def ask_login(parent=None):
# type: (Any) -> AccountInfo
"""Ask login with a dialog.
parent (QWidget, optional): Defaults to None. Parent widget.
Returns:
cgtwq.AccountInfo: Account logged in.
"""
_app = application()
dialog = QDialog(parent)
account_input = QLineEdit()
password_input = QLineEdit()
_setup_login_dialog(dialog, account_input, password_input)
while True:
dialog.exec_()
if dialog.result() == QDialog.Rejected:
raise ValueError("Rejected")
account, password = account_input.text(), password_input.text()
try:
return cgtwq.login(account, password)
except (ValueError, cgtwq.AccountNotFoundError, cgtwq.PasswordError) as ex:
msg = text_type(ex)
QMessageBox.critical(parent, "登录失败", msg)
def createPropertiesWidget(self, propertiesWidget):
baseCategory = CollapsibleFormWidget(headName="Base", modify=True)
# name
le_name = QLineEdit(self._rawVariable.name)
le_name.returnPressed.connect(lambda: self.setName(le_name.text()))
baseCategory.addWidget("Name", le_name)
# data type
cbTypes = EnumComboBox([
pin.__name__ for pin in getAllPinClasses() if pin.IsValuePin()
if pin.__name__ != "AnyPin"
])
cbTypes.setCurrentIndex(cbTypes.findText(self.dataType))
cbTypes.setEditable(False)
cbTypes.changeCallback.connect(self.setDataType)
propertiesWidget.addWidget(baseCategory)
# structure type
cbStructure = EnumComboBox(
[i.name for i in (PinStructure.Single, PinStructure.Array)])
cbStructure.setEditable(False)
cbStructure.setCurrentIndex(
cbStructure.findText(self._rawVariable.structure.name))
cbStructure.changeCallback.connect(self.onStructureChanged)
propertiesWidget.addWidget(baseCategory)
baseCategory.addWidget("Type", cbTypes)
baseCategory.addWidget("Structure", cbStructure)
valueCategory = CollapsibleFormWidget(headName="Value")
# current value
if self._rawVariable.structure == PinStructure.Single:
if not type(self._rawVariable.value) in {list, set, dict, tuple}:
def valSetter(x):
self._rawVariable.value = x
w = createInputWidget(
self._rawVariable.dataType, valSetter,
getPinDefaultValueByType(self._rawVariable.dataType))
if w:
w.setWidgetValue(self._rawVariable.value)
w.setObjectName(self._rawVariable.name)
valueCategory.addWidget(self._rawVariable.name, w)
# access level
cb = QComboBox()
cb.addItem('public', 0)
cb.addItem('private', 1)
cb.addItem('protected', 2)
def accessLevelChanged(x):
self._rawVariable.accessLevel = AccessLevel[x]
EditorHistory().saveState("Change variable access level",
modify=True)
cb.currentTextChanged.connect(accessLevelChanged)
cb.setCurrentIndex(self._rawVariable.accessLevel)
valueCategory.addWidget('Access level', cb)
propertiesWidget.addWidget(valueCategory)
def onUpdatePropertyView(self, formLayout):
# name
le_name = QLineEdit(self.name)
le_name.returnPressed.connect(lambda: self.setName(le_name.text()))
formLayout.addRow("Name", le_name)
# data type
cbTypes = VarTypeComboBox(self)
formLayout.addRow("Type", cbTypes)
# current value
def valSetter(x):
self.value = x
w = InputWidgets.getInputWidget(
self.dataType, valSetter,
Pins.getPinDefaultValueByType(self.dataType), None)
if w:
w.setWidgetValue(self.value)
w.setObjectName(self.name)
formLayout.addRow(self.name, w)
# access level
cb = QComboBox()
cb.addItem('public', 0)
cb.addItem('private', 1)
cb.addItem('protected', 2)
def accessLevelChanged(x):
self.accessLevel = x
cb.currentIndexChanged[int].connect(accessLevelChanged)
cb.setCurrentIndex(self.accessLevel)
formLayout.addRow('Access level', cb)
def createPropertiesWidget(self, propertiesWidget):
baseCategory = CollapsibleFormWidget(headName="Base")
# name
le_name = QLineEdit(self.getName())
le_name.setReadOnly(True)
# if self.isRenamable():
le_name.setReadOnly(False)
le_name.returnPressed.connect(lambda: self.setName(le_name.text()))
baseCategory.addWidget("Name", le_name)
# type
leType = QLineEdit(self.__class__.__name__)
leType.setReadOnly(True)
baseCategory.addWidget("Type", leType)
# pos
le_pos = QLineEdit("{0} x {1}".format(self.pos().x(), self.pos().y()))
baseCategory.addWidget("Pos", le_pos)
propertiesWidget.addWidget(baseCategory)
appearanceCategory = CollapsibleFormWidget(headName="Appearance")
pb = QPushButton("...")
