def __init__(self, parent, factor, main_color=None, *args, **kwargs):
super(HoudiniInputDragger, self).__init__(*args, **kwargs)
self._parent = parent
self._factor = factor
self._main_color = main_color if main_color else QColor(215, 128, 26).getRgb()
self._size = 35
self.setAttribute(Qt.WA_Hover)
self.setStyleSheet(self._get_style_sheet())
self.setMinimumHeight(self._size)
self.setMinimumWidth(self._size)
self.setMaximumHeight(self._size)
self.setMaximumWidth(self._size)
main_layout = layouts.VerticalLayout(margins=(0, 0, 0, 0))
self.setLayout(main_layout)
frame_layout = layouts.VerticalLayout(spacing=0, margins=(0, 0, 0, 0))
self._frame = QGroupBox()
self._frame.setLayout(frame_layout)
main_layout.addWidget(self._frame)
self._label = label.BaseLabel('+' + str(factor), parent=self)
font = self._label.font()
font.setPointSize(7)
self._label.setFont(font)
self._label.setAlignment(Qt.AlignCenter)
frame_layout.addWidget(self._label)
self.installEventFilter(self)
self._label.installEventFilter(self)
def __init__(self, dock_widget, renamable=False):
super(DockTitleBar, self).__init__(dock_widget)
self._renamable = renamable
main_layout = layouts.HorizontalLayout(margins=(0, 0, 0, 1))
self.setLayout(main_layout)
self._buttons_box = QGroupBox('')
self._buttons_box.setObjectName('Docked')
self._buttons_layout = layouts.HorizontalLayout(spacing=1, margins=(2, 2, 2, 2))
self._buttons_box.setLayout(self._buttons_layout)
main_layout.addWidget(self._buttons_box)
self._icon_label = QLabel(self)
self._title_label = QLabel(self)
self._title_label.setStyleSheet('background: transparent')
self._title_edit = QLineEdit(self)
self._title_edit.setVisible(False)
self._button_size = QSize(14, 14)
self._dock_btn = QToolButton(self)
self._dock_btn.setIcon(resources.icon('restore_window', theme='color'))
self._dock_btn.setMaximumSize(self._button_size)
self._dock_btn.setAutoRaise(True)
self._close_btn = QToolButton(self)
self._close_btn.setIcon(resources.icon('close_window', theme='color'))
self._close_btn.setMaximumSize(self._button_size)
self._close_btn.setAutoRaise(True)
self._buttons_layout.addSpacing(2)
self._buttons_layout.addWidget(self._icon_label)
self._buttons_layout.addWidget(self._title_label)
self._buttons_layout.addWidget(self._title_edit)
self._buttons_layout.addStretch()
self._buttons_layout.addSpacing(5)
self._buttons_layout.addWidget(self._dock_btn)
self._buttons_layout.addWidget(self._close_btn)
self._buttons_box.mouseDoubleClickEvent = self.mouseDoubleClickEvent
self._buttons_box.mousePressEvent = self.mousePressEvent
self._buttons_box.mouseMoveEvent = self.mouseMoveEvent
self._buttons_box.mouseReleaseEvent = self.mouseReleaseEvent
dock_widget.featuresChanged.connect(self._on_dock_features_changed)
self._title_edit.editingFinished.connect(self._on_finish_edit)
self._dock_btn.clicked.connect(self._on_dock_btn_clicked)
self._close_btn.clicked.connect(self._on_close_btn_clicked)
self._on_dock_features_changed(dock_widget.features())
self.set_title(dock_widget.windowTitle())
dock_widget.installEventFilter(self)
dock_widget.topLevelChanged.connect(self._on_change_floating_style)
if hasattr(dock_widget, 'icon') and callable(dock_widget.icon):
self._icon_label.setPixmap(dock_widget.icon().pixmap(QSize(16, 16)))
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 get_drives_widget(self):
"""
Returns a QGroupBox widget that contains all disk drivers of the PC in a vertical layout
:return: QGroupBox
"""
w = QGroupBox('')
w.setParent(self)
box = layouts.VerticalLayout()
box.setAlignment(Qt.AlignTop)
places = [(getpass.getuser(),
os.path.realpath(os.path.expanduser('~')))]
places += [
(q, q) for q in
[os.path.realpath(x.absolutePath()) for x in QDir().drives()]
]
for label, loc in places:
icon = QFileIconProvider().icon(QFileInfo(loc))
drive_btn = QRadioButton(label)
drive_btn.setIcon(icon)
drive_btn.setToolTip(loc)
drive_btn.setProperty('path', loc)
drive_btn.clicked.connect(self.go_to_drive)
self.places[loc] = drive_btn
box.addWidget(drive_btn)
w.setLayout(box)
return w
def ui(self):
super(AttributeEditor, self).ui()
self._main_group = QGroupBox()
self._main_group.setProperty('class', 'attr_main_group')
self._main_group.setFlat(False)
self._main_group.setTitle('')
self._main_group_layout = self.get_attributes_layout()
self._main_group.setLayout(self._main_group_layout)
scroll_area = QScrollArea()
scroll_area.setWidgetResizable(True)
scroll_area.setStyleSheet(
