.setColumnWidth(self.NAME_COL, 200)
layout.addWidget(self.tree, 0, 0, 3, 1)
restore_button = QPushButton("restore")
restore_button.clicked.connect(self.restore_selected)
layout.addWidget(restore_button, 0, 1)
nrg_plot_button = QPushButton("energy plot")
nrg_plot_button.clicked.connect(self.open_nrg_plot)
layout.addWidget(nrg_plot_button, 1, 1)
coordset_slider_button = QPushButton("movie slider")
coordset_slider_button.clicked.connect(self.open_movie_slider)
layout.addWidget(coordset_slider_button, 2, 1)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(placement="side")
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.setMinimumWidth(500)
self.table = QTableWidget()
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.itemChanged.connect(self._item_changed)
self.table.currentItemChanged.connect(self._current_item_changed)
self.table.horizontalHeader().hide()
self.table.verticalHeader().hide()
self.table.setColumnCount(3)
self.table.horizontalHeader().resizeSection(0, 200)
self.table.horizontalHeader().resizeSection(1, 200)
self.table.horizontalHeader().resizeSection(2, 20)
self.new = QPushButton('New variable')
self.new.clicked.connect(self._new)
self.color = Color()
self.color.changed.connect(self._color_changed)
layout = QGridLayout(self)
layout.addWidget(self.table)
layout.addWidget(self.color)
layout.addWidget(self.new)
def __init__(self, settings, *args, **kwargs):
super().__init__(*args, **kwargs)
layout = QGridLayout(self)
#layout.setContentsMargins(0, 0, 0, 0)
settings_tabs = QTabWidget()
layout.addWidget(settings_tabs)
form = 'Gaussian'
self.method = MethodOption(settings, form)
settings_tabs.addTab(self.method, "Method")
self.basis = BasisWidget(settings, form)
settings_tabs.addTab(self.basis, "Basis Sets")
#menu stuff
menu = QMenuBar()
self.presets_menu = menu.addMenu("Presets")
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.settings = settings
self.presets = {}
self.presets['Gaussian'] = loads(self.settings.gaussian_presets)
self.presets['ORCA'] = loads(self.settings.orca_presets)
self.presets['Psi4'] = loads(self.settings.psi4_presets)
self.refresh_presets()
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.hue = QSlider()
self.hue.setMaximum(100)
self.hue.setOrientation(Qt.Horizontal)
self.hue.valueChanged.connect(self._changed)
self.saturation = QSlider()
self.saturation.setMaximum(100)
self.saturation.setOrientation(Qt.Horizontal)
self.saturation.valueChanged.connect(self._changed)
self.value = QSlider()
self.value.setMaximum(100)
self.value.setOrientation(Qt.Horizontal)
self.value.valueChanged.connect(self._changed)
layout = QGridLayout(self)
layout.addWidget(QLabel("H"))
layout.addWidget(QLabel("S"))
layout.addWidget(QLabel("V"))
layout.addWidget(self.hue, 0, 1)
layout.addWidget(self.saturation, 1, 1)
layout.addWidget(self.value, 2, 1)
def initUI(self):
searchEdit = QLineEdit()
grid = QGridLayout()
grid.setSpacing(10)
grid.addWidget(searchEdit, 1, 0)
self.list = QListView()
# Create an empty model for the list's data
model = QStandardItemModel(self.list)
for gameName, gameId in self.Games.items():
game = QStandardItem(gameName)
game.setEditable(False)
model.appendRow(game)
self.list.doubleClicked.connect(self.OnDoubleClick) # Launch Game
# Apply the model to the list view
self.list.setModel(model)
self.list.setCurrentIndex(self.list.model().index(0, 0)) # Show the window and run the app
grid.addWidget(self.list, 2, 0)
self.setLayout(grid)
self.setGeometry(300, 300, 350, 300)
self.setWindowTitle('pySteamLauncher')
self.setWindowIcon(QIcon('logo.png'))
self.show()
def __init__(self,
parent=None,
dataSetCallback=None,
defaultValue=None,
userStructClass=None,
**kwds):
super(InputWidgetSingle,
self).__init__(parent=parent,
dataSetCallback=dataSetCallback,
defaultValue=defaultValue,
userStructClass=userStructClass,
**kwds)
# from widget
self.bWidgetSet = False
self.gridLayout = QGridLayout(self)
self.gridLayout.setSpacing(1)
self.gridLayout.setContentsMargins(0, 0, 0, 0)
self.gridLayout.setObjectName("gridLayout")
self.horizontalLayout = QHBoxLayout()
self.horizontalLayout.setObjectName("horizontalLayout")
spacerItem = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout.addItem(spacerItem)
self.pbReset = QPushButton(self)
self.pbReset.setMaximumSize(QtCore.QSize(25, 25))
self.pbReset.setText("")
self.pbReset.setObjectName("pbReset")
self.pbReset.setIcon(QtGui.QIcon(":/icons/resources/reset.png"))
self.horizontalLayout.addWidget(self.pbReset)
self.pbReset.clicked.connect(self.onResetValue)
self.gridLayout.addLayout(self.horizontalLayout, 0, 0, 1, 1)
self._index = 0
def __init__(self, name, session, nrg_fr, thermo_co, size, *args,
**kwargs):
super().__init__(*args, **kwargs)
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.session = session
self.nrg_fr = nrg_fr
self.thermo_co = thermo_co
layout = QGridLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
layout.setRowStretch(0, 1)
frame = QGroupBox(name)
frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
frame_layout = QGridLayout(frame)
frame_layout.setContentsMargins(0, 0, 0, 0)
frame_layout.setRowStretch(0, 1)
self.tree = QTreeWidget()
self.tree.setColumnCount(3)
self.tree.setHeaderLabels(["energy", "frequencies", "remove"])
self.tree.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.tree.setColumnWidth(0, size[0])
self.tree.setColumnWidth(1, size[1])
self.tree.resizeColumnToContents(2)
root_item = self.tree.invisibleRootItem()
plus = QTreeWidgetItem(root_item)
plus_button = QPushButton("add molecule")
plus_button.setFlat(True)
plus_button.clicked.connect(self.add_mol_group)
plus_button2 = QPushButton("")
plus_button2.setFlat(True)
plus_button2.clicked.connect(self.add_mol_group)
self.tree.setItemWidget(plus, 0, plus_button)
self.tree.setItemWidget(plus, 1, plus_button2)
self.tree.insertTopLevelItem(1, plus)
self.add_mol_group()
frame_layout.addWidget(self.tree)
layout.addWidget(frame)
def __init__(self, *args, **kwargs):
super(FileManagerViewer, self).__init__(*args, **kwargs)
self._lyt_grid = QGridLayout()
self._toolbar = ViewerToolbar()
self._build_ui()
self._build_connections()
self._setup_ui()
def _build_ui(self):
layout = QGridLayout()
self.text = QTextBrowser()
font = QFontDatabase.systemFont(QFontDatabase.FixedFont)
self.text.setFont(font)
layout.addWidget(self.text, 0, 0)
self.ui_area.setLayout(layout)
self.manage(None)
def _build_ui(self):
layout = QGridLayout()
self.ptable = PeriodicTable(initial_elements=[self.button.text()], select_multiple=False)
self.ptable.elementSelectionChanged.connect(self.element_changed)
layout.addWidget(self.ptable)
self.ui_area.setLayout(layout)
self.manage(None)
def _build_ui(self):
layout = QGridLayout()
self.lig_table = LigandTable(include_substituents=True)
self.lig_table.table.itemSelectionChanged.connect(self.refresh_selection)
layout.addWidget(self.lig_table)
self.ui_area.setLayout(layout)
self.manage(None)
def _build_ui(self):
layout = QGridLayout()
self.ring_table = RingTable()
self.ring_table.table.itemSelectionChanged.connect(self.refresh_selection)
layout.addWidget(self.ring_table)
self.ui_area.setLayout(layout)
self.manage(None)
def __init__(self):
super().__init__()
if separate_colorbars:
if rescale_colorbars:
self.vmins = tuple(np.min(u[0]) for u in U)
self.vmaxs = tuple(np.max(u[0]) for u in U)
else:
self.vmins = tuple(np.min(u) for u in U)
self.vmaxs = tuple(np.max(u) for u in U)
else:
if rescale_colorbars:
self.vmins = (min(np.min(u[0]) for u in U),) * len(U)
self.vmaxs = (max(np.max(u[0]) for u in U),) * len(U)
else:
self.vmins = (min(np.min(u) for u in U),) * len(U)
self.vmaxs = (max(np.max(u) for u in U),) * len(U)
