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 _build_ui(self):
#each group has an empty widget at the bottom so they resize the way I want while also having the
#labels where I want them
layout = QGridLayout()
self.tab_widget = QTabWidget()
layout.addWidget(self.tab_widget)
#layout for absolute thermo stuff
absolute_widget = QWidget()
absolute_layout = QGridLayout(absolute_widget)
#box for sp
sp_area_widget = QGroupBox("Single-point")
sp_layout = QFormLayout(sp_area_widget)
self.sp_selector = FilereaderComboBox(self.session,
otherItems=['energy'])
self.sp_selector.currentIndexChanged.connect(self.set_sp)
sp_layout.addRow(self.sp_selector)
self.sp_table = QTableWidget()
self.sp_table.setColumnCount(3)
self.sp_table.setShowGrid(False)
self.sp_table.horizontalHeader().hide()
self.sp_table.verticalHeader().hide()
self.sp_table.setFrameShape(QTableWidget.NoFrame)
self.sp_table.setSelectionMode(QTableWidget.NoSelection)
self.sp_table.insertRow(0)
sp_layout.addRow(self.sp_table)
#box for thermo
therm_area_widget = QGroupBox("Thermal corrections")
thermo_layout = QFormLayout(therm_area_widget)
self.thermo_selector = FilereaderComboBox(self.session,
otherItems=['frequency'])
self.thermo_selector.currentIndexChanged.connect(self.set_thermo_mdl)
thermo_layout.addRow(self.thermo_selector)
self.temperature_line = QDoubleSpinBox()
self.temperature_line.setMaximum(2**31 - 1)
self.temperature_line.setValue(298.15)
self.temperature_line.setSingleStep(10)
self.temperature_line.setSuffix(" K")
self.temperature_line.setMinimum(0)
self.temperature_line.valueChanged.connect(self.set_thermo)
thermo_layout.addRow("T =", self.temperature_line)
self.v0_edit = QDoubleSpinBox()
self.v0_edit.setMaximum(4000)
self.v0_edit.setValue(self.settings.w0)
self.v0_edit.setSingleStep(25)
self.v0_edit.setSuffix(" cm\u207b\u00b9")
self.v0_edit.valueChanged.connect(self.set_thermo)
self.v0_edit.setMinimum(0)
self.v0_edit.setToolTip(
"frequency parameter for quasi treatments of entropy")
thermo_layout.addRow("𝜔<sub>0</sub> =", self.v0_edit)
self.thermo_table = QTableWidget()
self.thermo_table.setColumnCount(3)
self.thermo_table.setShowGrid(False)
self.thermo_table.horizontalHeader().hide()
self.thermo_table.verticalHeader().hide()
self.thermo_table.setFrameShape(QTableWidget.NoFrame)
self.thermo_table.setSelectionMode(QTableWidget.NoSelection)
thermo_layout.addRow(self.thermo_table)
# for for total
sum_area_widget = QGroupBox("Thermochemistry")
sum_layout = QFormLayout(sum_area_widget)
self.sum_table = QTableWidget()
self.sum_table.setColumnCount(3)
self.sum_table.setShowGrid(False)
self.sum_table.horizontalHeader().hide()
self.sum_table.verticalHeader().hide()
self.sum_table.setFrameShape(QTableWidget.NoFrame)
self.sum_table.setSelectionMode(QTableWidget.NoSelection)
sum_layout.addRow(self.sum_table)
splitter = QSplitter(Qt.Horizontal)
splitter.setChildrenCollapsible(False)
splitter.addWidget(sp_area_widget)
splitter.addWidget(therm_area_widget)
splitter.addWidget(sum_area_widget)
absolute_layout.addWidget(splitter)
self.status = QStatusBar()
self.status.setSizeGripEnabled(False)
self.status.setStyleSheet("color: red")
absolute_layout.addWidget(self.status, 1, 0, 1, 1, Qt.AlignTop)
self.tab_widget.addTab(absolute_widget, "absolute")
relative_widget = QWidget()
relative_layout = QGridLayout(relative_widget)
size = [self.settings.ref_col_1, self.settings.ref_col_2]
self.ref_group = ThermoGroup("reference group", self.session,
self.nrg_fr, self.thermo_co, size)
self.ref_group.changes.connect(self.calc_relative_thermo)
relative_layout.addWidget(self.ref_group, 0, 0, 1, 3, Qt.AlignTop)
size = [self.settings.other_col_1, self.settings.other_col_2]
self.other_group = ThermoGroup("other group", self.session,
self.nrg_fr, self.thermo_co, size)
self.other_group.changes.connect(self.calc_relative_thermo)
relative_layout.addWidget(self.other_group, 0, 3, 1, 3, Qt.AlignTop)
self.relative_temperature = QDoubleSpinBox()
self.relative_temperature.setMaximum(2**31 - 1)
self.relative_temperature.setValue(self.settings.rel_temp)
self.relative_temperature.setSingleStep(10)
self.relative_temperature.setSuffix(" K")
self.relative_temperature.setMinimum(0)
self.relative_temperature.valueChanged.connect(