'QScrollArea { background-color: rgb(57,57,57);}')
scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
scroll_area.setWidget(self._main_group)
self.main_layout.addWidget(scroll_area)
self.setContextMenuPolicy(Qt.CustomContextMenu)
self.customContextMenuRequested.connect(self._on_create_context_menu)
class DockTitleBar(QWidget, object):
def __init__(self, dock_widget, renamable=False):
super(DockTitleBar, self).__init__(dock_widget)
self._renamable = renamable
main_layout = QHBoxLayout()
main_layout.setContentsMargins(0, 0, 0, 1)
self.setLayout(main_layout)
self._buttons_box = QGroupBox('')
self._buttons_box.setObjectName('Docked')
self._buttons_layout = QHBoxLayout()
self._buttons_layout.setSpacing(1)
self._buttons_layout.setMargin(2)
self._buttons_box.setLayout(self._buttons_layout)
main_layout.addWidget(self._buttons_box)
self._title_label = QLabel(self)
self._title_label.setStyleSheet('background: transparent')
self._title_edit = QLineEdit(self)
self._title_edit.setVisible(False)
self._button_size = QSize(14, 14)
self._dock_btn = QToolButton(self)
self._dock_btn.setIcon(resources.icon('restore_window', theme='color'))
self._dock_btn.setMaximumSize(self._button_size)
self._dock_btn.setAutoRaise(True)
self._close_btn = QToolButton(self)
self._close_btn.setIcon(resources.icon('close_window', theme='color'))
self._close_btn.setMaximumSize(self._button_size)
self._close_btn.setAutoRaise(True)
self._buttons_layout.addSpacing(2)
self._buttons_layout.addWidget(self._title_label)
self._buttons_layout.addWidget(self._title_edit)
self._buttons_layout.addStretch()
self._buttons_layout.addSpacing(5)
self._buttons_layout.addWidget(self._dock_btn)
self._buttons_layout.addWidget(self._close_btn)
self._buttons_box.mouseDoubleClickEvent = self.mouseDoubleClickEvent
self._buttons_box.mousePressEvent = self.mousePressEvent
self._buttons_box.mouseMoveEvent = self.mouseMoveEvent
self._buttons_box.mouseReleaseEvent = self.mouseReleaseEvent
dock_widget.featuresChanged.connect(self._on_dock_features_changed)
self._title_edit.editingFinished.connect(self._on_finish_edit)
self._dock_btn.clicked.connect(self._on_dock_btn_clicked)
self._close_btn.clicked.connect(self._on_close_btn_clicked)
self._on_dock_features_changed(dock_widget.features())
self.set_title(dock_widget.windowTitle())
dock_widget.installEventFilter(self)
dock_widget.topLevelChanged.connect(self._on_change_floating_style)
@property
def renamable(self):
return self._renamable
@renamable.setter
def renamable(self, flag):
self._renamable = flag
def eventFilter(self, obj, event):
if event.type() == QEvent.WindowTitleChange:
self.set_title(obj.windowTitle())
return super(DockTitleBar, self).eventFilter(obj, event)
def mouseMoveEvent(self, event):
event.ignore()
def mousePressEvent(self, event):
event.ignore()
def mouseReleaseEvent(self, event):
event.ignore()
def mouseDoubleClickEvent(self, event):
if event.pos().x() <= self._title_label.width() and self._renamable:
self._start_edit()
else:
super(DockTitleBar, self).mouseDoubleClickEvent(event)
def update(self, *args, **kwargs):
self._on_change_floating_style(self.parent().isFloating())
super(DockTitleBar, self).update(*args, **kwargs)
def set_title(self, title):
self._title_label.setText(title)
self._title_edit.setText(title)
def add_button(self, button):
button.setAutoRaise(True)
button.setMaximumSize(self._button_size)
self._buttons_layout.insertWidget(5, button)
def _start_edit(self):
self._title_label.hide()
self._title_edit.show()
self._title_edit.setFocus()
def _finish_edit(self):
self._title_edit.hide()
self._title_label.show()
self.parent().setWindowTitle(self._title_edit.text())
def _on_dock_features_changed(self, features):
if not features & QDockWidget.DockWidgetVerticalTitleBar:
self._close_btn.setVisible(features
& QDockWidget.DockWidgetClosable)
self._dock_btn.setVisible(features
& QDockWidget.DockWidgetFloatable)
else:
raise ValueError('Vertical title bar is not supported!')
def _on_finish_edit(self):
self._finish_edit()
def _on_dock_btn_clicked(self):
self.parent().setFloating(not self.parent().isFloating())
def _on_close_btn_clicked(self):
self.parent().toggleViewAction().setChecked(False)
self.parent().close()
def _on_change_floating_style(self, state):
pass
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 _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)
class HoudiniInputDragger(QWidget, object):
"""
Widget that allow to drag values when mid click over widget.