layout = QHBoxLayout()
plot_layout = QGridLayout()
self.colorbarwidgets = [cbar_widget(self, vmin=vmin, vmax=vmax) if cbar_widget else None
for vmin, vmax in zip(self.vmins, self.vmaxs)]
plots = [widget(self, grid, vmin=vmin, vmax=vmax, bounding_box=bounding_box, codim=codim)
for vmin, vmax in zip(self.vmins, self.vmaxs)]
if legend:
for i, plot, colorbar, l in zip(range(len(plots)), plots, self.colorbarwidgets, legend):
subplot_layout = QVBoxLayout()
caption = QLabel(l)
caption.setAlignment(Qt.AlignHCenter)
subplot_layout.addWidget(caption)
if not separate_colorbars or backend == 'matplotlib':
subplot_layout.addWidget(plot)
else:
hlayout = QHBoxLayout()
hlayout.addWidget(plot)
if colorbar:
hlayout.addWidget(colorbar)
subplot_layout.addLayout(hlayout)
plot_layout.addLayout(subplot_layout, int(i/columns), (i % columns), 1, 1)
else:
for i, plot, colorbar in zip(range(len(plots)), plots, self.colorbarwidgets):
if not separate_colorbars or backend == 'matplotlib':
plot_layout.addWidget(plot, int(i/columns), (i % columns), 1, 1)
else:
hlayout = QHBoxLayout()
hlayout.addWidget(plot)
if colorbar:
hlayout.addWidget(colorbar)
plot_layout.addLayout(hlayout, int(i/columns), (i % columns), 1, 1)
layout.addLayout(plot_layout)
if not separate_colorbars:
layout.addWidget(self.colorbarwidgets[0])
for w in self.colorbarwidgets[1:]:
w.setVisible(False)
self.setLayout(layout)
self.plots = plots
def __init__(self, parent=None, singleSelect=False):
super().__init__(parent)
layout = QGridLayout(self)
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels(
['name', 'conformers', 'conf. angle'])
self.add_subs()
for i in range(0, 3):
self.table.resizeColumnToContents(i)
self.table.horizontalHeader().setStretchLastSection(False)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.setSortingEnabled(True)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
if singleSelect:
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.filterEdit = QLineEdit()
self.filterEdit.textChanged.connect(self.apply_filter)
self.filterEdit.setClearButtonEnabled(True)
self.filter_columns = QComboBox()
self.filter_columns.addItem("name")
self.filter_columns.addItem("conformers")
self.filter_columns.addItem("conf. angle")
self.filter_columns.currentTextChanged.connect(
self.change_filter_method)
self.name_regex_option = QComboBox()
self.name_regex_option.addItem("case-insensitive")
self.name_regex_option.addItem("case-sensitive")
self.name_regex_option.currentTextChanged.connect(self.apply_filter)
self.name_regex_option.setVisible(
self.filter_columns.currentText() == "name")
layout.addWidget(self.table, 0, 0, 1, 4)
layout.addWidget(QLabel("filter based on"), 1, 0)
layout.addWidget(self.filter_columns, 1, 1)
layout.addWidget(self.name_regex_option, 1, 2)
layout.addWidget(self.filterEdit, 1, 3)
self.change_filter_method("name")
def __init__(self, settings, parent=None, description=None, pstvOnly=True):
super(ConfigDialog, self).__init__(parent)
self.setWindowTitle("Configure source")
self.layout = QGridLayout(self)
row = 0
self.widgets = {}
self.settings = settings
# Settings should be a dictionary
for name, val in settings.items():
label = QLabel(self)
label.setText(str(name))
self.layout.addWidget(label, row, 0, 1, 1)
# Check the type of each setting, and create widgets accordingly
if isinstance(val, str):
# A string of some kind
widget = QLineEdit(self)
widget.setText(val)
elif isinstance(val, list):
# A list of alternative values, first is selected
print("List: ", name)
continue
elif isinstance(val, bool):
widget = QCheckBox(self)
if val:
widget.setCheckState(Qt.CheckState.Checked)
else:
widget.setCheckState(Qt.CheckState.Unchecked)
elif isinstance(val, int):
widget = QLineEdit(self)
widget.setInputMask("9000000")
widget.setText(str(val).strip())
elif isinstance(val, float):
widget = QLineEdit(self)
if pstvOnly:
widget.setInputMask("0.000")
widget.setText(str(val).strip())
else:
print("Ignoring: " + name)
continue
widget.config = name
self.widgets[name] = widget
self.layout.addWidget(widget, row, 1, 1, 1)
row += 1
# Add OK and Cancel buttons
buttonbox = QDialogButtonBox(QDialogButtonBox.Ok
| QDialogButtonBox.Cancel)
buttonbox.accepted.connect(self.getValues)
buttonbox.rejected.connect(self.reject)
self.layout.addWidget(buttonbox, row, 1, 2, 1)
def __init__(self,
auto_resize=False,
single_row_select=True,
context_menu_callback=None,
last_column_stretch=True,
has_counters=False,
parent=None
):
QFrame.__init__(self, parent)
self._has_counters = has_counters
self.model = None
self.table_view = RowTableView(auto_resize, single_row_select, context_menu_callback, last_column_stretch)
self.table_view.doubleClicked.connect(self._double_clicked)
if has_counters:
self.counters = Counters()
self.counters.button_clicked.connect(self._counter_clicked)
self.search_bar = QLineEdit()
self.search_bar.setFixedHeight(SEARCHBAR_HEIGHT)
self.search_bar.textChanged.connect(self.set_search_text)
self.search_bar.setToolTip("Search bar")
self.auto_size_button = QPushButton('<>')
self.auto_size_button.setFixedSize(SEARCHBAR_HEIGHT, SEARCHBAR_HEIGHT)
self.auto_size_button.clicked.connect(self._auto_size_clicked)
self.auto_size_button.setToolTip("Auto size")
self.status_label = QLabel(STATUS_LABEL_MESSAGE.format(0, 0))
self.status_label.setFixedWidth(STATUS_LABEL_WIDTH)
self.progress_bar = QProgressBar()
self.progress_bar.setFormat('')
layout = QGridLayout()
layout.addWidget(self.search_bar, 0, 0, 1, 3)
layout.addWidget(self.auto_size_button, 0, 3)
if has_counters:
layout.addWidget(self.counters, 1, 0, 1, 2)
layout.addWidget(self.table_view, 1, 2, 1, 2)
else:
layout.addWidget(self.table_view, 1, 0, 1, 4)
layout.addWidget(self.status_label, 2, 0)
layout.addWidget(self.progress_bar, 2, 1, 1, 3)
layout.setColumnStretch(2, 100)
self.setLayout(layout)
def __init__(self, project_name):
self.project_name = project_name
self._app = QApplication.instance()
self._css_filepath = None
self.main_window = QWidget()
self.main_window.setWindowFlags(Qt.Tool)
self.main_window.setWindowTitle("CSS Editor - " + self.project_name)
self.variables = Variables()
self.variables.changed.connect(self._variables_changed)
self.variables.changed.connect(self._render_and_apply)
self.template = CSSTextEdit()
self.template.changed.connect(self._template_changed)
self.template.changed.connect(self._render_and_apply)
self.save = QPushButton('Save stylesheet to')
self.save.clicked.connect(self._save_stylesheet)
self.save_destination = QLineEdit()
self.save_destination.textChanged.connect(self._destination_changed)
self.splitter = QSplitter()
self.splitter.setOrientation(Qt.Vertical)
self.splitter.addWidget(self.variables)
self.splitter.addWidget(self.template)
layout = QGridLayout(self.main_window)
layout.addWidget(self.splitter, 0, 0, 1, 2)
layout.addWidget(self.save, 1, 0)
layout.addWidget(self.save_destination, 1, 1)
self.main_window.resize(800, 600)
self._project_dir = self._ensure_project_dir()
self._top_level_widgets = [
widget for widget in QApplication.topLevelWidgets() if
widget.windowTitle() != self.main_window.windowTitle()
]
self._variables = dict()
self._template = None
self._stylesheet = ""
self._app.aboutToQuit.connect(self._save_editor_state)
self._open()
self.save_destination.setText(self.css_filepath)
self.main_window.show()
def __init__(self, parent: QWidget = None):
super().__init__(parent)
self._in = QDataStream()
self.blockSize = 0
self.currentFortune = ""
self.hostLineEdit = QLineEdit("fortune")
self.getFortuneButton = QPushButton(self.tr("Get Fortune"))
self.statusLabel = QLabel(
self.tr(
"This examples requires that you run the Local Fortune Server example as well."