self.calc_relative_thermo)
relative_layout.addWidget(QLabel("T ="), 1, 0, 1, 1,
Qt.AlignRight | Qt.AlignVCenter)
relative_layout.addWidget(self.relative_temperature, 1, 1, 1, 5,
Qt.AlignLeft | Qt.AlignVCenter)
self.relative_v0 = QDoubleSpinBox()
self.relative_v0.setMaximum(2**31 - 1)
self.relative_v0.setValue(self.settings.w0)
self.relative_v0.setSingleStep(25)
self.relative_v0.setSuffix(" cm\u207b\u00b9")
self.relative_v0.setMinimum(0)
self.relative_v0.setToolTip(
"frequency parameter for quasi treatments of entropy")
self.relative_v0.valueChanged.connect(self.calc_relative_thermo)
relative_layout.addWidget(QLabel("𝜔<sub>0</sub> ="), 2, 0, 1, 1,
Qt.AlignRight | Qt.AlignVCenter)
relative_layout.addWidget(self.relative_v0, 2, 1, 1, 5,
Qt.AlignLeft | Qt.AlignVCenter)
relative_layout.addWidget(
QLabel("Boltzmann-weighted relative energies in kcal/mol:"), 3, 0,
1, 6, Qt.AlignVCenter | Qt.AlignLeft)
self.relative_table = QTextBrowser()
self.relative_table.setMaximumHeight(
4 * self.relative_table.fontMetrics().boundingRect("Q").height())
relative_layout.addWidget(self.relative_table, 4, 0, 1, 6, Qt.AlignTop)
relative_layout.setRowStretch(0, 1)
relative_layout.setRowStretch(1, 0)
relative_layout.setRowStretch(2, 0)
relative_layout.setRowStretch(3, 0)
relative_layout.setRowStretch(4, 0)
self.tab_widget.addTab(relative_widget, "relative")
#menu stuff
menu = QMenuBar()
export = menu.addMenu("&Export")
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
self.copy = copy
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QGridLayout()
layout.addWidget(QLabel("center of rotation:"), 0, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.cor_button = QComboBox()
self.cor_button.addItems(
["automatic", "select atoms", "view's center of rotation"])
layout.addWidget(self.cor_button, 0, 1, 1, 1, Qt.AlignTop)
self.set_cor_selection = QPushButton("set selection")
self.cor_button.currentTextChanged.connect(
lambda t, widget=self.set_cor_selection: widget.setEnabled(
t == "select atoms"))
self.set_cor_selection.clicked.connect(self.manual_cor)
layout.addWidget(self.set_cor_selection, 0, 2, 1, 1, Qt.AlignTop)
self.set_cor_selection.setEnabled(False)
layout.addWidget(QLabel("rotation vector:"), 1, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.vector_option = QComboBox()
self.vector_option.addItems([
"axis", "view axis", "bond", "perpendicular to plane",
"centroid of atoms", "custom"
])
layout.addWidget(self.vector_option, 1, 1, 1, 1, Qt.AlignVCenter)
vector = QWidget()
vector.setToolTip("vector will be normalized before rotating")
vector_layout = QHBoxLayout(vector)
vector_layout.setContentsMargins(0, 0, 0, 0)
self.vector_x = QDoubleSpinBox()
self.vector_y = QDoubleSpinBox()
self.vector_z = QDoubleSpinBox()
self.vector_z.setValue(1.0)
for c, t in zip([self.vector_x, self.vector_y, self.vector_z],
[" x", " y", " z"]):
c.setSingleStep(0.01)
c.setRange(-100, 100)
# c.setSuffix(t)
c.valueChanged.connect(self.show_rot_vec)
vector_layout.addWidget(c)
layout.addWidget(vector, 1, 2, 1, 1, Qt.AlignTop)
vector.setVisible(self.vector_option.currentText() == "custom")
self.vector_option.currentTextChanged.connect(
lambda text, widget=vector: widget.setVisible(text == "custom"))
self.view_axis = QComboBox()
self.view_axis.addItems(["z", "y", "x"])
layout.addWidget(self.view_axis, 1, 2, 1, 1, Qt.AlignTop)
self.view_axis.setVisible(
self.vector_option.currentText() == "view axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.view_axis: widget.setVisible(text ==
"view axis"))
self.axis = QComboBox()
self.axis.addItems(["z", "y", "x"])
layout.addWidget(self.axis, 1, 2, 1, 1, Qt.AlignTop)
self.axis.setVisible(self.vector_option.currentText() == "axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.axis: widget.setVisible(text == "axis"))
self.bond_button = QPushButton("set selected bond")
self.bond_button.clicked.connect(self.set_bonds)
layout.addWidget(self.bond_button, 1, 2, 1, 1, Qt.AlignTop)
self.bond_button.setVisible(self.vector_option.currentText() == "bond")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.bond_button: widget.setVisible(text ==
"bond"))
self.perp_button = QPushButton("set selected atoms")