Right Drag increments values and Left Drag decreases value
"""
def __init__(self, parent, factor, main_color=None, *args, **kwargs):
super(HoudiniInputDragger, self).__init__(*args, **kwargs)
self._parent = parent
self._factor = factor
self._main_color = main_color if main_color else QColor(215, 128, 26).getRgb()
self._size = 35
self.setAttribute(Qt.WA_Hover)
self.setStyleSheet(self._get_style_sheet())
self.setMinimumHeight(self._size)
self.setMinimumWidth(self._size)
self.setMaximumHeight(self._size)
self.setMaximumWidth(self._size)
main_layout = layouts.VerticalLayout(margins=(0, 0, 0, 0))
self.setLayout(main_layout)
frame_layout = layouts.VerticalLayout(spacing=0, margins=(0, 0, 0, 0))
self._frame = QGroupBox()
self._frame.setLayout(frame_layout)
main_layout.addWidget(self._frame)
self._label = label.BaseLabel('+' + str(factor), parent=self)
font = self._label.font()
font.setPointSize(7)
self._label.setFont(font)
self._label.setAlignment(Qt.AlignCenter)
frame_layout.addWidget(self._label)
self.installEventFilter(self)
self._label.installEventFilter(self)
def eventFilter(self, obj, event):
if event.type() == QEvent.HoverEnter:
self.setStyleSheet(self._get_style_sheet(hover_style=True))
self._parent.active_drag = self
for drag in self._parent.drags:
if drag != self:
drag.setStyleSheet(self._get_style_sheet())
if event.type() == QEvent.HoverLeave:
if event.pos().y() > self.height() or event.pos().y() < 0:
self.setStyleSheet(self._get_style_sheet())
if event.type() == QEvent.MouseMove:
self._parent.eventFilter(self, event)
return False
@property
def factor(self):
return self._factor
def _get_style_sheet(self, hover_style=False):
if hover_style:
return """
QGroupBox{
border: 0.5 solid darkgrey;
background : %s;
color: white;
}
QLabel{
background: transparent;
border: 0 solid transparent;
color: white;
}
""" % "rgba%s" % str(self._main_color)
else:
return """
def _build_ui(self):
layout = QFormLayout()
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)
layout.addRow("radii:", self.radii_option)
self.L_option = QComboBox()
self.L_option.addItems([
"to centroid of coordinating atoms",
"bisect angle between coordinating atoms"
])
ndx = self.L_option.findText(self.settings.L_option, Qt.MatchExactly)
self.L_option.setCurrentIndex(ndx)
layout.addRow("L axis:", self.L_option)
self.sterimol2vec = QGroupBox("Sterimol2Vec")
sterimol2vec_layout = QFormLayout(self.sterimol2vec)
self.at_L = QDoubleSpinBox()
self.at_L.setRange(-10, 30)
self.at_L.setDecimals(2)
self.at_L.setSingleStep(0.25)
self.at_L.setValue(self.settings.at_L)
sterimol2vec_layout.addRow("L value:", self.at_L)
layout.addRow(self.sterimol2vec)
self.sterimol2vec.setCheckable(True)
self.sterimol2vec.toggled.connect(lambda x: self.at_L.setEnabled(x))
self.sterimol2vec.setChecked(self.settings.sterimol2vec)
self.display_vectors = QCheckBox()
self.display_vectors.setChecked(self.settings.display_vectors)
layout.addRow("show vectors:", self.display_vectors)
self.display_radii = QCheckBox()
self.display_radii.setChecked(self.settings.display_radii)
layout.addRow("show radii:", self.display_radii)
calc_sterimol_button = QPushButton(
"calculate parameters for selected ligands")
calc_sterimol_button.clicked.connect(self.calc_sterimol)
layout.addRow(calc_sterimol_button)
self.calc_sterimol_button = calc_sterimol_button
remove_sterimol_button = QPushButton("remove Sterimol visualizations")
remove_sterimol_button.clicked.connect(self.del_sterimol)
layout.addRow(remove_sterimol_button)
self.remove_sterimol_button = remove_sterimol_button
self.table = QTableWidget()
self.table.setColumnCount(8)
self.table.setHorizontalHeaderLabels([
'model',
'coord. atoms',
'B\u2081',
'B\u2082',
'B\u2083',
'B\u2084',
'B\u2085',
'L',
])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.resizeColumnToContents(3)
self.table.resizeColumnToContents(4)
self.table.resizeColumnToContents(5)
self.table.resizeColumnToContents(6)
self.table.resizeColumnToContents(7)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
4, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
5, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
6, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
7, QHeaderView.Stretch)
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)
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)
class LigandSterimol(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Ligand-Sterimol-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.settings = _SterimolSettings(self.session, name)
self._build_ui()
def _build_ui(self):
layout = QFormLayout()
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)
layout.addRow("radii:", self.radii_option)
self.L_option = QComboBox()
self.L_option.addItems([
"to centroid of coordinating atoms",
"bisect angle between coordinating atoms"
])
ndx = self.L_option.findText(self.settings.L_option, Qt.MatchExactly)
self.L_option.setCurrentIndex(ndx)
layout.addRow("L axis:", self.L_option)
self.sterimol2vec = QGroupBox("Sterimol2Vec")
sterimol2vec_layout = QFormLayout(self.sterimol2vec)
self.at_L = QDoubleSpinBox()
self.at_L.setRange(-10, 30)
self.at_L.setDecimals(2)
self.at_L.setSingleStep(0.25)
self.at_L.setValue(self.settings.at_L)
sterimol2vec_layout.addRow("L value:", self.at_L)
layout.addRow(self.sterimol2vec)
self.sterimol2vec.setCheckable(True)
self.sterimol2vec.toggled.connect(lambda x: self.at_L.setEnabled(x))
self.sterimol2vec.setChecked(self.settings.sterimol2vec)
self.display_vectors = QCheckBox()
self.display_vectors.setChecked(self.settings.display_vectors)
layout.addRow("show vectors:", self.display_vectors)
self.display_radii = QCheckBox()
self.display_radii.setChecked(self.settings.display_radii)
layout.addRow("show radii:", self.display_radii)
calc_sterimol_button = QPushButton(
"calculate parameters for selected ligands")
calc_sterimol_button.clicked.connect(self.calc_sterimol)
layout.addRow(calc_sterimol_button)
self.calc_sterimol_button = calc_sterimol_button
remove_sterimol_button = QPushButton("remove Sterimol visualizations")
remove_sterimol_button.clicked.connect(self.del_sterimol)
layout.addRow(remove_sterimol_button)
self.remove_sterimol_button = remove_sterimol_button
self.table = QTableWidget()
self.table.setColumnCount(8)
self.table.setHorizontalHeaderLabels([
'model',
'coord. atoms',
'B\u2081',
'B\u2082',
'B\u2083',
'B\u2084',
'B\u2085',
'L',
])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.resizeColumnToContents(3)
self.table.resizeColumnToContents(4)
self.table.resizeColumnToContents(5)
self.table.resizeColumnToContents(6)
self.table.resizeColumnToContents(7)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
4, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
5, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
6, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
7, QHeaderView.Stretch)
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)
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 clear_table(self):
are_you_sure = QMessageBox.question(
None,
"Clear table?",
"Are you sure you want to clear the data table?",
)
if are_you_sure != QMessageBox.Yes:
return
self.table.setRowCount(0)
def calc_sterimol(self, *args):
self.settings.radii = self.radii_option.currentText()
self.settings.display_radii = self.display_radii.checkState(
) == Qt.Checked
self.settings.display_vectors = self.display_vectors.checkState(
) == Qt.Checked
self.settings.at_L = self.at_L.value()
self.settings.sterimol2vec = self.sterimol2vec.isChecked()
self.settings.L_option = self.L_option.currentText()
targets, neighbors, datas = sterimol_cmd(
self.session,
selected_atoms(self.session),
radii=self.radii_option.currentText(),
showVectors=self.display_vectors.checkState() == Qt.Checked,
showRadii=self.display_radii.checkState() == Qt.Checked,
return_values=True,
at_L=self.at_L.value() if self.sterimol2vec.isChecked() else None,
bisect_L=self.L_option.currentText() ==
"bisect angle between coordinating atoms",
)
if len(targets) == 0:
return
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
# self.table.setRowCount(0)
for t, b, data in zip(targets, neighbors, datas):
row = self.table.rowCount()
self.table.insertRow(row)
targ = QTableWidgetItem()
targ.setData(Qt.DisplayRole, t)
self.table.setItem(row, 0, targ)