pb.clicked.connect(lambda: self.onChangeColor(True))
appearanceCategory.addWidget("Color", pb)
propertiesWidget.addWidget(appearanceCategory)
infoCategory = CollapsibleFormWidget(headName="Info")
doc = QTextBrowser()
doc.setOpenExternalLinks(True)
doc.setHtml(self.description())
infoCategory.addWidget("", doc)
propertiesWidget.addWidget(infoCategory)
def onUpdatePropertyView(self, formLayout):
# name
le_name = QLineEdit(self.getName())
le_name.setReadOnly(True)
if self.label().IsRenamable():
le_name.setReadOnly(False)
le_name.returnPressed.connect(lambda: self.setName(le_name.text()))
formLayout.addRow("Name", le_name)
# uid
leUid = QLineEdit(str(self.uid))
leUid.setReadOnly(True)
#formLayout.addRow("Uuid", leUid)
# type
leType = QLineEdit(self.__class__.__name__)
leType.setReadOnly(True)
formLayout.addRow("Type", leType)
# pos
#le_pos = QLineEdit("{0} x {1}".format(self.pos().x(), self.pos().y()))
#formLayout.addRow("Pos", le_pos)
# inputs
if len([i for i in self.inputs.values()]) != 0:
for inp in self.inputs.values():
dataSetter = inp.call if inp.dataType == DataTypes.Exec else inp.setData
if not inp.hasConnections():
w = getInputWidget(inp.dataType, dataSetter,
inp.defaultValue(), inp.getUserStruct())
if w:
w.setWidgetValue(inp.currentData())
w.setObjectName(inp.getName())
formLayout.addRow(inp.name, w)
if inp.hasConnections():
w.setEnabled(False)
w.hide()
if self.asGraphSides:
# outputs
if len([i for i in self.outputs.values()]) != 0:
for out in self.outputs.values():
dataSetter = out.call if out.dataType == DataTypes.Exec else out.setData
w = getInputWidget(out.dataType, dataSetter,
out.defaultValue(), out.getUserStruct())
if w:
w.setWidgetValue(out.currentData())
w.setObjectName(out.getName())
formLayout.addRow(out.name, w)
if out.hasConnections():
w.setEnabled(True)
doc_lb = QLabel()
doc_lb.setStyleSheet("background-color: black;")
doc_lb.setText("Description")
#formLayout.addRow("", doc_lb)
doc = QTextBrowser()
doc.setOpenExternalLinks(True)
doc.setHtml(self.description())
class StringEditor(BaseEditor, object):
attr_type = 'str'
def __init__(self, parent=None, **kwargs):
super(StringEditor, self).__init__(parent=parent, **kwargs)
self._default_value = ""
self._clean_value = kwargs.get('clean', True)
self.value_line = QLineEdit(self)
reg_exp = QRegExp('^([a-zA-Z0-9_]+)')
self.main_layout.addWidget(self.value_line)
self.value_line.textEdited.connect(self._validate_text)
self.value_line.editingFinished.connect(self.OnValueUpdated)
self.value_line.returnPressed.connect(self.OnValueUpdated)
def get_value(self):
return str(self.value_line.text())
value = property(get_value)
def initialize_editor(self):
editor_value = self.default_value
node_values = self.values
if node_values:
if len(node_values) > 1:
pass
elif len(node_values) == 1:
if node_values[0]:
editor_value = node_values[0]
self.value_line.blockSignals(True)
self.value_line.setText(str(editor_value))
self.value_line.blockSignals(False)
def set_connected(self, conn):
if conn != self._connection:
self._connection = conn
self.value_line.setText(conn)
self.value_line.setEnabled(False)
self.value_line.setProperty('class', 'Connected')
def _validate_text(self, text):
"""
Validates the given value and update the current text
:param text: str, text to validate
"""
current_text = self.value
if self._clean_value:
cursor_pos = self.value_line.cursorPosition()
cleaned = string_utils.clean_string(text=text)
self.value_line.blockSignals(True)