self.perp_button.clicked.connect(self.set_perpendicular)
layout.addWidget(self.perp_button, 1, 2, 1, 1, Qt.AlignTop)
self.perp_button.setVisible(
self.vector_option.currentText() == "perpendicular to plane")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.perp_button: widget.setVisible(
text == "perpendicular to plane"))
self.group_button = QPushButton("set selected atoms")
self.group_button.clicked.connect(self.set_group)
layout.addWidget(self.group_button, 1, 2, 1, 1, Qt.AlignTop)
self.group_button.setVisible(
self.vector_option.currentText() == "centroid of atoms")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.group_button: widget.setVisible(
text == "centroid of atoms"))
layout.addWidget(QLabel("angle:"), 2, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.angle = QDoubleSpinBox()
self.angle.setRange(-360, 360)
self.angle.setSingleStep(5)
self.angle.setSuffix("°")
layout.addWidget(self.angle, 2, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
layout.addWidget(QLabel("preview rotation axis:"), 3, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.display_rot_vec = QCheckBox()
self.display_rot_vec.setCheckState(Qt.Checked)
self.display_rot_vec.stateChanged.connect(self.show_rot_vec)
layout.addWidget(self.display_rot_vec, 3, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
rotate_button = QPushButton("rotate selected atoms")
rotate_button.clicked.connect(self.do_rotate)
layout.addWidget(rotate_button, 4, 0, 1, 3, Qt.AlignTop)
self.rotate_button = rotate_button
self.status_bar = QStatusBar()
self.status_bar.setSizeGripEnabled(False)
layout.addWidget(self.status_bar, 5, 0, 1, 3, Qt.AlignTop)
self.vector_option.currentTextChanged.connect(self.show_auto_status)
self.cor_button.currentIndexChanged.connect(
lambda *args: self.show_auto_status("select atoms"))
self.cor_button.currentIndexChanged.connect(self.show_rot_vec)
self.set_cor_selection.clicked.connect(self.show_rot_vec)
self.vector_option.currentIndexChanged.connect(self.show_rot_vec)
self.axis.currentIndexChanged.connect(self.show_rot_vec)
self.view_axis.currentIndexChanged.connect(self.show_rot_vec)
self.bond_button.clicked.connect(self.show_rot_vec)
self.perp_button.clicked.connect(self.show_rot_vec)
self.group_button.clicked.connect(self.show_rot_vec)
layout.setRowStretch(0, 0)
layout.setRowStretch(1, 0)
layout.setRowStretch(2, 0)
layout.setRowStretch(3, 0)
layout.setRowStretch(4, 0)
layout.setRowStretch(5, 1)
layout.setColumnStretch(0, 0)
layout.setColumnStretch(1, 1)
layout.setColumnStretch(2, 1)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
self.tree = QTreeWidget()
self.tree.setSelectionMode(QTreeWidget.ExtendedSelection)
self.tree.setHeaderLabels([
"name", "status", "server", "prioritize", "kill", "delete",
"browse"
])
self.tree.setUniformRowHeights(True)
self.tree.setColumnWidth(0, 150)
layout.addWidget(self.tree, 0, 0, 6, 1, Qt.AlignTop)
row = 0
pause_button = QPushButton(
"pause new jobs"
if not self.session.seqcrow_job_manager.paused else "resume jobs")
pause_button.setCheckable(True)
pause_button.clicked.connect(lambda check: pause_button.setText(
"pause new jobs" if not check else "resume jobs"))
pause_button.setChecked(self.session.seqcrow_job_manager.paused)
pause_button.clicked.connect(self.pause_queue)
layout.addWidget(pause_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
open_button = QPushButton("open structure")
open_button.clicked.connect(self.open_jobs)
layout.addWidget(open_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
log_button = QPushButton("log")
log_button.clicked.connect(self.open_log)
layout.addWidget(log_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
output_button = QPushButton("raw output")
output_button.clicked.connect(self.open_output)
layout.addWidget(output_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
refresh_button = QToolButton()
refresh_button.setSizePolicy(QSizePolicy.Fixed,
QSizePolicy.MinimumExpanding)
refresh_button.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
refresh_button.setIcon(
QIcon(refresh_button.style().standardIcon(
QStyle.SP_BrowserReload)))
refresh_button.setText('check jobs')
refresh_button.clicked.connect(
lambda *args: self.session.seqcrow_job_manager.triggers.