neigh = QTableWidgetItem()
neigh.setData(Qt.DisplayRole, delim.join(b))
self.table.setItem(row, 1, neigh)
l = np.linalg.norm(data["L"][1] - data["L"][0])
b1 = np.linalg.norm(data["B1"][1] - data["B1"][0])
b2 = np.linalg.norm(data["B2"][1] - data["B2"][0])
b3 = np.linalg.norm(data["B3"][1] - data["B3"][0])
b4 = np.linalg.norm(data["B4"][1] - data["B4"][0])
b5 = np.linalg.norm(data["B5"][1] - data["B5"][0])
li = QTableWidgetItem()
li.setData(Qt.DisplayRole, "%.2f" % l)
self.table.setItem(row, 7, li)
b1i = QTableWidgetItem()
b1i.setData(Qt.DisplayRole, "%.2f" % b1)
self.table.setItem(row, 2, b1i)
b2i = QTableWidgetItem()
b2i.setData(Qt.DisplayRole, "%.2f" % b2)
self.table.setItem(row, 3, b2i)
b3i = QTableWidgetItem()
b3i.setData(Qt.DisplayRole, "%.2f" % b3)
self.table.setItem(row, 4, b3i)
b4i = QTableWidgetItem()
b4i.setData(Qt.DisplayRole, "%.2f" % b4)
self.table.setItem(row, 5, b4i)
b5i = QTableWidgetItem()
b5i.setData(Qt.DisplayRole, "%.2f" % b5)
self.table.setItem(row, 6, b5i)
for i in range(0, 7):
if i == 1:
continue
self.table.resizeColumnToContents(i)
def header_check(self, state):
"""user has [un]checked the 'include header' option on the menu"""
if state:
self.settings.include_header = True
else:
self.settings.include_header = False
def get_csv(self):
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
if self.settings.include_header:
s = delim.join([
"substituent_atom", "bonded_atom", "B1", "B2", "B3", "B4",
"B5", "L"
])
s += "\n"
else:
s = ""
for i in range(0, self.table.rowCount()):
s += delim.join([
item.data(Qt.DisplayRole)
for item in [self.table.item(i, j) for j in range(0, 8)]
])
s += "\n"
return s
def copy_csv(self):
app = QApplication.instance()
clipboard = app.clipboard()
csv = self.get_csv()
clipboard.setText(csv)
self.session.logger.status("copied to clipboard")
def save_csv(self):
"""save data on current tab to CSV file"""
filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)")
if filename:
s = self.get_csv()
with open(filename, 'w') as f:
f.write(s.strip())
self.session.logger.status("saved to %s" % filename)
def del_sterimol(self):
for model in self.session.models.list(type=Generic3DModel):
if model.name.startswith("Sterimol"):
model.delete()
def display_help(self):
"""Show the help for this tool in the help viewer."""
from chimerax.core.commands import run
run(self.session,
'open %s' % self.help if self.help is not None else "")
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)
class AttributeEditor(base.BaseWidget, object):
def __init__(self,
name='AttributeEditor',
label='Attribute Editor',
parent=None):
self._label = label
self._objects = list()
super(AttributeEditor, self).__init__(parent=parent)
self.setObjectName(name)
def get_objects(self):
return self._objects
objects = property(get_objects)
def ui(self):
super(AttributeEditor, self).ui()
self._main_group = QGroupBox()
self._main_group.setProperty('class', 'attr_main_group')
self._main_group.setFlat(False)
self._main_group.setTitle('')
self._main_group_layout = self.get_attributes_layout()
self._main_group.setLayout(self._main_group_layout)
scroll_area = QScrollArea()
scroll_area.setWidgetResizable(True)
scroll_area.setStyleSheet(
'QScrollArea { background-color: rgb(57,57,57);}')
scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
scroll_area.setWidget(self._main_group)
self.main_layout.addWidget(scroll_area)
self.setContextMenuPolicy(Qt.CustomContextMenu)
self.customContextMenuRequested.connect(self._on_create_context_menu)
def get_attributes_layout(self):
"""
Returns layout used for the attributes
:return: QLayout
"""
attributes_layout = layouts.HorizontalLayout(margins=(5, 5, 5, 5))
attributes_layout.setAlignment(Qt.AlignTop)
return attributes_layout
def set_title(self, new_title):
self._main_group.setTitle(new_title)
def clear_layout(self, reset_title=True):
"""
Clears main layout and resetes editor title
"""
qtutils.clear_layout(self._main_group_layout)
if reset_title:
self._main_group.setTitle('')
def _build_layout(self):
pass
def _on_create_context_menu(self):
pass
def create_coord_items(tool, layout, allow_minimization=True, default_ele="Ca"):
"""