self.value_line.setText(cleaned)
self.value_line.blockSignals(False)
self.value_line.setCursorPosition(cursor_pos)
def createPropertiesWidget(self, propertiesWidget):
baseCategory = CollapsibleFormWidget(headName="Base")
# name
le_name = QLineEdit(self._rawVariable.name)
le_name.returnPressed.connect(lambda: self.setName(le_name.text()))
baseCategory.addWidget("Name", le_name)
# data type
cbTypes = VarTypeComboBox(self)
baseCategory.addWidget("Type", cbTypes)
propertiesWidget.addWidget(baseCategory)
valueCategory = CollapsibleFormWidget(headName="Value")
# current value
def valSetter(x):
self._rawVariable.value = x
w = createInputWidget(
self._rawVariable.dataType, valSetter,
getPinDefaultValueByType(self._rawVariable.dataType))
if w:
w.setWidgetValue(self._rawVariable.value)
w.setObjectName(self._rawVariable.name)
valueCategory.addWidget(self._rawVariable.name, w)
# access level
cb = QComboBox()
cb.addItem('public', 0)
cb.addItem('private', 1)
cb.addItem('protected', 2)
def accessLevelChanged(x):
self._rawVariable.accessLevel = AccessLevel[x]
cb.currentTextChanged.connect(accessLevelChanged)
cb.setCurrentIndex(self._rawVariable.accessLevel)
valueCategory.addWidget('Access level', cb)
propertiesWidget.addWidget(valueCategory)
def onUpdatePropertyView(self, formLayout):
# name
le_name = QLineEdit(self.getName())
le_name.setReadOnly(True)
if self.label().IsRenamable():
le_name.setReadOnly(False)
le_name.returnPressed.connect(lambda: self.setName(le_name.text()))
formLayout.addRow("Name", le_name)
# uid
leUid = QLineEdit(str(self.uid))
leUid.setReadOnly(True)
formLayout.addRow("Uuid", leUid)
# type
leType = QLineEdit(self.__class__.__name__)
leType.setReadOnly(True)
formLayout.addRow("Type", leType)
# pos
le_pos = QLineEdit("{0} x {1}".format(self.pos().x(), self.pos().y()))
formLayout.addRow("Pos", le_pos)
pb = QPushButton("...")
pb.clicked.connect(self.onChangeColor)
formLayout.addRow("Color", pb)
doc_lb = QLabel()
doc_lb.setStyleSheet("background-color: black;")
doc_lb.setText("Description")
formLayout.addRow("", doc_lb)
doc = QTextBrowser()
doc.setOpenExternalLinks(True)
doc.setHtml(self.description())
formLayout.addRow("", doc)
class BaseFileFolderDialog(BaseDialog,
abstract_dialog.AbstractFileFolderDialog):
"""
Base dialog classes for folders and files
"""
def_title = 'Select File'
def_size = (200, 125)
def_use_app_browser = False
def __init__(self, name='BaseFileFolder', parent=None, **kwargs):
super(BaseFileFolderDialog, self).__init__(name=name, parent=parent)
self.directory = None
self.filters = None
self._use_app_browser = kwargs.pop('use_app_browser',
self.def_use_app_browser)
self.set_filters('All Files (*.*)')
# By default, we set the directory to the user folder
self.set_directory(os.path.expanduser('~'))
self.center()
def open_app_browser(self):
return
def ui(self):
super(BaseFileFolderDialog, self).ui()
from tpDcc.libs.qt.widgets import directory
self.places = dict()
self.grid = layouts.GridLayout()
sub_grid = layouts.GridLayout()
self.grid.addWidget(QLabel('Path:'), 0, 0, Qt.AlignRight)
self.path_edit = QLineEdit(self)
self.path_edit.setReadOnly(True)
self.filter_box = QComboBox(self)
self.file_edit = QLineEdit(self)
self.view = directory.FileListWidget(self)
self.view.setWrapping(True)
self.view.setFocusPolicy(Qt.StrongFocus)
self.open_button = QPushButton('Select', self)
self.cancel_button = QPushButton('Cancel', self)
size = QSize(32, 24)
self.up_button = QPushButton('Up')