activate_trigger(JOB_QUEUED, "refresh"))
layout.addWidget(refresh_button, row, 1, 1, 1, Qt.AlignTop)
row += 1
for i in range(0, row - 1):
layout.setRowStretch(i, 0)
layout.setRowStretch(row - 1, 1)
layout.setColumnStretch(0, 1)
layout.setColumnStretch(1, 0)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def __init__(self, *args, initial_elements=[], select_multiple=True, **kwargs):
super().__init__(*args, **kwargs)
layout = QGridLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
self._elements = {ele: ElementButton(ele) for ele in ELEMENTS if not any(ele == x for x in ['Bq', 'X'])}
for ele in self._elements.keys():
self._elements[ele].setTristate(False)
if select_multiple:
self._elements[ele].stateChanged.connect(lambda state, ele=ele: self.elementSelectionChanged.emit())
else:
self._elements[ele].stateChanged.connect(lambda state, ele=ele: self._single_ele_clicked(state, ele))
elements_widget = QWidget()
elements_layout = QGridLayout(elements_widget)
elements_layout.setContentsMargins(0, 0, 0, 0)
elements_layout.addWidget(self._elements['H'], 0, 0, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['He'], 0, 17, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Li'], 1, 0, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Be'], 1, 1, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['B'], 1, 12, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['C'], 1, 13, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['N'], 1, 14, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['O'], 1, 15, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['F'], 1, 16, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ne'], 1, 17, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Na'], 2, 0, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Mg'], 2, 1, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Al'], 2, 12, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Si'], 2, 13, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['P'], 2, 14, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['S'], 2, 15, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Cl'], 2, 16, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ar'], 2, 17, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['K'], 3, 0, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ca'], 3, 1, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Sc'], 3, 2, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ti'], 3, 3, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['V'], 3, 4, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Cr'], 3, 5, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Mn'], 3, 6, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Fe'], 3, 7, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Co'], 3, 8, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ni'], 3, 9, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Cu'], 3, 10, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Zn'], 3, 11, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ga'], 3, 12, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ge'], 3, 13, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['As'], 3, 14, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Se'], 3, 15, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Br'], 3, 16, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Kr'], 3, 17, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Rb'], 4, 0, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Sr'], 4, 1, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Y'], 4, 2, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Zr'], 4, 3, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Nb'], 4, 4, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Mo'], 4, 5, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Tc'], 4, 6, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ru'], 4, 7, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Rh'], 4, 8, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Pd'], 4, 9, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ag'], 4, 10, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Cd'], 4, 11, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['In'], 4, 12, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Sn'], 4, 13, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Sb'], 4, 14, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Te'], 4, 15, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['I'], 4, 16, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Xe'], 4, 17, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Cs'], 5, 0, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ba'], 5, 1, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Hf'], 5, 3, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ta'], 5, 4, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['W'], 5, 5, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Re'], 5, 6, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Os'], 5, 7, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ir'], 5, 8, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Pt'], 5, 9, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Au'], 5, 10, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Hg'], 5, 11, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Tl'], 5, 12, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Pb'], 5, 13, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Bi'], 5, 14, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Po'], 5, 15, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['At'], 5, 16, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Rn'], 5, 17, Qt.AlignLeft | Qt.AlignTop)
if 'Fr' in ELEMENTS:
elements_layout.addWidget(self._elements['Fr'], 6, 0, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ra'], 6, 1, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Rf'], 6, 3, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Db'], 6, 4, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Sg'], 6, 5, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Bh'], 6, 6, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Hs'], 6, 7, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Mt'], 6, 8, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ds'], 6, 9, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Rg'], 6, 10, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Cn'], 6, 11, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Nh'], 6, 12, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Fl'], 6, 13, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Mc'], 6, 14, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Lv'], 6, 15, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ts'], 6, 16, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Og'], 6, 17, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['La'], 7, 2, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ce'], 7, 3, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Pr'], 7, 4, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Nd'], 7, 5, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Pm'], 7, 6, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Sm'], 7, 7, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Eu'], 7, 8, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Gd'], 7, 9, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Tb'], 7, 10, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Dy'], 7, 11, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Ho'], 7, 12, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Er'], 7, 13, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Tm'], 7, 14, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Yb'], 7, 15, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Lu'], 7, 16, Qt.AlignLeft | Qt.AlignTop)
if 'Ac' in ELEMENTS:
elements_layout.addWidget(self._elements['Ac'], 8, 2, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Th'], 8, 3, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Pa'], 8, 4, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['U'], 8, 5, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Np'], 8, 6, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Pu'], 8, 7, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Am'], 8, 8, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Cm'], 8, 9, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Bk'], 8, 10, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Cf'], 8, 11, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Es'], 8, 12, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Fm'], 8, 13, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Md'], 8, 14, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['No'], 8, 15, Qt.AlignLeft | Qt.AlignTop)
elements_layout.addWidget(self._elements['Lr'], 8, 16, Qt.AlignLeft | Qt.AlignTop)
if select_multiple:
organic_button = QPushButton("organic chemists'")
organic_button.setCheckable(True)
organic_button.clicked.connect(self._select_ochem)
#layout.addWidget(organic_button, 9, col, Qt.AlignTop)
z_lt_37_button = QPushButton("H-Kr")
z_lt_37_button.setCheckable(True)
z_lt_37_button.clicked.connect(self._select_z_lt_37)
layout.addWidget(z_lt_37_button, 9, 0, Qt.AlignTop)
