def ui(self):
super(FallofCurveWidget, self).ui()
base_rect = QRect(0, 0, self._base_size, self._base_size)
self._scene = CurveNodeScene(base_rect)
self._scene.base_size = self._base_size
self._view = CurveNodeView(parent=self)
self._view.setScene(self._scene)
self._view.setGeometry(base_rect)
self._menu_bar = QMenuBar(self)
self._menu_bar.addAction(self._scene.undo_action)
self._menu_bar.addAction(self._scene.redo_action)
bottom_layout = layouts.HorizontalLayout(spacing=2, margins=(2, 2, 2, 2))
self._bezier_type_combo = combobox.BaseComboBox(parent=self)
self._snap_cbx = checkbox.BaseCheckBox('Snap', parent=self)
bottom_layout.addWidget(self._bezier_type_combo)
bottom_layout.addWidget(self._snap_cbx)
self.main_layout.addWidget(self._menu_bar)
self.main_layout.addWidget(dividers.Divider(parent=self))
self.main_layout.addWidget(self._view)
self.main_layout.addWidget(dividers.Divider(parent=self))
self.main_layout.addLayout(bottom_layout)
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 _build_ui(self):
layout = QFormLayout()
self.cone_option = QComboBox()
self.cone_option.addItems(["Tolman (Unsymmetrical)", "Exact"])
ndx = self.cone_option.findText(self.settings.cone_option,
Qt.MatchExactly)
self.cone_option.setCurrentIndex(ndx)
layout.addRow("method:", self.cone_option)
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.display_cone = QCheckBox()
self.display_cone.setChecked(self.settings.display_cone)
layout.addRow("show cone:", self.display_cone)
self.display_radii = QCheckBox()
self.display_radii.setChecked(self.settings.display_radii)
layout.addRow("show radii:", self.display_radii)
set_ligand_button = QPushButton("set ligand to current selection")
set_ligand_button.clicked.connect(self.set_ligand)
layout.addRow(set_ligand_button)
self.set_ligand_button = set_ligand_button
calc_cone_button = QPushButton(
"calculate cone angle for ligand on selected center")
calc_cone_button.clicked.connect(self.calc_cone)
layout.addRow(calc_cone_button)
self.calc_cone_button = calc_cone_button
remove_cone_button = QPushButton("remove cone visualizations")
remove_cone_button.clicked.connect(self.del_cone)
layout.addRow(remove_cone_button)
self.remove_cone_button = remove_cone_button
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels([
'model',
'center',
'cone angle (°)',
])
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(
2, 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 _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 FallofCurveWidget(base.BaseWidget, object):
curveUpdated = Signal(list)
def __init__(self, parent=None):
self._base_size = 300
self._bezier_dict = {
'bezier': [
QPoint(0, 0), QPoint(75, 0),
QPoint(225, 300), QPoint(300, 300)],
'linear': [
QPointF(0.000000, 0.000000), QPointF(75.000000, 75.000000),
QPointF(225.000000, 225.000000), QPointF(300.000000, 300.000000)]
}
super(FallofCurveWidget, self).__init__(parent=parent)
self.setObjectName('Falloff Curve')
self.show()
self.refresh()
def ui(self):
super(FallofCurveWidget, self).ui()
base_rect = QRect(0, 0, self._base_size, self._base_size)
self._scene = CurveNodeScene(base_rect)
self._scene.base_size = self._base_size
self._view = CurveNodeView(parent=self)
self._view.setScene(self._scene)
self._view.setGeometry(base_rect)
self._menu_bar = QMenuBar(self)
self._menu_bar.addAction(self._scene.undo_action)
self._menu_bar.addAction(self._scene.redo_action)
bottom_layout = layouts.HorizontalLayout(spacing=2, margins=(2, 2, 2, 2))
self._bezier_type_combo = combobox.BaseComboBox(parent=self)
self._snap_cbx = checkbox.BaseCheckBox('Snap', parent=self)
bottom_layout.addWidget(self._bezier_type_combo)
bottom_layout.addWidget(self._snap_cbx)
self.main_layout.addWidget(self._menu_bar)
self.main_layout.addWidget(dividers.Divider(parent=self))
self.main_layout.addWidget(self._view)
self.main_layout.addWidget(dividers.Divider(parent=self))
self.main_layout.addLayout(bottom_layout)
def setup_signals(self):
self._bezier_type_combo.currentTextChanged.connect(self._on_change_curve)
self._snap_cbx.toggled.connect(self._on_change_snap)
self._scene.curveUpdated.connect(self._on_curve_updated)
def resizeEvent(self, event):
super(FallofCurveWidget, self).resizeEvent(event)
self.update_view()
def update_view(self):
self._view.fitInView(self._scene.itemsBoundingRect(), Qt.KeepAspectRatio)