)
)
self.socket = QLocalSocket()
self.setWindowFlags(self.windowFlags() & ~Qt.WindowContextHelpButtonHint)
hostLabel = QLabel(self.tr("&Server name:"))
hostLabel.setBuddy(self.hostLineEdit)
self.statusLabel.setWordWrap(True)
self.getFortuneButton.setDefault(True)
quitButton = QPushButton(self.tr("Quit"))
buttonBox = QDialogButtonBox()
buttonBox.addButton(self.getFortuneButton, QDialogButtonBox.ActionRole)
buttonBox.addButton(quitButton, QDialogButtonBox.RejectRole)
self._in.setDevice(self.socket)
self._in.setVersion(QDataStream.Qt_5_10)
self.hostLineEdit.textChanged.connect(self.enableGetFortuneButton)
self.getFortuneButton.clicked.connect(self.requestNewFortune)
quitButton.clicked.connect(self.close)
self.socket.readyRead.connect(self.readFortune)
self.socket.errorOccurred.connect(self.displayError)
mainLayout = QGridLayout(self)
mainLayout.addWidget(hostLabel, 0, 0)
mainLayout.addWidget(self.hostLineEdit, 0, 1)
mainLayout.addWidget(self.statusLabel, 2, 0, 1, 2)
mainLayout.addWidget(buttonBox, 3, 0, 1, 2)
self.setWindowTitle(QGuiApplication.applicationDisplayName())
self.hostLineEdit.setFocus()
def initPenColorButtons(self):
self.colorSet = QWidget(self)
self.colorLayout = QHBoxLayout()
self.colorLayout.setSpacing(5)
self.colorLayout.setContentsMargins(5, 0, 5, 0)
self.colorSet.setLayout(self.colorLayout)
self.presentColor = QPushButton(self.colorSet)
self.presentColor.setFixedSize(self.iconWidth, self.iconHeight)
self.presentColor.setEnabled(False)
# adjust pen color
self.colorPick = QWidget(self.colorSet)
self.colorGrid = QGridLayout()
self.colorGrid.setSpacing(0)
self.colorGrid.setContentsMargins(5, 0, 5, 0)
self.colorPick.setLayout(self.colorGrid)
self.colorList = [('white', '#ffffff'), ('red', '#ff0000'),
('green', '#00ff00'), ('blue', '#0000ff'),
('cyan', '#00ffff'), ('magenta', '#ff00ff'),
('yellow', '#ffff00'), ('gray', '#a0a0a4'),
('black', '#000000'), ('darkRed', '#800000'),
('darkGreen', '#008000'), ('darkBlue', '#000080'),
('darkCyan', '#008080'), ('darkMagenta', '#800080'),
('darkYellow', '#808000'), ('darkGray', '#808080')]
self.generateButtons()
self.colorButtonGroup = QButtonGroup(self)
for button in self.colorButtons:
self.colorButtonGroup.addButton(button)
self.colorButtonGroup.buttonClicked.connect(self.colorButtonToggled)
# set the layout
tmp = 0
for x in range(0, 2):
for y in range(0, int(len(self.colorList) / 2)):
self.colorGrid.addWidget(self.colorButtons[tmp], x, y)
tmp += 1
self.colorGrid.setSpacing(0)
self.colorGrid.setContentsMargins(0, 0, 0, 0)
self.colorLayout.addWidget(self.presentColor)
self.colorLayout.addWidget(self.colorPick)
def __init__(self, name, report, parent=None):
QDialog.__init__(self, parent)
icon = self.style().standardIcon(QStyle.SP_MessageBoxCritical)
self.setWindowTitle('Error reporting')
self.setWindowIcon(icon)
try:
font = QFontDatabase().systemFont(QFontDatabase.FixedFont)
except AttributeError as e:
font = QFont()
font.setStyleHint(QFont.TypeWriter)
self.text = QPlainTextEdit()
self.text.setFont(font)
self.text.setReadOnly(True)
self.text.setLineWrapMode(QPlainTextEdit.NoWrap)
self.text.setPlainText(report)
TracebackHighlighter(self.text.document())
icon_label = QLabel()
icon_label.setPixmap(icon.pixmap(ICON_SIZE, ICON_SIZE))
label = QLabel("{} error !".format(name))
label.setFont(QFont('default', pointSize=14))
button_copy = QPushButton('Copy to clipboard')
button_copy.clicked.connect(self._copy)
layout = QGridLayout(self)
layout.addWidget(icon_label, 0, 0)
layout.addWidget(label, 0, 1)
layout.addWidget(self.text, 1, 0, 1, 2)
layout.addWidget(button_copy, 2, 0, 1, 2)
layout.setColumnStretch(1, 100)
self.setModal(True)
self.resize(600, 400)
def _build_ui(self):
layout = QGridLayout()
library_tabs = QTabWidget()
#ligand tab
ligand_tab = QWidget()
ligand_layout = QFormLayout(ligand_tab)
self.ligand_name = QLineEdit()
self.ligand_name.setText("")
self.ligand_name.setPlaceholderText("leave blank to preview")
self.ligand_name.setToolTip(
"name of ligand you are adding to your ligand library\nleave blank to open a new model with just the ligand"
)
ligand_layout.addRow("ligand name:", self.ligand_name)
ligand_key_atoms = QPushButton("set key atoms to current selection")
ligand_key_atoms.clicked.connect(self.update_key_atoms)
ligand_key_atoms.setToolTip(
"the current selection will be the key atoms for the ligand\nleave blank to automatically determine key atoms"
)
ligand_layout.addRow(ligand_key_atoms)
libadd_ligand = QPushButton("add current selection to library")
libadd_ligand.clicked.connect(self.libadd_ligand)
ligand_layout.addRow(libadd_ligand)
#substituent tab
sub_tab = QWidget()
sub_layout = QFormLayout(sub_tab)
self.sub_name = QLineEdit()
self.sub_name.setText("")
self.sub_name.setPlaceholderText("leave blank to preview")
self.sub_name.setToolTip(
"name of substituent you are adding to your substituent library\nleave blank to open a new model with just the substituent"
)
sub_layout.addRow("substituent name:", self.sub_name)
self.sub_confs = QSpinBox()
self.sub_confs.setMinimum(1)
sub_layout.addRow("number of conformers:", self.sub_confs)
self.sub_angle = QSpinBox()
self.sub_angle.setRange(0, 180)
self.sub_angle.setSingleStep(30)
sub_layout.addRow("angle between conformers:", self.sub_angle)
libadd_sub = QPushButton("add current selection to library")
libadd_sub.clicked.connect(self.libadd_substituent)
sub_layout.addRow(libadd_sub)
#ring tab
ring_tab = QWidget()
ring_layout = QFormLayout(ring_tab)
self.ring_name = QLineEdit()
self.ring_name.setText("")
self.ring_name.setPlaceholderText("leave blank to preview")
self.ring_name.setToolTip(
"name of ring you are adding to your ring library\nleave blank to open a new model with just the ring"
)
ring_layout.addRow("ring name:", self.ring_name)
libadd_ring = QPushButton("add ring with selected walk to library")
libadd_ring.clicked.connect(self.libadd_ring)
ring_layout.addRow(libadd_ring)
library_tabs.addTab(sub_tab, "substituent")
library_tabs.addTab(ring_tab, "ring")
library_tabs.addTab(ligand_tab, "ligand")
self.library_tabs = library_tabs
layout.addWidget(library_tabs)
whats_this = QLabel()
whats_this.setText(
"<a href=\"req\" style=\"text-decoration: none;\">what's this?</a>"
)
whats_this.setTextFormat(Qt.RichText)
whats_this.setTextInteractionFlags(Qt.TextBrowserInteraction)
whats_this.linkActivated.connect(self.open_link)
whats_this.setToolTip(
"click for more information about AaronTools libraries")
layout.addWidget(whats_this)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QGridLayout()
tab_widget = QTabWidget()
layout.addWidget(tab_widget)
structure_widget = QWidget()
structure_layout = QGridLayout(structure_widget)
tab_widget.addTab(structure_widget, "structure")
self.structure_source = QComboBox()
self.structure_source.addItems(
["AARON template", "file", "coordination complexes", "SMILES"])
structure_layout.addWidget(QLabel("structure source:"), 0, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
structure_layout.addWidget(
self.structure_source,
0,
1,
1,
1,
)
open_button = QPushButton("open")
open_button.clicked.connect(self.open_template)
structure_layout.addWidget(
open_button,
0,
2,
1,
1,
)
# SMILES options
self.smiles_options = QGroupBox("SMILES options")
smiles_layout = QFormLayout(self.smiles_options)
structure_layout.addWidget(self.smiles_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
self.smiles_line = QLineEdit()
smiles_layout.addRow("SMILES string:", self.smiles_line)
self.smiles_options.setVisible(
self.structure_source.currentText() == "SMILES")
self.structure_source.currentTextChanged.connect(
lambda text: self.smiles_options.setVisible(text == "SMILES"))
# coordination complexes options
self.coord_comp_options = QGroupBox("Coordination Complex Options")
coord_layout = QFormLayout(self.coord_comp_options)
structure_layout.addWidget(self.coord_comp_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
create_coord_items(self,
coord_layout,
allow_minimization=False,
default_ele="Pd")
self.coord_comp_options.setVisible(
self.structure_source.currentText() == "coordination complexes")
self.structure_source.currentTextChanged.connect(
lambda text: self.coord_comp_options.setVisible(
text == "coordination complexes"))
# aaron template options
self.aaron_options = QGroupBox("AARON template structures")
aaron_layout = QFormLayout(self.aaron_options)
structure_layout.addWidget(self.aaron_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
self.aaron_options.setVisible(
self.structure_source.currentText() == "AARON template")
self.structure_source.currentTextChanged.connect(
lambda text: self.aaron_options.setVisible(text == "AARON template"
))
# file options
self.file_options = QGroupBox("single file options")
file_layout = QFormLayout(self.file_options)
structure_layout.addWidget(self.file_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
file_widget = QWidget()
file_browse_layout = QGridLayout(file_widget)
self.template_file = QLineEdit()
file_browse_layout.addWidget(self.template_file, 0, 0, 1, 1,
Qt.AlignCenter)
browse_button = QPushButton("browse...")