z_ge_37_button = QPushButton("row 5+")
z_ge_37_button.setCheckable(True)
z_ge_37_button.clicked.connect(self._select_z_ge_37)
layout.addWidget(z_ge_37_button, 9, 1, Qt.AlignTop)
z_le_86_button = QPushButton("H-Rn")
z_le_86_button.setCheckable(True)
z_le_86_button.clicked.connect(self._select_z_le_86)
layout.addWidget(z_le_86_button, 9, 2, Qt.AlignTop)
tm_button = QPushButton("transition metals")
tm_button.setCheckable(True)
tm_button.clicked.connect(self._select_tm)
layout.addWidget(tm_button, 9, 3, Qt.AlignTop)
all_button = QPushButton("all")
all_button.clicked.connect(self._select_all)
all_button.clicked.connect(lambda *args: organic_button.setChecked(False))
all_button.clicked.connect(lambda *args: tm_button.setChecked(False))
all_button.clicked.connect(lambda *args: organic_button.setChecked(False))
all_button.clicked.connect(lambda *args: z_lt_37_button.setChecked(False))
all_button.clicked.connect(lambda *args: z_ge_37_button.setChecked(False))
all_button.clicked.connect(lambda *args: z_le_86_button.setChecked(False))
layout.addWidget(all_button, 10, 0, Qt.AlignTop)
invert = QPushButton("invert")
invert.clicked.connect(self._invert)
invert.clicked.connect(lambda *args: organic_button.setChecked(False))
invert.clicked.connect(lambda *args: tm_button.setChecked(False))
invert.clicked.connect(lambda *args: organic_button.setChecked(False))
invert.clicked.connect(lambda *args: z_lt_37_button.setChecked(False))
invert.clicked.connect(lambda *args: z_ge_37_button.setChecked(False))
invert.clicked.connect(lambda *args: z_le_86_button.setChecked(False))
layout.addWidget(invert, 10, 2, Qt.AlignTop)
clear = QPushButton("clear")
clear.clicked.connect(self._clear)
clear.clicked.connect(lambda *args: organic_button.setChecked(False))
clear.clicked.connect(lambda *args: tm_button.setChecked(False))
clear.clicked.connect(lambda *args: organic_button.setChecked(False))
clear.clicked.connect(lambda *args: z_lt_37_button.setChecked(False))
clear.clicked.connect(lambda *args: z_ge_37_button.setChecked(False))
clear.clicked.connect(lambda *args: z_le_86_button.setChecked(False))
layout.addWidget(clear, 10, 1, Qt.AlignTop)
reset = QPushButton("reset")
reset.clicked.connect(self._reset)
reset.clicked.connect(lambda *args: organic_button.setChecked(False))
reset.clicked.connect(lambda *args: tm_button.setChecked(False))
reset.clicked.connect(lambda *args: organic_button.setChecked(False))
reset.clicked.connect(lambda *args: z_lt_37_button.setChecked(False))
reset.clicked.connect(lambda *args: z_ge_37_button.setChecked(False))
reset.clicked.connect(lambda *args: z_le_86_button.setChecked(False))
layout.addWidget(reset, 10, 3, Qt.AlignTop)
layout.addWidget(elements_widget, 0, 0, 7, 4, Qt.AlignLeft | Qt.AlignTop)
self.setSelectedElements(initial_elements)
self._initial_elements = initial_elements
layout.setRowStretch(0, 0)
layout.setRowStretch(1, 0)
layout.setRowStretch(2, 0)
layout.setRowStretch(3, 0)
layout.setRowStretch(4, 0)
layout.setRowStretch(5, 0)
layout.setRowStretch(6, 0)
layout.setRowStretch(7, 0)
layout.setRowStretch(8, 0)
layout.setRowStretch(9, 0)
layout.setRowStretch(10, 1)
layout.setColumnStretch(0, 0)
layout.setColumnStretch(1, 1)
layout.setColumnStretch(2, 1)
layout.setColumnStretch(3, 1)
else:
layout.addWidget(elements_widget)
if len(initial_elements) > 0:
self.setSelectedElements([initial_elements[0]])
self._initial_elements = [initial_elements[0]]
def _build_ui(self):
layout = QGridLayout()
self.alchemy_tabs = QTabWidget()
#substitute
substitute_tab = QWidget()
substitute_layout = QGridLayout(substitute_tab)
sublabel = QLabel("substituent name:")
substitute_layout.addWidget(sublabel, 0, 0, Qt.AlignVCenter)
self.subname = QLineEdit()
# self.subname.setText("Et")
sub_completer = NameCompleter(Substituent.list(), self.subname)
self.subname.setCompleter(sub_completer)
self.subname.setToolTip("name of substituent in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
substitute_layout.addWidget(self.subname, 0, 1, Qt.AlignVCenter)
open_sub_lib = QPushButton("from library...")
open_sub_lib.clicked.connect(self.open_sub_selector)
substitute_layout.addWidget(open_sub_lib, 0, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_sub = QCheckBox()
self.close_previous_sub.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_sub.setChecked(self.settings.modify)
self.close_previous_sub.stateChanged.connect(self.close_previous_change)
substitute_layout.addWidget(self.close_previous_sub, 1, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("relax substituent:"), 2, 0, 1, 1, Qt.AlignVCenter)