add widgets to the layout and set appropriate attributes for tool
this is used by this tool and the AaronJr input builder
"""
tool.element = ElementButton(default_ele, single_state=True)
tool.element.clicked.connect(lambda *args, t=tool: open_ptable(t))
layout.addRow("element:", tool.element)
tool.vsepr = QComboBox()
tool.vsepr.addItems([
"trigonal pyramidal", # 1
"tetrahedral", # 2
"seesaw", # 3
"square planar", # 4
"trigonal bipyramidal", # 5
"square pyramidal", # 6
"pentagonal", # 7
"octahedral", # 8
"hexagonal", # 9
"trigonal prismatic", #10
"pentagonal pyramidal", #11
"capped octahedral", #12
"capped trigonal prismatic", #13
"heptagonal", #14
"hexagonal pyramidal", #15
"pentagonal bipyramidal", #16
])
tool.vsepr.setCurrentIndex(7)
tool.vsepr.insertSeparator(11)
tool.vsepr.insertSeparator(7)
tool.vsepr.insertSeparator(4)
layout.addRow("geometry:", tool.vsepr)
if allow_minimization:
tool.minimize = QCheckBox()
tool.minimize.setCheckState(Qt.Checked)
tool.minimize.setToolTip("rotate substituents on ligands to mitigate steric clashing")
layout.addRow("relax ligands:", tool.minimize)
ligand_box = QGroupBox("ligands")
ligand_layout = QFormLayout(ligand_box)
layout.addRow(ligand_box)
tool.ligand_table = QTableWidget()
tool.ligand_table.setColumnCount(3)
tool.ligand_table.setHorizontalHeaderLabels(["name", "C\u2082-symmetric", "remove"])
tool.ligand_table.cellClicked.connect(
lambda row, column, t=tool:ligand_table_clicked(t, row, column)
)
tool.ligand_table.setEditTriggers(QTableWidget.NoEditTriggers)
add_ligand(tool)
tool.ligand_table.resizeColumnToContents(0)
tool.ligand_table.resizeColumnToContents(1)
tool.ligand_table.resizeColumnToContents(2)
tool.ligand_table.horizontalHeader().setStretchLastSection(False)
tool.ligand_table.horizontalHeader().setSectionResizeMode(0, QHeaderView.Stretch)
tool.ligand_table.horizontalHeader().setSectionResizeMode(1, QHeaderView.Fixed)
tool.ligand_table.horizontalHeader().setSectionResizeMode(2, QHeaderView.Fixed)
ligand_layout.addRow(tool.ligand_table)
def ui(self):
super(NameIt, self).ui()
tools_toolbar = toolbar.ToolBar('Main ToolBar', parent=self)
tools_toolbar.setMovable(False)
# tools_toolbar.setAllowedAreas(Qt.TopToolBarArea | Qt.BottomToolBarArea)
self.main_layout.addWidget(tools_toolbar)
refresh_btn = buttons.BaseToolButton(parent=tools_toolbar)
refresh_btn.setIcon(resources.icon('refresh'))
refresh_btn.clicked.connect(self._on_refresh)
self._refresh_btn = tools_toolbar.addWidget(refresh_btn)
self._refresh_btn.setEnabled(False)
save_btn = buttons.BaseToolButton(parent=tools_toolbar)
save_btn.setIcon(resources.icon('save'))
save_btn.clicked.connect(self._on_save)
self._save_btn = tools_toolbar.addWidget(save_btn)
self._save_btn.setEnabled(False)
if self._is_renamer_tool_available():
renamer_btn = buttons.BaseToolButton(parent=tools_toolbar)
renamer_btn.setIcon(resources.icon('rename'))
renamer_btn.clicked.connect(self._on_open_renamer_tool)
tools_toolbar.addWidget(renamer_btn)
self._name_file_line = directory.SelectFile(label_text='Naming File',
parent=tools_toolbar)
tools_toolbar.addWidget(self._name_file_line)
base_layout = layouts.HorizontalLayout(spacing=0, margins=(0, 0, 0, 0))
self.main_layout.addLayout(base_layout)
panels_splitter = QSplitter(parent=self)
panels_splitter.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
base_layout.addWidget(panels_splitter)
left_panel_widget = QWidget()
left_panel_layout = layouts.VerticalLayout(margins=(5, 0, 5, 0))
left_panel_widget.setLayout(left_panel_layout)
panels_splitter.addWidget(left_panel_widget)
# Tab Widget
rules_tab = QWidget()
tokens_tab = QWidget()
templates_tab = QWidget()
templates_tokens_tab = QWidget()
self.tabs = tabs.BaseTabWidget()
self.tabs.addTab(rules_tab, 'Rules')
self.tabs.addTab(tokens_tab, 'Tokens')
self.tabs.addTab(templates_tab, 'Templates')
self.tabs.addTab(templates_tokens_tab, 'Templates Tokens')
left_panel_layout.addWidget(self.tabs)
# Rules Tab
rules_main_layout = layouts.VerticalLayout(spacing=0,
margins=(5, 5, 5, 5))
self.rules_list = QListWidget()
rules_main_layout.addWidget(self.rules_list)
left_panel_buttons_layout_rules = layouts.HorizontalLayout(margins=(5,