# browse_button.clicked.connect(self.browse_file_template)
file_browse_layout.addWidget(browse_button, 0, 1, 1, 1, Qt.AlignCenter)
file_browse_layout.setColumnStretch(0, 1)
file_browse_layout.setColumnStretch(1, 0)
margins = file_browse_layout.contentsMargins()
file_browse_layout.setContentsMargins(margins.left(), 0,
margins.right(), 0)
file_layout.addRow("file:", file_widget)
self.file_options.setVisible(
self.structure_source.currentText() == "file")
self.structure_source.currentTextChanged.connect(
lambda text: self.file_options.setVisible(text == "file"))
self.optimize_template = QCheckBox()
self.optimize_template.setCheckState(Qt.Checked)
structure_layout.addWidget(
QLabel("optimize template:"),
2,
0,
1,
1,
Qt.AlignLeft | Qt.AlignVCenter,
)
structure_layout.addWidget(
self.optimize_template,
2,
1,
1,
2,
Qt.AlignLeft | Qt.AlignVCenter,
)
structure_layout.setColumnStretch(0, 0)
structure_layout.setColumnStretch(1, 1)
structure_layout.setColumnStretch(2, 0)
# structure changes
changes_widget = QWidget()
changes_layout = QGridLayout(changes_widget)
tab_widget.addTab(changes_widget, "changes")
# HPC settings
hpc_widget = QWidget()
hpc_layout = QGridLayout(hpc_widget)
tab_widget.addTab(hpc_widget, "HPC")
# theory settings
theory_widget = QWidget()
theory_layout = QGridLayout(theory_widget)
tab_widget.addTab(theory_widget, "theory")
# results
results_widget = QWidget()
results_layout = QGridLayout(results_widget)
tab_widget.addTab(results_widget, "results")
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QGridLayout()
tabs = QTabWidget()
layout.addWidget(tabs)
ts_bond_tab = QWidget()
ts_options = QFormLayout(ts_bond_tab)
self.tsbond_color = ColorButton(has_alpha_channel=False,
max_size=(16, 16))
self.tsbond_color.set_color(self.settings.tsbond_color)
ts_options.addRow("color:", self.tsbond_color)
self.tsbond_transparency = QSpinBox()
self.tsbond_transparency.setRange(1, 99)
self.tsbond_transparency.setValue(self.settings.tsbond_transparency)
self.tsbond_transparency.setSuffix("%")
ts_options.addRow("transparency:", self.tsbond_transparency)
self.tsbond_radius = QDoubleSpinBox()
self.tsbond_radius.setRange(0.01, 1)
self.tsbond_radius.setDecimals(3)
self.tsbond_radius.setSingleStep(0.005)
self.tsbond_radius.setSuffix(" \u212B")
self.tsbond_radius.setValue(self.settings.tsbond_radius)
ts_options.addRow("radius:", self.tsbond_radius)
draw_tsbonds = QPushButton("draw TS bonds on selected atoms/bonds")
draw_tsbonds.clicked.connect(self.run_tsbond)
ts_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_tsbonds = QPushButton("erase selected TS bonds")
erase_tsbonds.clicked.connect(self.run_erase_tsbond)
ts_options.addRow(erase_tsbonds)
self.erase_tsbonds = erase_tsbonds
bond_tab = QWidget()
bond_options = QFormLayout(bond_tab)
self.bond_halfbond = QCheckBox()
self.bond_halfbond.setChecked(self.settings.bond_halfbond)
self.bond_halfbond.setToolTip(
"each half of the bond will be colored according to the atom's color"
)
bond_options.addRow("half-bond:", self.bond_halfbond)
self.bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.bond_color.set_color(self.settings.bond_color)
self.bond_color.setEnabled(
self.bond_halfbond.checkState() != Qt.Checked)
self.bond_halfbond.stateChanged.connect(
lambda state, widget=self.bond_color: self.bond_color.setEnabled(
state != Qt.Checked))
bond_options.addRow("color:", self.bond_color)
self.bond_radius = QDoubleSpinBox()
self.bond_radius.setRange(0.01, 1)
self.bond_radius.setDecimals(3)
self.bond_radius.setSingleStep(0.005)
self.bond_radius.setSuffix(" \u212B")
self.bond_radius.setValue(self.settings.bond_radius)
bond_options.addRow("radius:", self.bond_radius)
draw_tsbonds = QPushButton("draw bond between selected atoms")
draw_tsbonds.clicked.connect(self.run_bond)
bond_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_bonds = QPushButton("erase selected bonds")
erase_bonds.clicked.connect(
lambda *, ses=self.session: run(ses, "delete bonds sel"))
bond_options.addRow(erase_bonds)
self.erase_bonds = erase_bonds
hbond_tab = QWidget()
hbond_options = QFormLayout(hbond_tab)
self.hbond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.hbond_color.set_color(self.settings.hbond_color)
hbond_options.addRow("color:", self.hbond_color)
self.hbond_radius = QDoubleSpinBox()
self.hbond_radius.setDecimals(3)
self.hbond_radius.setSuffix(" \u212B")
self.hbond_radius.setValue(self.settings.hbond_radius)
hbond_options.addRow("radius:", self.hbond_radius)
self.hbond_dashes = QSpinBox()
self.hbond_dashes.setRange(0, 28)
self.hbond_dashes.setSingleStep(2)
self.hbond_radius.setSingleStep(0.005)
self.hbond_dashes.setValue(self.settings.hbond_dashes)
hbond_options.addRow("dashes:", self.hbond_dashes)
draw_hbonds = QPushButton("draw H-bonds")
draw_hbonds.clicked.connect(self.run_hbond)
hbond_options.addRow(draw_hbonds)
self.draw_hbonds = draw_hbonds
erase_hbonds = QPushButton("erase all H-bonds")
erase_hbonds.clicked.connect(
lambda *, ses=self.session: run(ses, "~hbonds"))
hbond_options.addRow(erase_hbonds)
self.erase_hbonds = erase_hbonds
tm_bond_tab = QWidget()
tm_bond_options = QFormLayout(tm_bond_tab)
self.tm_bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.tm_bond_color.set_color(self.settings.tm_bond_color)
tm_bond_options.addRow("color:", self.tm_bond_color)
self.tm_bond_radius = QDoubleSpinBox()
self.tm_bond_radius.setDecimals(3)
self.tm_bond_radius.setSuffix(" \u212B")
self.tm_bond_radius.setValue(self.settings.tm_bond_radius)
tm_bond_options.addRow("radius:", self.tm_bond_radius)
self.tm_bond_dashes = QSpinBox()
self.tm_bond_dashes.setRange(0, 28)
self.tm_bond_dashes.setSingleStep(2)
self.tm_bond_radius.setSingleStep(0.005)
self.tm_bond_dashes.setValue(self.settings.tm_bond_dashes)
tm_bond_options.addRow("dashes:", self.tm_bond_dashes)
draw_tm_bonds = QPushButton("draw metal coordination bonds")
draw_tm_bonds.clicked.connect(self.run_tm_bond)
tm_bond_options.addRow(draw_tm_bonds)
self.draw_tm_bonds = draw_tm_bonds
erase_tm_bonds = QPushButton("erase all metal coordination bonds")
erase_tm_bonds.clicked.connect(self.del_tm_bond)
tm_bond_options.addRow(erase_tm_bonds)
self.erase_tm_bonds = erase_tm_bonds
bond_length_tab = QWidget()
bond_length_layout = QFormLayout(bond_length_tab)
self.bond_distance = QDoubleSpinBox()
self.bond_distance.setRange(0.5, 10.0)
self.bond_distance.setSingleStep(0.05)
self.bond_distance.setValue(1.51)
self.bond_distance.setSuffix(" \u212B")
bond_length_layout.addRow("bond length:", self.bond_distance)
self.move_fragment = QComboBox()
self.move_fragment.addItems(["both", "smaller", "larger"])
bond_length_layout.addRow("move side:", self.move_fragment)
bond_lookup = QGroupBox("bond length lookup:")
bond_lookup_layout = QGridLayout(bond_lookup)
bond_lookup_layout.addWidget(
QLabel("elements:"),
0,
0,
)
self.ele1 = ElementButton("C", single_state=True)
self.ele1.clicked.connect(
lambda *args, button=self.ele1: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele1, 0, 1,
Qt.AlignRight | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("-"), 0, 2,
Qt.AlignHCenter | Qt.AlignVCenter)
self.ele2 = ElementButton("C", single_state=True)
self.ele2.clicked.connect(
lambda *args, button=self.ele2: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele2, 0, 3,
Qt.AlignLeft | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("bond order:"), 1, 0)
self.bond_order = BondOrderSpinBox()
self.bond_order.setRange(1., 3.)