self.minimize = QCheckBox()
self.minimize.setToolTip("spin the added substituents to try to minimize the LJ potential energy")
self.minimize.setChecked(self.settings.minimize)
substitute_layout.addWidget(self.minimize, 2, 1, 1, 1, Qt.AlignTop)
substitute_layout.addWidget(QLabel("guess previous substituent:"), 3, 0, 1, 1, Qt.AlignVCenter)
self.guess_old = QCheckBox()
self.guess_old.setToolTip("checked: leave the longest connected fragment in the residue\nunchecked: previous substituent must be selected")
self.guess_old.setChecked(self.settings.guess)
self.guess_old.stateChanged.connect(lambda state, settings=self.settings: settings.__setattr__("guess", True if state == Qt.Checked else False))
substitute_layout.addWidget(self.guess_old, 3, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("new residue:"), 5, 0, 1, 1, Qt.AlignVCenter)
self.new_residue = QCheckBox()
self.new_residue.setToolTip("put the new substituent in its own residue instead\nof adding it to the residue of the old substituent")
self.new_residue.setChecked(self.settings.new_residue)
self.new_residue.stateChanged.connect(lambda state, settings=self.settings: settings.__setattr__("new_residue", True if state == Qt.Checked else False))
substitute_layout.addWidget(self.new_residue, 5, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("use distance names:"), 4, 0, 1, 1, Qt.AlignVCenter)
self.use_greek = QCheckBox()
self.use_greek.setChecked(self.settings.use_greek)
self.use_greek.setToolTip("indicate distance from point of attachment with atom name")
substitute_layout.addWidget(self.use_greek, 4, 1, 1, 1, Qt.AlignTop)
substitute_layout.addWidget(QLabel("change residue name:"), 6, 0, 1, 1, Qt.AlignVCenter)
self.new_sub_name = QLineEdit()
self.new_sub_name.setToolTip("change name of modified residues")
self.new_sub_name.setPlaceholderText("leave blank to keep current")
substitute_layout.addWidget(self.new_sub_name, 6, 1, 1, 2, Qt.AlignTop)
substitute_button = QPushButton("substitute current selection")
substitute_button.clicked.connect(self.do_substitute)
substitute_layout.addWidget(substitute_button, 7, 0, 1, 3, Qt.AlignTop)
self.substitute_button = substitute_button
substitute_layout.setRowStretch(0, 0)
substitute_layout.setRowStretch(1, 0)
substitute_layout.setRowStretch(2, 0)
substitute_layout.setRowStretch(3, 0)
substitute_layout.setRowStretch(4, 0)
substitute_layout.setRowStretch(5, 0)
substitute_layout.setRowStretch(6, 0)
substitute_layout.setRowStretch(7, 1)
#map ligand
maplig_tab = QWidget()
maplig_layout = QGridLayout(maplig_tab)
liglabel = QLabel("ligand name:")
maplig_layout.addWidget(liglabel, 0, 0, Qt.AlignVCenter)
self.ligname = QLineEdit()
lig_completer = NameCompleter(Component.list(), self.ligname)
self.ligname.setCompleter(lig_completer)
self.ligname.setToolTip("name of ligand in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
maplig_layout.addWidget(self.ligname, 0, 1, Qt.AlignVCenter)
open_lig_lib = QPushButton("from library...")
open_lig_lib.clicked.connect(self.open_lig_selector)
maplig_layout.addWidget(open_lig_lib, 0, 2, Qt.AlignTop)
maplig_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_lig = QCheckBox()
self.close_previous_lig.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_lig.setChecked(self.settings.modify)
self.close_previous_lig.stateChanged.connect(self.close_previous_change)
maplig_layout.addWidget(self.close_previous_lig, 1, 1, 1, 2, Qt.AlignTop)
maplig_button = QPushButton("swap ligand with selected coordinating atoms")
maplig_button.clicked.connect(self.do_maplig)
maplig_layout.addWidget(maplig_button, 2, 0, 1, 3, Qt.AlignTop)
self.maplig_button = maplig_button
start_structure_button = QPushButton("place in:")
self.lig_model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_lig)
maplig_layout.addWidget(start_structure_button, 3, 0, 1, 1, Qt.AlignTop)
maplig_layout.addWidget(self.lig_model_selector, 3, 1, 1, 2, Qt.AlignTop)
maplig_layout.setRowStretch(0, 0)
maplig_layout.setRowStretch(1, 0)
maplig_layout.setRowStretch(2, 0)
maplig_layout.setRowStretch(3, 1)
#close ring
closering_tab = QWidget()
closering_layout = QGridLayout(closering_tab)
ringlabel = QLabel("ring name:")
closering_layout.addWidget(ringlabel, 0, 0, Qt.AlignVCenter)
self.ringname = QLineEdit()
ring_completer = NameCompleter(Ring.list(), self.ringname)
self.ringname.setCompleter(ring_completer)
self.ringname.setToolTip("name of ring in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
closering_layout.addWidget(self.ringname, 0, 1, Qt.AlignVCenter)
open_ring_lib = QPushButton("from library...")