def refresh(self):
self.update_view()
self._bezier_type_combo.clear()
for key, value in self._bezier_dict.items():
self._bezier_type_combo.addItem(key)
self._scene.undo_stack.clear()
def curve_as_points(self):
points = self._scene.bezier_curve.points
points_list = list()
for point in points:
points_list.append([point.x(), point.y()])
return points_list
def get_division_data(self, divisions=11):
percentage = 1 / (divisions - 1.0)
divisions_list = list()
for i in range(divisions):
divisions_list.append(i * percentage)
return self.get_data_on_points(divisions_list)
def get_data_on_percentage(self, percentage, points_list=None):
points_list = points_list or self.curve_as_points()
return bezier.get_data_on_percentage(percentage, points_list)
def get_data_on_points(self, in_list=None):
in_list = in_list or [0.0, 0.2, 0.25, 0.5, 0.6, 0.66, 0.8, 1.0]
percentage_list = list()
for point in in_list:
percentage_list.append(self.get_data_on_percentage(point))
return percentage_list
def _on_change_curve(self, text):
curve_points = self._bezier_dict[text]
self._scene.undo_stack.push(CurveNodeSwitchUndoCommand(self._scene, self._scene.get_points(), curve_points))
curve_points = self.curve_as_points()
self.curveUpdated.emit(curve_points)
def _on_change_snap(self, flag):
if not flag:
self._scene.set_snap(False)
else:
self._scene.set_snap(250)
def _on_curve_updated(self):
curve_points = self.curve_as_points()
self.curveUpdated.emit(curve_points)
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 _build_ui(self):
layout = QVBoxLayout()
self.file_selector = FilereaderComboBox(self.session)
self.file_selector.currentIndexChanged.connect(self.fill_table)
layout.insertWidget(0, self.file_selector, 0)
tabs = QTabWidget()
self.tabs = tabs
layout.insertWidget(1, self.tabs, 1)
general_info = QWidget()
general_layout = QVBoxLayout(general_info)
tabs.addTab(general_info, "general")
self.table = QTableWidget()
self.table.setColumnCount(2)
self.table.setHorizontalHeaderLabels(['Data', 'Value'])
self.table.horizontalHeader().setStretchLastSection(False)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Interactive)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Stretch)
self.table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
general_layout.insertWidget(1, self.table, 1)
self.filter = QLineEdit()
self.filter.setPlaceholderText("filter data")
self.filter.textChanged.connect(self.apply_filter)
self.filter.setClearButtonEnabled(True)
general_layout.insertWidget(2, self.filter, 0)
freq_info = QWidget()
freq_layout = QVBoxLayout(freq_info)
tabs.addTab(freq_info, "harmonic frequencies")
self.freq_table = QTableWidget()
self.freq_table.setColumnCount(4)
self.freq_table.setHorizontalHeaderLabels([
"Frequency (cm\u207b\u00b9)",
"symmetry",
"IR intensity",
"force constant (mDyne/\u212B)",
])
self.freq_table.setSortingEnabled(True)
self.freq_table.setEditTriggers(QTableWidget.NoEditTriggers)
for i in range(0, 4):
self.freq_table.resizeColumnToContents(i)
self.freq_table.horizontalHeader().setStretchLastSection(False)
self.freq_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.freq_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.freq_table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Fixed)
self.freq_table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.freq_table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
freq_layout.insertWidget(1, self.freq_table, 1)
anharm_info = QWidget()
anharm_layout = QVBoxLayout(anharm_info)
tabs.addTab(anharm_info, "anharmonic frequencies")
anharm_layout.insertWidget(0, QLabel("fundamentals:"), 0)
self.fundamental_table = QTableWidget()
self.fundamental_table.setColumnCount(3)
self.fundamental_table.setHorizontalHeaderLabels([
"Fundamental (cm\u207b\u00b9)",
"Δ\u2090\u2099\u2095 (cm\u207b\u00b9)",
"IR intensity",
])
self.fundamental_table.setSortingEnabled(True)
self.fundamental_table.setEditTriggers(QTableWidget.NoEditTriggers)
for i in range(0, 3):
self.fundamental_table.resizeColumnToContents(i)
self.fundamental_table.horizontalHeader().setStretchLastSection(False)
self.fundamental_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.fundamental_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.fundamental_table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.fundamental_table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