self.bond_order.setValue(1)
self.bond_order.setSingleStep(0.5)
self.bond_order.setDecimals(1)
self.bond_order.valueChanged.connect(self.check_bond_lengths)
bond_lookup_layout.addWidget(self.bond_order, 1, 1, 1, 3)
bond_lookup_layout.setColumnStretch(0, 0)
bond_lookup_layout.setColumnStretch(1, 0)
bond_lookup_layout.setColumnStretch(2, 0)
bond_lookup_layout.setColumnStretch(3, 1)
bond_length_layout.addRow(bond_lookup)
self.status = QStatusBar()
self.status.setSizeGripEnabled(False)
bond_lookup_layout.addWidget(self.status, 2, 0, 1, 4)
self.do_bond_change = QPushButton("change selected bond lengths")
self.do_bond_change.clicked.connect(self.change_bond_length)
bond_length_layout.addRow(self.do_bond_change)
tabs.addTab(bond_tab, "covalent bonds")
tabs.addTab(ts_bond_tab, "TS bonds")
tabs.addTab(hbond_tab, "H-bonds")
tabs.addTab(tm_bond_tab, "coordination bonds")
tabs.addTab(bond_length_tab, "bond length")
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def fill_tree(self, trigger_name=None, trigger_job=None):
item_stack = [self.tree.invisibleRootItem()]
self.tree.clear()
jobs = self.session.seqcrow_job_manager.jobs
for job in jobs:
name = job.name
parent = item_stack[0]
item = QTreeWidgetItem(parent)
item_stack.append(item)
item.setData(self.NAME_COL, Qt.DisplayRole, job)
item.setText(self.NAME_COL, name)
if isinstance(job, LocalJob):
if job.killed:
item.setText(self.STATUS_COL, "killed")
del_job_widget = QWidget()
del_job_layout = QGridLayout(del_job_widget)
del_job = QPushButton()
del_job.clicked.connect(
lambda *args, job=job: self.remove_job(job))
del_job.setIcon(
QIcon(del_job_widget.style().standardIcon(
QStyle.SP_DialogDiscardButton)))
del_job.setFlat(True)
del_job_layout.addWidget(del_job, 0, 0, 1, 1,
Qt.AlignHCenter)
del_job_layout.setColumnStretch(0, 1)
del_job_layout.setContentsMargins(0, 0, 0, 0)
self.tree.setItemWidget(item, self.DEL_COL, del_job_widget)
elif job.isRunning():
if job in self.session.seqcrow_job_manager.unknown_status_jobs:
unk_widget = QWidget()
unk_layout = QGridLayout(unk_widget)
unk = QPushButton()
unk.setIcon(
QIcon(unk_widget.style().standardIcon(
QStyle.SP_MessageBoxQuestion)))
unk.setFlat(True)
unk.clicked.connect(lambda *args, job=job: self.
show_ask_if_running(job))
unk_layout.addWidget(unk, 0, 0, 1, 1, Qt.AlignHCenter)
unk_layout.setColumnStretch(0, 1)
unk_layout.setContentsMargins(0, 0, 0, 0)
self.tree.setItemWidget(item, self.STATUS_COL,
unk_widget)
else:
item.setText(self.STATUS_COL, "running")
kill_widget = QWidget()
kill_layout = QGridLayout(kill_widget)
kill = QPushButton()
kill.setIcon(
QIcon(kill_widget.style().standardIcon(
QStyle.SP_DialogCancelButton)))
kill.setFlat(True)
kill.clicked.connect(lambda *args, job=job: job.kill())
kill.clicked.connect(
lambda *args, session=self.session: session.
seqcrow_job_manager.triggers.activate_trigger(
JOB_QUEUED, "resume"))
kill_layout.addWidget(kill, 0, 0, 1, 1, Qt.AlignLeft)
kill_layout.setColumnStretch(0, 0)
kill_layout.setContentsMargins(0, 0, 0, 0)
self.tree.setItemWidget(item, self.KILL_COL,
kill_widget)
elif job.isFinished():
if not job.error:
item.setText(self.STATUS_COL, "finished")
else:
error_widget = QWidget()
error_layout = QGridLayout(error_widget)
error = QPushButton()
error.setIcon(
QIcon(error_widget.style().standardIcon(
QStyle.SP_MessageBoxWarning)))
error.setFlat(True)
error.setToolTip(
"job did not finish without errors or output file cannot be found"
)
error_layout.addWidget(error, 0, 0, 1, 1,
Qt.AlignHCenter)
error_layout.setColumnStretch(0, 1)
error_layout.setContentsMargins(0, 0, 0, 0)
self.tree.setItemWidget(item, self.STATUS_COL,
error_widget)
del_job_widget = QWidget()
del_job_layout = QGridLayout(del_job_widget)
del_job = QPushButton()
del_job.clicked.connect(
lambda *args, job=job: self.remove_job(job))
del_job.setIcon(
QIcon(del_job_widget.style().standardIcon(
QStyle.SP_DialogDiscardButton)))
del_job.setFlat(True)
del_job_layout.addWidget(del_job, 0, 0, 1, 1,
Qt.AlignHCenter)
del_job_layout.setColumnStretch(0, 1)
del_job_layout.setContentsMargins(0, 0, 0, 0)
self.tree.setItemWidget(item, self.DEL_COL, del_job_widget)
else:
item.setText(self.STATUS_COL, "queued")
priority_widget = QWidget()
priority_layout = QGridLayout(priority_widget)
inc_priority = QPushButton()
inc_priority.setIcon(
QIcon(priority_widget.style().standardIcon(
QStyle.SP_ArrowUp)))
inc_priority.setFlat(True)
inc_priority.clicked.connect(
lambda *args, job=job: self.session.seqcrow_job_manager
.increase_priotity(job))
priority_layout.addWidget(inc_priority, 0, 0, 1, 1,
Qt.AlignRight)
dec_priority = QPushButton()
dec_priority.setIcon(
QIcon(priority_widget.style().standardIcon(
QStyle.SP_ArrowDown)))
dec_priority.setFlat(True)
dec_priority.clicked.connect(
lambda *args, job=job: self.session.seqcrow_job_manager
.decrease_priotity(job))
priority_layout.addWidget(dec_priority, 0, 1, 1, 1,
Qt.AlignLeft)
priority_layout.setColumnStretch(0, 1)
priority_layout.setColumnStretch(1, 1)
priority_layout.setContentsMargins(0, 0, 0, 0)
self.tree.setItemWidget(item, self.CHANGE_PRIORITY,
priority_widget)
kill_widget = QWidget()
kill_layout = QGridLayout(kill_widget)
kill = QPushButton()
kill.setIcon(
QIcon(kill_widget.style().standardIcon(
QStyle.SP_DialogCancelButton)))
kill.setFlat(True)
kill.clicked.connect(lambda *args, job=job: job.kill())
kill.clicked.connect(
lambda *args, session=self.session: session.