5,
5,
0))
rules_main_layout.addLayout(left_panel_buttons_layout_rules)
self.add_rule_btn = buttons.BaseButton(parent=self)
self.remove_rule_btn = buttons.BaseButton(parent=self)
self.add_rule_btn.setIcon(resources.icon('plus'))
self.remove_rule_btn.setIcon(resources.icon('minus'))
left_panel_buttons_layout_rules.addStretch()
left_panel_buttons_layout_rules.addWidget(self.add_rule_btn)
left_panel_buttons_layout_rules.addWidget(self.remove_rule_btn)
rules_tab.setLayout(rules_main_layout)
# Tokens Tab
tokens_main_layout = layouts.VerticalLayout(margins=(5, 5, 5, 5))
tokens_main_layout.setSpacing(0)
self.tokens_list = QListWidget()
tokens_main_layout.addWidget(self.tokens_list)
left_panel_buttons_layout_tokens = layouts.HorizontalLayout(
margins=(5, 5, 5, 0))
tokens_main_layout.addLayout(left_panel_buttons_layout_tokens)
self.add_token_btn = buttons.BaseButton(parent=self)
self.remove_token_btn = buttons.BaseButton(parent=self)
self.add_token_btn.setIcon(resources.icon('plus'))
self.remove_token_btn.setIcon(resources.icon('minus'))
left_panel_buttons_layout_tokens.addStretch()
left_panel_buttons_layout_tokens.addWidget(self.add_token_btn)
left_panel_buttons_layout_tokens.addWidget(self.remove_token_btn)
tokens_tab.setLayout(tokens_main_layout)
# Templates Tab
templates_main_layout = layouts.VerticalLayout(spacing=0,
margins=(5, 5, 5, 5))
self.templates_list = QListWidget()
templates_main_layout.addWidget(self.templates_list)
left_panel_buttons_layout_templates = layouts.HorizontalLayout(
margins=(5, 5, 5, 0))
templates_main_layout.addLayout(left_panel_buttons_layout_templates)
self.add_template_btn = buttons.BaseButton(parent=self)
self.remove_template_btn = buttons.BaseButton(parent=self)
self.add_template_btn.setIcon(resources.icon('plus'))
self.remove_template_btn.setIcon(resources.icon('minus'))
left_panel_buttons_layout_templates.addStretch()
left_panel_buttons_layout_templates.addWidget(self.add_template_btn)
left_panel_buttons_layout_templates.addWidget(self.remove_template_btn)
templates_tab.setLayout(templates_main_layout)
# Template Tokens Tab
templates_tokens_main_layout = layouts.VerticalLayout(spacing=0,
margins=(5, 5, 5,
5))
self.template_tokens_list = QListWidget()
templates_tokens_main_layout.addWidget(self.template_tokens_list)
left_panel_buttons_layout_templates_tokens = layouts.HorizontalLayout(
margins=(5, 5, 5, 0))
left_panel_buttons_layout_templates_tokens.setContentsMargins(
5, 5, 5, 0)
templates_tokens_main_layout.addLayout(
left_panel_buttons_layout_templates_tokens)
self.add_template_token_btn = buttons.BaseButton(parent=self)
self.remove_template_token_btn = buttons.BaseButton(parent=self)
self.add_template_token_btn.setIcon(resources.icon('plus'))
self.remove_template_token_btn.setIcon(resources.icon('minus'))
left_panel_buttons_layout_templates_tokens.addStretch()
left_panel_buttons_layout_templates_tokens.addWidget(
self.add_template_token_btn)
left_panel_buttons_layout_templates_tokens.addWidget(
self.remove_template_token_btn)
templates_tokens_tab.setLayout(templates_tokens_main_layout)
# === PROPERTIES === #
main_group = QGroupBox('Properties')
panels_splitter.addWidget(main_group)
self.group_layout = layouts.VerticalLayout(spacing=0,
margins=(5, 5, 5, 5))
main_group.setLayout(self.group_layout)
# Rules Panel
self.rules_widget = QWidget(self)
rules_layout = layouts.GridLayout()
self.rules_widget.setLayout(rules_layout)
expression_lbl = label.BaseLabel('Expression', parent=self)
self.expression_line = lineedit.BaseLineEdit(parent=self)
self.expression_btn = buttons.BaseButton(' <', parent=self)
self.expression_btn.setEnabled(False)
self.expression_btn.setStyleSheet(
"QPushButton::menu-indicator{image:url(none.jpg);}")
self.expression_menu = QMenu(self)
self.expression_btn.setMenu(self.expression_menu)
iterator_lbl = label.BaseLabel('Iterator', parent=self)
self.iterator_cbx = combobox.BaseComboBox(parent=self)
for it_format in [
'@', '@^', '#', '##', '###', '####', '#####', 'None'
]:
self.iterator_cbx.addItem(it_format)
description_rule_lbl = label.BaseLabel('Description', parent=self)