anharm_layout.insertWidget(1, self.fundamental_table, 1)
# self.overtone_table = QTableWidget()
# self.overtone_table.setColumnCount(3)
# self.overtone_table.setHorizontalHeaderLabels(
# [
# "Fundamental (cm\u207b\u00b9)",
# "Overtone (cm\u207b\u00b9)",
# "IR intensity",
# ]
# )
# self.overtone_table.setSortingEnabled(True)
# self.overtone_table.setEditTriggers(QTableWidget.NoEditTriggers)
# for i in range(0, 3):
# self.overtone_table.resizeColumnToContents(i)
#
# self.overtone_table.horizontalHeader().setStretchLastSection(False)
# self.overtone_table.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
# self.overtone_table.horizontalHeader().setSectionResizeMode(1, QHeaderView.Fixed)
# self.overtone_table.horizontalHeader().setSectionResizeMode(2, QHeaderView.Stretch)
#
# self.overtone_table.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding)
# anharm_layout.insertWidget(2, self.overtone_table, 1)
anharm_layout.insertWidget(2, QLabel("combinations and overtones:"), 0)
self.combo_table = QTableWidget()
self.combo_table.setColumnCount(4)
self.combo_table.setHorizontalHeaderLabels([
"Fundamental (cm\u207b\u00b9)",
"Fundamental (cm\u207b\u00b9)",
"Combination (cm\u207b\u00b9)",
"IR intensity",
])
self.combo_table.setSortingEnabled(True)
self.combo_table.setEditTriggers(QTableWidget.NoEditTriggers)
for i in range(0, 3):
self.combo_table.resizeColumnToContents(i)
self.combo_table.horizontalHeader().setStretchLastSection(False)
self.combo_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.combo_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.combo_table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Fixed)
self.combo_table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.combo_table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
anharm_layout.insertWidget(3, self.combo_table, 1)
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)
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)
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
archive = QAction("Include archive if present",
self.tool_window.ui_area,
checkable=True)
archive.triggered.connect(
lambda checked: setattr(self.settings, "archive", checked))
archive.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
archive.setChecked(self.settings.archive)
export.addAction(archive)
unit = menu.addMenu("&Units")
energy = unit.addMenu("energy")
hartree = QAction("Hartree", self.tool_window.ui_area, checkable=True)
hartree.setChecked(self.settings.energy == "Hartree")
kcal = QAction("kcal/mol", self.tool_window.ui_area, checkable=True)
kcal.setChecked(self.settings.energy == "kcal/mol")
kjoule = QAction("kJ/mol", self.tool_window.ui_area, checkable=True)
kjoule.setChecked(self.settings.energy == "kJ/mol")
energy.addAction(hartree)
energy.addAction(kcal)
energy.addAction(kjoule)
hartree.triggered.connect(
lambda *args, val="Hartree": setattr(self.settings, "energy", val))
hartree.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
hartree.triggered.connect(
lambda *args, action=kcal: action.setChecked(False))
hartree.triggered.connect(
lambda *args, action=kjoule: action.setChecked(False))
kcal.triggered.connect(lambda *args, val="kcal/mol": setattr(
self.settings, "energy", val))
kcal.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
kcal.triggered.connect(
lambda *args, action=hartree: action.setChecked(False))
kcal.triggered.connect(
lambda *args, action=kjoule: action.setChecked(False))
kjoule.triggered.connect(
lambda *args, val="kJ/mol": setattr(self.settings, "energy", val))
kjoule.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
kjoule.triggered.connect(
lambda *args, action=hartree: action.setChecked(False))
kjoule.triggered.connect(
lambda *args, action=kcal: action.setChecked(False))
mass = unit.addMenu("mass")
kg = QAction("kg", self.tool_window.ui_area, checkable=True)
kg.setChecked(self.settings.mass == "kg")
amu = QAction("Da", self.tool_window.ui_area, checkable=True)
amu.setChecked(self.settings.mass == "Da")
mass.addAction(kg)
mass.addAction(amu)
kg.triggered.connect(
lambda *args, val="kg": setattr(self.settings, "mass", val))
kg.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
kg.triggered.connect(
lambda *args, action=amu: action.setChecked(False))