self.up_button.setToolTip('Go up')
self.up_button.setMinimumSize(size)
self.up_button.setMaximumSize(size)
size = QSize(56, 24)
self.refresh_button = QPushButton('Reload')
self.refresh_button.setToolTip('Reload file list')
self.refresh_button.setMinimumSize(size)
self.refresh_button.setMaximumSize(size)
self.show_hidden = QCheckBox('Hidden')
self.show_hidden.setChecked(False)
self.show_hidden.setToolTip('Toggle show hidden files')
sub_grid.addWidget(self.up_button, 0, 1)
sub_grid.addWidget(self.path_edit, 0, 2)
sub_grid.addWidget(self.refresh_button, 0, 3)
sub_grid.addWidget(self.show_hidden, 0, 4)
self.grid.addLayout(sub_grid, 0, 1)
self.grid.addWidget(self.get_drives_widget(), 1, 0)
self.grid.addWidget(self.view, 1, 1)
self.grid.addWidget(QLabel('File name:'), 7, 0, Qt.AlignRight)
self.grid.addWidget(self.file_edit, 7, 1)
self.filter_label = QLabel('Filter:')
self.grid.addWidget(self.filter_label, 8, 0, Qt.AlignRight)
self.grid.addWidget(self.filter_box, 8, 1)
hbox = layouts.GridLayout()
hbox.addWidget(self.open_button, 0, 0, Qt.AlignRight)
hbox.addWidget(self.cancel_button, 0, 1, Qt.AlignRight)
self.grid.addLayout(hbox, 9, 1, Qt.AlignRight)
self.main_layout.addLayout(self.grid)
self.setGeometry(200, 100, 600, 400)
self.open_button.clicked.connect(self.accept)
self.cancel_button.clicked.connect(self.reject)
self.up_button.clicked.connect(self.go_up)
self.refresh_button.clicked.connect(self.update_view)
self.show_hidden.stateChanged.connect(self.update_view)
self.view.directory_activated.connect(
self.activate_directory_from_view)
self.view.file_activated.connect(self.activate_file_from_view)
self.view.file_selected.connect(self.select_file_item)
self.view.folder_selected.connect(self.select_folder_item)
self.view.up_requested.connect(self.go_up)
self.view.update_requested.connect(self.update_view)
def exec_(self, *args, **kwargs):
if self._use_app_browser:
return self.open_app_browser()
else:
self.update_view()
self.filter_box.currentIndexChanged.connect(self.update_view)
accepted = super(BaseFileFolderDialog, self).exec_()
self.filter_box.currentIndexChanged.disconnect(self.update_view)
return self.get_result() if accepted == 1 else None
def set_filters(self, filters, selected=0):
self.filter_box.clear()
filter_types = filters.split(';;')
for ft in filter_types:
extensions = string.extract(ft, '(', ')')
filter_name = string.rstrips(ft, '({})'.format(extensions))
extensions = extensions.split(' ')
self.filter_box.addItem(
'{} ({})'.format(filter_name, ','.join(extensions)),
extensions)
if 0 <= selected < self.filter_box.count():
self.filter_box.setCurrentIndex(selected)
self.filters = filters
def get_drives_widget(self):
"""
Returns a QGroupBox widget that contains all disk drivers of the PC in a vertical layout
:return: QGroupBox
"""
w = QGroupBox('')
w.setParent(self)
box = layouts.VerticalLayout()
box.setAlignment(Qt.AlignTop)
places = [(getpass.getuser(),
os.path.realpath(os.path.expanduser('~')))]
places += [
(q, q) for q in
[os.path.realpath(x.absolutePath()) for x in QDir().drives()]
]
for label, loc in places:
icon = QFileIconProvider().icon(QFileInfo(loc))
drive_btn = QRadioButton(label)
drive_btn.setIcon(icon)
drive_btn.setToolTip(loc)
drive_btn.setProperty('path', loc)
drive_btn.clicked.connect(self.go_to_drive)
self.places[loc] = drive_btn
box.addWidget(drive_btn)
w.setLayout(box)
return w
def go_to_drive(self):
"""
Updates widget to show the content of the selected disk drive
"""
sender = self.sender()