seqcrow_job_manager.triggers.activate_trigger(
JOB_QUEUED, "resume"))
kill_layout.addWidget(kill, 0, 0, 1, 1, Qt.AlignLeft)
kill_layout.setColumnStretch(0, 0)
kill_layout.setContentsMargins(0, 0, 0, 0)
self.tree.setItemWidget(item, self.KILL_COL, kill_widget)
item.setText(self.SERVER_COL, "local")
if job.scratch_dir and os.path.exists(job.scratch_dir):
browse_widget = QWidget()
browse_layout = QGridLayout(browse_widget)
browse = QPushButton()
browse.clicked.connect(
lambda *args, job=job: self.browse_local(job))
browse.setIcon(
QIcon(browse_widget.style().standardIcon(
QStyle.SP_DirOpenIcon)))
browse.setFlat(True)
browse_layout.addWidget(browse, 0, 0, 1, 1, Qt.AlignLeft)
browse_layout.setColumnStretch(0, 1)
browse_layout.setContentsMargins(0, 0, 0, 0)
self.tree.setItemWidget(item, self.BROWSE_COL,
browse_widget)
self.tree.expandItem(item)
self.tree.resizeColumnToContents(self.STATUS_COL)
self.tree.resizeColumnToContents(self.SERVER_COL)
self.tree.resizeColumnToContents(self.CHANGE_PRIORITY)
self.tree.resizeColumnToContents(self.KILL_COL)
self.tree.resizeColumnToContents(self.DEL_COL)
self.tree.resizeColumnToContents(self.BROWSE_COL)
def _build_ui(self):
layout = QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
self.tree = QTreeWidget()
self.tree.setSelectionMode(QTreeWidget.ExtendedSelection)
self.tree.setHeaderLabels([
"name", "status", "server", "prioritize", "kill", "delete",
"browse"
])
self.tree.setUniformRowHeights(True)
self.tree.setColumnWidth(0, 150)
layout.addWidget(self.tree, 0, 0, 6, 1, Qt.AlignTop)
row = 0
pause_button = QPushButton(
"pause new jobs"
if not self.session.seqcrow_job_manager.paused else "resume jobs")
pause_button.setCheckable(True)
pause_button.clicked.connect(lambda check: pause_button.setText(
"pause new jobs" if not check else "resume jobs"))
pause_button.setChecked(self.session.seqcrow_job_manager.paused)
pause_button.clicked.connect(self.pause_queue)
layout.addWidget(pause_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
open_button = QPushButton("open structure")
open_button.clicked.connect(self.open_jobs)
layout.addWidget(open_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
log_button = QPushButton("log")
log_button.clicked.connect(self.open_log)
layout.addWidget(log_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
output_button = QPushButton("raw output")
output_button.clicked.connect(self.open_output)
layout.addWidget(output_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
refresh_button = QToolButton()
refresh_button.setSizePolicy(QSizePolicy.Fixed,
QSizePolicy.MinimumExpanding)
refresh_button.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
refresh_button.setIcon(
QIcon(refresh_button.style().standardIcon(
QStyle.SP_BrowserReload)))
refresh_button.setText('check jobs')
refresh_button.clicked.connect(
lambda *args: self.session.seqcrow_job_manager.triggers.
activate_trigger(JOB_QUEUED, "refresh"))
layout.addWidget(refresh_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
for i in range(0, row - 1):
layout.setRowStretch(i, 0)
layout.setRowStretch(row - 1, 1)
layout.setColumnStretch(0, 1)
layout.setColumnStretch(1, 0)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
#each group has an empty widget at the bottom so they resize the way I want while also having the
#labels where I want them
layout = QGridLayout()
self.tab_widget = QTabWidget()
layout.addWidget(self.tab_widget)
#layout for absolute thermo stuff
absolute_widget = QWidget()
absolute_layout = QGridLayout(absolute_widget)
#box for sp
sp_area_widget = QGroupBox("Single-point")
sp_layout = QFormLayout(sp_area_widget)
self.sp_selector = FilereaderComboBox(self.session,
otherItems=['energy'])
self.sp_selector.currentIndexChanged.connect(self.set_sp)
sp_layout.addRow(self.sp_selector)
self.sp_table = QTableWidget()
self.sp_table.setColumnCount(3)
self.sp_table.setShowGrid(False)
self.sp_table.horizontalHeader().hide()
self.sp_table.verticalHeader().hide()
self.sp_table.setFrameShape(QTableWidget.NoFrame)
self.sp_table.setSelectionMode(QTableWidget.NoSelection)
self.sp_table.insertRow(0)
sp_layout.addRow(self.sp_table)
#box for thermo
therm_area_widget = QGroupBox("Thermal corrections")
thermo_layout = QFormLayout(therm_area_widget)
self.thermo_selector = FilereaderComboBox(self.session,
otherItems=['frequency'])
self.thermo_selector.currentIndexChanged.connect(self.set_thermo_mdl)
thermo_layout.addRow(self.thermo_selector)
self.temperature_line = QDoubleSpinBox()
self.temperature_line.setMaximum(2**31 - 1)
self.temperature_line.setValue(298.15)
self.temperature_line.setSingleStep(10)
self.temperature_line.setSuffix(" K")
self.temperature_line.setMinimum(0)
self.temperature_line.valueChanged.connect(self.set_thermo)
thermo_layout.addRow("T =", self.temperature_line)
self.v0_edit = QDoubleSpinBox()
self.v0_edit.setMaximum(4000)
self.v0_edit.setValue(self.settings.w0)
self.v0_edit.setSingleStep(25)
self.v0_edit.setSuffix(" cm\u207b\u00b9")
self.v0_edit.valueChanged.connect(self.set_thermo)
self.v0_edit.setMinimum(0)
self.v0_edit.setToolTip(
"frequency parameter for quasi treatments of entropy")
thermo_layout.addRow("𝜔<sub>0</sub> =", self.v0_edit)
self.thermo_table = QTableWidget()
self.thermo_table.setColumnCount(3)
self.thermo_table.setShowGrid(False)
self.thermo_table.horizontalHeader().hide()
self.thermo_table.verticalHeader().hide()
self.thermo_table.setFrameShape(QTableWidget.NoFrame)
self.thermo_table.setSelectionMode(QTableWidget.NoSelection)
thermo_layout.addRow(self.thermo_table)
# for for total
sum_area_widget = QGroupBox("Thermochemistry")
sum_layout = QFormLayout(sum_area_widget)
self.sum_table = QTableWidget()
self.sum_table.setColumnCount(3)
self.sum_table.setShowGrid(False)
self.sum_table.horizontalHeader().hide()
self.sum_table.verticalHeader().hide()
self.sum_table.setFrameShape(QTableWidget.NoFrame)
self.sum_table.setSelectionMode(QTableWidget.NoSelection)
sum_layout.addRow(self.sum_table)
splitter = QSplitter(Qt.Horizontal)
splitter.setChildrenCollapsible(False)
splitter.addWidget(sp_area_widget)
splitter.addWidget(therm_area_widget)
splitter.addWidget(sum_area_widget)
absolute_layout.addWidget(splitter)
self.status = QStatusBar()
self.status.setSizeGripEnabled(False)
self.status.setStyleSheet("color: red")
absolute_layout.addWidget(self.status, 1, 0, 1, 1, Qt.AlignTop)
self.tab_widget.addTab(absolute_widget, "absolute")
relative_widget = QWidget()
relative_layout = QGridLayout(relative_widget)
size = [self.settings.ref_col_1, self.settings.ref_col_2]
self.ref_group = ThermoGroup("reference group", self.session,
self.nrg_fr, self.thermo_co, size)
self.ref_group.changes.connect(self.calc_relative_thermo)
relative_layout.addWidget(self.ref_group, 0, 0, 1, 3, Qt.AlignTop)
size = [self.settings.other_col_1, self.settings.other_col_2]
self.other_group = ThermoGroup("other group", self.session,
self.nrg_fr, self.thermo_co, size)
self.other_group.changes.connect(self.calc_relative_thermo)
relative_layout.addWidget(self.other_group, 0, 3, 1, 3, Qt.AlignTop)
self.relative_temperature = QDoubleSpinBox()
self.relative_temperature.setMaximum(2**31 - 1)
self.relative_temperature.setValue(self.settings.rel_temp)
self.relative_temperature.setSingleStep(10)
self.relative_temperature.setSuffix(" K")
self.relative_temperature.setMinimum(0)
self.relative_temperature.valueChanged.connect(
self.calc_relative_thermo)
relative_layout.addWidget(QLabel("T ="), 1, 0, 1, 1,
Qt.AlignRight | Qt.AlignVCenter)
relative_layout.addWidget(self.relative_temperature, 1, 1, 1, 5,
Qt.AlignLeft | Qt.AlignVCenter)
self.relative_v0 = QDoubleSpinBox()
self.relative_v0.setMaximum(2**31 - 1)