amu.triggered.connect(
lambda *args, val="Da": setattr(self.settings, "mass", val))
amu.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
amu.triggered.connect(
lambda *args, action=kg: action.setChecked(False))
rot_const = unit.addMenu("rotational constants")
temperature = QAction("K", self.tool_window.ui_area, checkable=True)
temperature.setChecked(self.settings.rot_const == "K")
hertz = QAction("GHz", self.tool_window.ui_area, checkable=True)
hertz.setChecked(self.settings.rot_const == "GHz")
rot_const.addAction(temperature)
rot_const.addAction(hertz)
temperature.triggered.connect(
lambda *args, val="K": setattr(self.settings, "rot_const", val))
temperature.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
temperature.triggered.connect(
lambda *args, action=hertz: action.setChecked(False))
hertz.triggered.connect(
lambda *args, val="GHz": setattr(self.settings, "rot_const", val))
hertz.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
hertz.triggered.connect(
lambda *args, action=temperature: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
if len(self.session.filereader_manager.list()) > 0:
self.fill_table(0)
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):
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_style = QComboBox()
self.L_style.addItems(["FORTRAN", "AaronTools"])
ndx = self.L_style.findText(self.settings.L_style, Qt.MatchExactly)
self.L_style.setCurrentIndex(ndx)
self.L_style.setToolTip(
"""FORTRAN: Add 0.4 + the ideal X-H bond length to the length
of the substituent
AaronTools: add VDW radius to the length of the substituent""")
layout.addRow("L correction:", self.L_style)
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 substituents")
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',
'substituent atom',
'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 _build_ui(self):
layout = QGridLayout()
self.figure = Figure(figsize=(2, 2))
self.canvas = Canvas(self.figure)
ax = self.figure.add_axes((0.15, 0.20, 0.80, 0.70))
fr = self.filereader
if fr.all_geom is None:
self.opened = False
return
data = []
for step in fr.all_geom:
info = [
item for item in step
if isinstance(item, dict) and "energy" in item
]
if len(info) < 1:
#we will be unable to load an enegy plot because some structure does not have an associated energy
self.opened = False
self.session.logger.error(
"not enough iterations to plot - %i found" % len(info))
return
else:
info = info[0]
data.append(info["energy"])
if self.structure.num_coordsets > len(data):
data.append(fr.other["energy"])
self.ys = data
se = np.ptp(data)
self.nrg_plot = ax.plot(self.structure.coordset_ids,
data,
marker='o',
c='gray',
markersize=3)
self.nrg_plot = self.nrg_plot[0]
ax.set_xlabel('iteration')
ax.set_ylabel(r'energy ($E_h$)')
ax.set_ylim(bottom=(min(data) - se / 10), top=(max(data) + se / 10))
minlocs = [
self.structure.coordset_ids[i]
for i in range(0, self.structure.num_coordsets)
if data[i] == min(data)
]
mins = [min(data) for m in minlocs]
maxlocs = [
self.structure.coordset_ids[i]
for i in range(0, self.structure.num_coordsets)
if data[i] == max(data)
]
maxs = [max(data) for m in maxlocs]
ax.plot(minlocs, mins, marker='*', c='blue', markersize=5)
ax.plot(maxlocs, maxs, marker='*', c='red', markersize=5)
ax.ticklabel_format(axis='y',
style='sci',
scilimits=(0, 0),
useOffset=True)
ax.ticklabel_format(axis='x', style='plain', useOffset=False)
self.canvas.mpl_connect('button_release_event', self.unclick)
self.canvas.mpl_connect('button_press_event', self.onclick)
self.canvas.mpl_connect('motion_notify_event', self.drag)
self.canvas.mpl_connect('scroll_event', self.zoom)
self.annotation = ax.annotate("",
xy=(0, 0),
xytext=(0, 10),
textcoords="offset points",
fontfamily='Arial')
self.annotation.set_visible(False)
ax.autoscale()
self.canvas.draw()
self.canvas.setMinimumWidth(400)
self.canvas.setMinimumHeight(200)
layout.addWidget(self.canvas)
toolbar_widget = QWidget()
toolbar = NavigationToolbar(self.canvas, toolbar_widget)
toolbar.setMaximumHeight(32)
self.toolbar = toolbar
layout.addWidget(toolbar)
#menu bar for saving stuff
menu = QMenuBar()
file = menu.addMenu("&Export")
file.addAction("&Save CSV...")
file.triggered.connect(self.save)
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
self.opened = True