open_ring_lib.clicked.connect(self.open_ring_selector)
closering_layout.addWidget(open_ring_lib, 0, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_ring = QCheckBox()
self.close_previous_ring.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_ring.setChecked(self.settings.modify)
self.close_previous_ring.stateChanged.connect(self.close_previous_change)
closering_layout.addWidget(self.close_previous_ring, 1, 1, 1, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("try multiple:"), 2, 0, 1, 1, Qt.AlignVCenter)
self.minimize_ring = QCheckBox()
self.minimize_ring.setToolTip("try to use other versions of this ring in the library to find the one that fits best")
self.minimize_ring.setChecked(self.settings.minimize_ring)
closering_layout.addWidget(self.minimize_ring, 2, 1, 1, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("new residue name:"), 3, 0, 1, 1, Qt.AlignVCenter)
self.new_ring_name = QLineEdit()
self.new_ring_name.setToolTip("change name of modified residues")
self.new_ring_name.setPlaceholderText("leave blank to keep current")
closering_layout.addWidget(self.new_ring_name, 3, 1, 1, 2, Qt.AlignTop)
closering_button = QPushButton("put a ring on current selection")
closering_button.clicked.connect(self.do_fusering)
closering_layout.addWidget(closering_button, 4, 0, 1, 3, Qt.AlignTop)
self.closering_button = closering_button
start_structure_button = QPushButton("place in:")
self.ring_model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_ring)
closering_layout.addWidget(start_structure_button, 5, 0, 1, 1, Qt.AlignTop)
closering_layout.addWidget(self.ring_model_selector, 5, 1, 1, 2, Qt.AlignTop)
closering_layout.setRowStretch(0, 0)
closering_layout.setRowStretch(1, 0)
closering_layout.setRowStretch(2, 0)
closering_layout.setRowStretch(3, 0)
closering_layout.setRowStretch(4, 0)
closering_layout.setRowStretch(5, 1)
#change element
changeelement_tab = QWidget()
changeelement_layout = QFormLayout(changeelement_tab)
self.element = ElementButton("C", single_state=True)
self.element.clicked.connect(self.open_ptable)
changeelement_layout.addRow("element:", self.element)
self.vsepr = QComboBox()
self.vsepr.addItems([
"do not change", # 0
"linear (1 bond)", # 1
"linear (2 bonds)", # 2
"trigonal planar (2 bonds)", # 3
"tetrahedral (2 bonds)", # 4
"trigonal planar", # 5
"tetrahedral (3 bonds)", # 6
"T-shaped", # 7
"trigonal pyramidal", # 8
"tetrahedral", # 9
"sawhorse", #10
"seesaw", #11
"square planar", #12
"trigonal bipyramidal", #13
"square pyramidal", #14
"pentagonal", #15
"octahedral", #16
"hexagonal", #17
"trigonal prismatic", #18
"pentagonal pyramidal", #19
"capped octahedral", #20
"capped trigonal prismatic", #21
"heptagonal", #22
"hexagonal pyramidal", #23
"pentagonal bipyramidal", #24
"biaugmented trigonal prismatic", #25
"cubic", #26
"elongated trigonal bipyramidal", #27
"hexagonal bipyramidal", #28
"heptagonal pyramidal", #29
"octagonal", #30
"square antiprismatic", #31
"trigonal dodecahedral", #32
"capped cube", #33
"capped square antiprismatic", #34
"enneagonal", #35
"heptagonal bipyramidal", #36
"hula-hoop", #37
"triangular cupola", #38
"tridiminished icosahedral", #39
"muffin", #40
"octagonal pyramidal", #41
"tricapped trigonal prismatic", #42
])
self.vsepr.setCurrentIndex(9)
self.vsepr.insertSeparator(33)
self.vsepr.insertSeparator(25)
self.vsepr.insertSeparator(20)
self.vsepr.insertSeparator(16)
self.vsepr.insertSeparator(13)
self.vsepr.insertSeparator(8)
self.vsepr.insertSeparator(5)
self.vsepr.insertSeparator(2)
self.vsepr.insertSeparator(1)
self.vsepr.insertSeparator(0)
changeelement_layout.addRow("geometry:", self.vsepr)
self.change_bonds = QCheckBox()
self.change_bonds.setChecked(self.settings.change_bonds)
changeelement_layout.addRow("adjust bond lengths:", self.change_bonds)
change_element_button = QPushButton("change selected elements")
change_element_button.clicked.connect(self.do_change_element)
changeelement_layout.addRow(change_element_button)
self.change_element_button = change_element_button
start_structure_button = QPushButton("place in:")
self.model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_atom)
changeelement_layout.addRow(start_structure_button, self.model_selector)
delete_atoms_button = QPushButton("delete selected atoms")
delete_atoms_button.clicked.connect(self.delete_atoms)
changeelement_layout.addRow(delete_atoms_button)
self.alchemy_tabs.addTab(substitute_tab, "substitute")
self.alchemy_tabs.addTab(maplig_tab, "swap ligand")
self.alchemy_tabs.addTab(closering_tab, "fuse ring")
self.alchemy_tabs.addTab(changeelement_tab, "change element")
layout.addWidget(self.alchemy_tabs)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