self.description_rule_text = QTextEdit(parent=self)
self.group_layout.addWidget(self.rules_widget)
rules_layout.addWidget(expression_lbl, 0, 0, Qt.AlignRight)
rules_layout.addWidget(self.expression_line, 0, 1)
rules_layout.addWidget(self.expression_btn, 0, 2)
rules_layout.addWidget(iterator_lbl, 1, 0, Qt.AlignRight | Qt.AlignTop)
rules_layout.addWidget(self.iterator_cbx, 1, 1, 1, 2)
rules_layout.addWidget(description_rule_lbl, 2, 0,
Qt.AlignRight | Qt.AlignTop)
rules_layout.addWidget(self.description_rule_text, 2, 1, 1, 2)
# Tokens Panel
self.tokens_widget = QWidget(parent=self)
tokens_layout = layouts.GridLayout()
self.tokens_widget.setLayout(tokens_layout)
values_lbl = label.BaseLabel('Values')
data = {'key': list(), 'value': list()}
self.values_table = TokensTable(data, 0, 2)
self.values_table.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
values_buttons_layout = layouts.HorizontalLayout(margins=(5, 5, 5, 0))
self.add_key_value_btn = buttons.BaseButton(parent=self)
self.remove_key_value_btn = buttons.BaseButton(parent=self)
self.add_key_value_btn.setIcon(resources.icon('plus'))
self.remove_key_value_btn.setIcon(resources.icon('minus'))
values_buttons_layout.addWidget(self.add_key_value_btn)
values_buttons_layout.addWidget(self.remove_key_value_btn)
values_buttons_layout.addStretch()
default_lbl = label.BaseLabel('Default', parent=self)
self.default_cbx = combobox.BaseComboBox(parent=self)
description_tokens_lbl = label.BaseLabel('Description', parent=self)
self.description_token_text = QTextEdit(parent=self)
self.group_layout.addWidget(self.tokens_widget)
self.tokens_widget.hide()
tokens_layout.addWidget(values_lbl, 0, 0, Qt.AlignRight | Qt.AlignTop)
tokens_layout.addWidget(self.values_table, 0, 1, 2, 1)
tokens_layout.addLayout(values_buttons_layout, 0, 2)
tokens_layout.addWidget(default_lbl, 4, 0, Qt.AlignRight)
tokens_layout.addWidget(self.default_cbx, 4, 1, 1, 2)
tokens_layout.addWidget(description_tokens_lbl, 5, 0,
Qt.AlignRight | Qt.AlignTop)
tokens_layout.addWidget(self.description_token_text, 5, 1, 1, 2)
# Templates Panel
self.templates_widget = QWidget(parent=self)
templates_layout = layouts.VerticalLayout()
self.templates_widget.setLayout(templates_layout)
pattern_layout = layouts.HorizontalLayout(spacing=5,
margins=(5, 5, 5, 5))
pattern_lbl = label.BaseLabel('Pattern: ', parent=self)
self.pattern_line = lineedit.BaseLineEdit(parent=self)
pattern_layout.addWidget(pattern_lbl)
pattern_layout.addWidget(self.pattern_line)
templates_layout.addLayout(pattern_layout)
templates_layout.addLayout(dividers.DividerLayout())
self.template_tokens_layout = layouts.GridLayout()
self.template_tokens_layout.setAlignment(Qt.AlignTop)
template_tokens_frame = QFrame(parent=self)
template_tokens_frame.setFrameShape(QFrame.StyledPanel)
template_tokens_frame.setFrameShadow(QFrame.Sunken)
template_tokens_frame.setLayout(self.template_tokens_layout)
templates_layout.addWidget(template_tokens_frame)
self.group_layout.addWidget(self.templates_widget)
self.templates_widget.hide()
# Templates Tokens Panel
self.templates_tokens_widget = QWidget(parent=self)
templates_tokens_layout = layouts.VerticalLayout()
self.templates_tokens_widget.setLayout(templates_tokens_layout)
description_templates_token_layout = layouts.HorizontalLayout(
spacing=5, margins=(5, 5, 5, 5))
description_tokens_layout = layouts.VerticalLayout()
description_templates_token_lbl = label.BaseLabel('Description: ',
parent=self)
description_tokens_layout.addWidget(description_templates_token_lbl)
description_tokens_layout.addStretch()
self.description_templates_token_text = QTextEdit(parent=self)
description_templates_token_layout.addLayout(description_tokens_layout)
description_templates_token_layout.addWidget(
self.description_templates_token_text)
templates_tokens_layout.addLayout(description_templates_token_layout)
self.group_layout.addWidget(self.templates_tokens_widget)
self.templates_tokens_widget.hide()
# Initialize database
self._init_db()
# First update of the UI
self.update_expression_menu()
self.update_tokens_properties_state()
self.update_rules_properties_state()
self.update_templates_properties_state()