self.relative_v0.setValue(self.settings.w0)
self.relative_v0.setSingleStep(25)
self.relative_v0.setSuffix(" cm\u207b\u00b9")
self.relative_v0.setMinimum(0)
self.relative_v0.setToolTip(
"frequency parameter for quasi treatments of entropy")
self.relative_v0.valueChanged.connect(self.calc_relative_thermo)
relative_layout.addWidget(QLabel("𝜔<sub>0</sub> ="), 2, 0, 1, 1,
Qt.AlignRight | Qt.AlignVCenter)
relative_layout.addWidget(self.relative_v0, 2, 1, 1, 5,
Qt.AlignLeft | Qt.AlignVCenter)
relative_layout.addWidget(
QLabel("Boltzmann-weighted relative energies in kcal/mol:"), 3, 0,
1, 6, Qt.AlignVCenter | Qt.AlignLeft)
self.relative_table = QTextBrowser()
self.relative_table.setMaximumHeight(
4 * self.relative_table.fontMetrics().boundingRect("Q").height())
relative_layout.addWidget(self.relative_table, 4, 0, 1, 6, Qt.AlignTop)
relative_layout.setRowStretch(0, 1)
relative_layout.setRowStretch(1, 0)
relative_layout.setRowStretch(2, 0)
relative_layout.setRowStretch(3, 0)
relative_layout.setRowStretch(4, 0)
self.tab_widget.addTab(relative_widget, "relative")
#menu stuff
menu = QMenuBar()
export = menu.addMenu("&Export")
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
self.copy = copy
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QGridLayout()
tabs = QTabWidget()
calc_widget = QWidget()
calc_layout = QFormLayout(calc_widget)
settings_widget = QWidget()
settings_layout = QFormLayout(settings_widget)
steric_map_widget = QWidget()
steric_layout = QFormLayout(steric_map_widget)
cutout_widget = QWidget()
vol_cutout_layout = QFormLayout(cutout_widget)
layout.addWidget(tabs)
tabs.addTab(calc_widget, "calculation")
tabs.addTab(settings_widget, "settings")
tabs.addTab(steric_map_widget, "steric map")
tabs.addTab(cutout_widget, "volume cutout")
self.radii_option = QComboBox()
self.radii_option.addItems(["Bondi", "UMN"])
ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
self.radii_option.setCurrentIndex(ndx)
settings_layout.addRow("radii:", self.radii_option)
self.scale = QDoubleSpinBox()
self.scale.setValue(self.settings.vdw_scale)
self.scale.setSingleStep(0.01)
self.scale.setRange(1., 1.5)
settings_layout.addRow("VDW scale:", self.scale)
set_ligand_atoms = QPushButton("set ligands to current selection")
set_ligand_atoms.clicked.connect(self.set_ligand_atoms)
set_ligand_atoms.setToolTip(
"specify atoms to use in calculation\n" +
"by default, all atoms will be used unless a single center is specified\n"
+
"in the case of a single center, all atoms except the center is used"
)
calc_layout.addRow(set_ligand_atoms)
self.set_ligand_atoms = set_ligand_atoms
self.radius = QDoubleSpinBox()
self.radius.setValue(self.settings.center_radius)
self.radius.setSuffix(" \u212B")
self.radius.setDecimals(1)
self.radius.setSingleStep(0.1)
self.radius.setRange(1., 15.)
settings_layout.addRow("radius around center:", self.radius)
self.method = QComboBox()
self.method.addItems(["Lebedev", "Monte-Carlo"])
self.method.setToolTip("Lebedev: deterministic method\n" +
"Monte-Carlo: non-deterministic method")
ndx = self.method.findText(self.settings.method, Qt.MatchExactly)
self.method.setCurrentIndex(ndx)
settings_layout.addRow("integration method:", self.method)
leb_widget = QWidget()
leb_layout = QFormLayout(leb_widget)
leb_layout.setContentsMargins(0, 0, 0, 0)
self.radial_points = QComboBox()
self.radial_points.addItems(["20", "32", "64", "75", "99", "127"])
self.radial_points.setToolTip(
"more radial points will give more accurate results, but integration will take longer"
)
ndx = self.radial_points.findText(self.settings.radial_points,
Qt.MatchExactly)
self.radial_points.setCurrentIndex(ndx)
leb_layout.addRow("radial points:", self.radial_points)
self.angular_points = QComboBox()
self.angular_points.addItems([
"110", "194", "302", "590", "974", "1454", "2030", "2702", "5810"
])
self.angular_points.setToolTip(
"more angular points will give more accurate results, but integration will take longer"
)
ndx = self.angular_points.findText(self.settings.angular_points,
Qt.MatchExactly)
self.angular_points.setCurrentIndex(ndx)
leb_layout.addRow("angular points:", self.angular_points)
settings_layout.addRow(leb_widget)
mc_widget = QWidget()
mc_layout = QFormLayout(mc_widget)
mc_layout.setContentsMargins(0, 0, 0, 0)
self.min_iter = QSpinBox()
self.min_iter.setValue(self.settings.minimum_iterations)
self.min_iter.setRange(0, 10000)
self.min_iter.setToolTip(
"each iteration is 3000 points\n" +
"iterations continue until convergence criteria are met")
mc_layout.addRow("minimum interations:", self.min_iter)
settings_layout.addRow(mc_widget)
if self.settings.method == "Lebedev":
mc_widget.setVisible(False)
elif self.settings.method == "Monte-Carlo":
leb_widget.setVisible(False)
self.report_component = QComboBox()
self.report_component.addItems(["total", "quadrants", "octants"])
ndx = self.report_component.findText(self.settings.report_component,
Qt.MatchExactly)
self.report_component.setCurrentIndex(ndx)
settings_layout.addRow("report volume:", self.report_component)
self.use_scene = QCheckBox()
self.use_scene.setChecked(self.settings.use_scene)
self.use_scene.setToolTip(
"quadrants/octants will use the orientation the molecule is displayed in"
)
settings_layout.addRow("use display orientation:", self.use_scene)
self.method.currentTextChanged.connect(
lambda text, widget=leb_widget: widget.setVisible(text == "Lebedev"
))
self.method.currentTextChanged.connect(
lambda text, widget=mc_widget: widget.setVisible(text ==
"Monte-Carlo"))
self.use_centroid = QCheckBox()
self.use_centroid.setChecked(self.settings.use_centroid)
self.use_centroid.setToolTip(
"place the center between selected atoms\n" +
"might be useful for polydentate ligands")
calc_layout.addRow("use centroid of centers:", self.use_centroid)
self.steric_map = QCheckBox()
self.steric_map.setChecked(self.settings.steric_map)
self.steric_map.setToolTip(
"produce a 2D projection of steric bulk\ncauses buried volume to be reported for individual quadrants"
)
steric_layout.addRow("create steric map:", self.steric_map)
self.num_pts = QSpinBox()
self.num_pts.setRange(25, 250)
self.num_pts.setValue(self.settings.num_pts)
self.num_pts.setToolTip("number of points along x and y axes")
steric_layout.addRow("number of points:", self.num_pts)
self.include_vbur = QCheckBox()
self.include_vbur.setChecked(self.settings.include_vbur)
steric_layout.addRow("label quadrants with %V<sub>bur</sub>",
self.include_vbur)
self.map_shape = QComboBox()
self.map_shape.addItems(["circle", "square"])
ndx = self.map_shape.findText(self.settings.map_shape, Qt.MatchExactly)
self.map_shape.setCurrentIndex(ndx)
steric_layout.addRow("map shape:", self.map_shape)
self.auto_minmax = QCheckBox()
self.auto_minmax.setChecked(self.settings.auto_minmax)
steric_layout.addRow("automatic min. and max.:", self.auto_minmax)
self.map_min = QDoubleSpinBox()
self.map_min.setRange(-15., 0.)
self.map_min.setSuffix(" \u212B")
self.map_min.setSingleStep(0.1)
self.map_min.setValue(self.settings.map_min)
steric_layout.addRow("minimum value:", self.map_min)
self.map_max = QDoubleSpinBox()
self.map_max.setRange(0., 15.)
self.map_max.setSuffix(" \u212B")
self.map_max.setSingleStep(0.1)
self.map_max.setValue(self.settings.map_max)
steric_layout.addRow("maximum value:", self.map_max)
self.num_pts.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.num_pts: widget.setEnabled(state == Qt.
Checked))
self.include_vbur.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.include_vbur: widget.setEnabled(
state == Qt.Checked))
self.map_shape.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_shape: widget.setEnabled(state == Qt.
Checked))
self.auto_minmax.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.auto_minmax: widget.setEnabled(
state == Qt.Checked))
self.map_min.setEnabled(not self.settings.auto_minmax
and self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_min, widget2=self.auto_minmax: widget
.setEnabled(state == Qt.Checked and not widget2.isChecked()))
self.auto_minmax.stateChanged.connect(
lambda state, widget=self.map_min, widget2=self.steric_map: widget.
setEnabled(not state == Qt.Checked and widget2.isChecked()))
self.map_max.setEnabled(not self.settings.auto_minmax
and self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_max, widget2=self.auto_minmax: widget
.setEnabled(state == Qt.Checked and not widget2.isChecked()))
self.auto_minmax.stateChanged.connect(
lambda state, widget=self.map_max, widget2=self.steric_map: widget.
setEnabled(not state == Qt.Checked and widget2.isChecked()))
self.display_cutout = QComboBox()
self.display_cutout.addItems(["no", "free", "buried"])
ndx = self.display_cutout.findText(self.settings.display_cutout,
Qt.MatchExactly)
self.display_cutout.setCurrentIndex(ndx)
self.display_cutout.setToolTip("show free or buried volume")
vol_cutout_layout.addRow("display volume:", self.display_cutout)
self.point_spacing = QDoubleSpinBox()
self.point_spacing.setDecimals(3)
self.point_spacing.setRange(0.01, 0.5)
self.point_spacing.setSingleStep(0.005)
self.point_spacing.setSuffix(" \u212B")
self.point_spacing.setValue(self.settings.point_spacing)
self.point_spacing.setToolTip(
"distance between points on cutout\n" +
"smaller spacing will narrow gaps, but increase time to create the cutout"
)
vol_cutout_layout.addRow("point spacing:", self.point_spacing)
self.intersection_scale = QDoubleSpinBox()
self.intersection_scale.setDecimals(2)
self.intersection_scale.setRange(1., 10.)
self.intersection_scale.setSingleStep(0.5)
self.intersection_scale.setSuffix("x")
self.intersection_scale.setToolTip(
"relative density of points where VDW radii intersect\n" +
"higher density will narrow gaps, but increase time to create cutout"
)
self.intersection_scale.setValue(self.settings.intersection_scale)
vol_cutout_layout.addRow("intersection density:",
self.intersection_scale)
self.cutout_labels = QComboBox()
self.cutout_labels.addItems(["none", "quadrants", "octants"])
ndx = self.cutout_labels.findText(self.settings.cutout_labels,
Qt.MatchExactly)
self.cutout_labels.setCurrentIndex(ndx)
vol_cutout_layout.addRow("label sections:", self.cutout_labels)
self.point_spacing.setEnabled(self.settings.display_cutout != "no")
self.intersection_scale.setEnabled(
self.settings.display_cutout != "no")
self.cutout_labels.setEnabled(self.settings.display_cutout != "no")
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.point_spacing: widget.setEnabled(text !=
"no"))
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.intersection_scale: widget.setEnabled(
text != "no"))
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.cutout_labels: widget.setEnabled(text !=
"no"))
calc_vbur_button = QPushButton(
"calculate % buried volume for selected centers")
calc_vbur_button.clicked.connect(self.calc_vbur)
calc_layout.addRow(calc_vbur_button)
self.calc_vbur_button = calc_vbur_button
remove_vbur_button = QPushButton(
"remove % buried volume visualizations")
remove_vbur_button.clicked.connect(self.del_vbur)
vol_cutout_layout.addRow(remove_vbur_button)
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels(['model', 'center', '%Vbur'])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Interactive)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Interactive)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
calc_layout.addRow(self.table)
menu = QMenuBar()
export = menu.addMenu("&Export")
clear = QAction("Clear data table", self.tool_window.ui_area)
clear.triggered.connect(self.clear_table)
export.addAction(clear)
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
self.copy = copy
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
self.layout = QGridLayout()
self.ui_area.setLayout(self.layout)
self.manage(None)
def _build_ui(self):
layout = QGridLayout()
layout.addWidget(QLabel("center of rotation:"), 0, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.cor_button = QComboBox()
self.cor_button.addItems(
["automatic", "select atoms", "view's center of rotation"])
layout.addWidget(self.cor_button, 0, 1, 1, 1, Qt.AlignTop)
self.set_cor_selection = QPushButton("set selection")
self.cor_button.currentTextChanged.connect(
lambda t, widget=self.set_cor_selection: widget.setEnabled(
t == "select atoms"))
self.set_cor_selection.clicked.connect(self.manual_cor)
layout.addWidget(self.set_cor_selection, 0, 2, 1, 1, Qt.AlignTop)
self.set_cor_selection.setEnabled(False)
layout.addWidget(QLabel("rotation vector:"), 1, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.vector_option = QComboBox()
self.vector_option.addItems([
"axis", "view axis", "bond", "perpendicular to plane",
"centroid of atoms", "custom"
])
layout.addWidget(self.vector_option, 1, 1, 1, 1, Qt.AlignVCenter)
vector = QWidget()
vector.setToolTip("vector will be normalized before rotating")
vector_layout = QHBoxLayout(vector)
vector_layout.setContentsMargins(0, 0, 0, 0)
self.vector_x = QDoubleSpinBox()
self.vector_y = QDoubleSpinBox()
self.vector_z = QDoubleSpinBox()
self.vector_z.setValue(1.0)
for c, t in zip([self.vector_x, self.vector_y, self.vector_z],
[" x", " y", " z"]):
c.setSingleStep(0.01)
c.setRange(-100, 100)
# c.setSuffix(t)
c.valueChanged.connect(self.show_rot_vec)
vector_layout.addWidget(c)
layout.addWidget(vector, 1, 2, 1, 1, Qt.AlignTop)
vector.setVisible(self.vector_option.currentText() == "custom")
self.vector_option.currentTextChanged.connect(
lambda text, widget=vector: widget.setVisible(text == "custom"))
self.view_axis = QComboBox()
self.view_axis.addItems(["z", "y", "x"])
layout.addWidget(self.view_axis, 1, 2, 1, 1, Qt.AlignTop)
self.view_axis.setVisible(
self.vector_option.currentText() == "view axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.view_axis: widget.setVisible(text ==
"view axis"))
self.axis = QComboBox()
self.axis.addItems(["z", "y", "x"])
layout.addWidget(self.axis, 1, 2, 1, 1, Qt.AlignTop)
self.axis.setVisible(self.vector_option.currentText() == "axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.axis: widget.setVisible(text == "axis"))
self.bond_button = QPushButton("set selected bond")
self.bond_button.clicked.connect(self.set_bonds)
layout.addWidget(self.bond_button, 1, 2, 1, 1, Qt.AlignTop)
self.bond_button.setVisible(self.vector_option.currentText() == "bond")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.bond_button: widget.setVisible(text ==
"bond"))
self.perp_button = QPushButton("set selected atoms")
self.perp_button.clicked.connect(self.set_perpendicular)
layout.addWidget(self.perp_button, 1, 2, 1, 1, Qt.AlignTop)
self.perp_button.setVisible(
self.vector_option.currentText() == "perpendicular to plane")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.perp_button: widget.setVisible(
text == "perpendicular to plane"))
self.group_button = QPushButton("set selected atoms")
self.group_button.clicked.connect(self.set_group)
layout.addWidget(self.group_button, 1, 2, 1, 1, Qt.AlignTop)
self.group_button.setVisible(
self.vector_option.currentText() == "centroid of atoms")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.group_button: widget.setVisible(
text == "centroid of atoms"))
layout.addWidget(QLabel("angle:"), 2, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.angle = QDoubleSpinBox()
self.angle.setRange(-360, 360)
self.angle.setSingleStep(5)
self.angle.setSuffix("°")
layout.addWidget(self.angle, 2, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
layout.addWidget(QLabel("preview rotation axis:"), 3, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.display_rot_vec = QCheckBox()
self.display_rot_vec.setCheckState(Qt.Checked)
self.display_rot_vec.stateChanged.connect(self.show_rot_vec)
layout.addWidget(self.display_rot_vec, 3, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
rotate_button = QPushButton("rotate selected atoms")
rotate_button.clicked.connect(self.do_rotate)
layout.addWidget(rotate_button, 4, 0, 1, 3, Qt.AlignTop)
self.rotate_button = rotate_button
self.status_bar = QStatusBar()
self.status_bar.setSizeGripEnabled(False)
layout.addWidget(self.status_bar, 5, 0, 1, 3, Qt.AlignTop)
self.vector_option.currentTextChanged.connect(self.show_auto_status)
self.cor_button.currentIndexChanged.connect(
lambda *args: self.show_auto_status("select atoms"))
self.cor_button.currentIndexChanged.connect(self.show_rot_vec)
self.set_cor_selection.clicked.connect(self.show_rot_vec)
self.vector_option.currentIndexChanged.connect(self.show_rot_vec)
self.axis.currentIndexChanged.connect(self.show_rot_vec)
self.view_axis.currentIndexChanged.connect(self.show_rot_vec)
self.bond_button.clicked.connect(self.show_rot_vec)
self.perp_button.clicked.connect(self.show_rot_vec)
self.group_button.clicked.connect(self.show_rot_vec)
layout.setRowStretch(0, 0)
layout.setRowStretch(1, 0)
layout.setRowStretch(2, 0)
layout.setRowStretch(3, 0)
layout.setRowStretch(4, 0)
layout.setRowStretch(5, 1)
layout.setColumnStretch(0, 0)
layout.setColumnStretch(1, 1)
layout.setColumnStretch(2, 1)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)