self.set_directory(sender.property('path'), False)
def get_result(self):
tf = self.file_edit.text()
sf = self.get_file_path(tf)
return sf, os.path.dirname(sf), tf.split(os.pathsep)
def get_filter_patterns(self):
"""
Get list of filter patterns that are being used by the widget
:return: list<str>
"""
idx = self.filter_box.currentIndex()
if idx >= 0:
return self.filter_box.itemData(idx)
else:
return []
def get_file_path(self, file_name):
"""
Returns file path of the given file name taking account the selected directory
:param file_name: str, name of the file without path
:return: str
"""
sname = file_name.split(os.pathsep)[0]
return os.path.realpath(
os.path.join(os.path.abspath(self.directory), sname))
# def accept(self):
# self._overlay.close()
# super(BaseFileFolderDialog, self).accept()
#
#
# def reject(self):
# self._overlay.close()
# super(BaseFileFolderDialog, self).reject()
def update_view(self):
"""
Updates file/folder view
:return:
"""
self.view.clear()
qdir = QDir(self.directory)
qdir.setNameFilters(self.get_filter_patterns())
filters = QDir.Dirs | QDir.AllDirs | QDir.Files | QDir.NoDot | QDir.NoDotDot
if self.show_hidden.isChecked():
filters = filters | QDir.Hidden
entries = qdir.entryInfoList(filters=filters,
sort=QDir.DirsFirst | QDir.Name)
file_path = self.get_file_path('..')
if os.path.exists(file_path) and file_path != self.directory:
icon = QFileIconProvider().icon(QFileInfo(self.directory))
QListWidgetItem(icon, '..', self.view, 0)
for info in entries:
icon = QFileIconProvider().icon(info)
suf = info.completeSuffix()
name, tp = (info.fileName(), 0) if info.isDir() else (
'%s%s' % (info.baseName(), '.%s' % suf if suf else ''), 1)
QListWidgetItem(icon, name, self.view, tp)
self.view.setFocus()
def set_directory(self, path, check_drive=True):
"""
Sets the directory that you want to explore
:param path: str, valid path
:param check_drive: bool,
:return:
"""
self.directory = os.path.realpath(path)
self.path_edit.setText(self.directory)
self.file_edit.setText('')
# If necessary, update selected disk driver
if check_drive:
for loc in self.places:
rb = self.places[loc]
rb.setAutoExclusive(False)
rb.setChecked(loc.lower() == self.directory.lower())
rb.setAutoExclusive(True)
self.update_view()
self.up_button.setEnabled(not self.cant_go_up())
def go_up(self):
"""
Updates the current directory to go to its parent directory
"""
self.set_directory(os.path.dirname(self.directory))
def cant_go_up(self):
"""
Checks whether we can naviage to current selected parent directory or not
:return: bool
"""
return os.path.dirname(self.directory) == self.directory
def activate_directory_from_view(self, name):
"""
Updates selected directory
:param name: str, name of the directory
"""
self.set_directory(os.path.join(self.directory, name))
def activate_file_from_view(self, name):
"""
Updates selected file text and returns its info by accepting it
:param name: str, name of the file
"""
self.select_file_item(name=name)
self.accept()
def select_file_item(self, name):
"""
Updates selected file text and returns its info by accepting it
:param name: str, name of the file
"""
self.file_edit.setText(name)
def select_folder_item(self, name):
"""
Updates selected folder text and returns its info by accepting it
:param name: str, name of the folder
"""
self.file_edit.setText(name)
class LigandTable(QWidget):
def __init__(
self,
parent=None,
singleSelect=False,
maxDenticity=None,
include_substituents=False,
):
super().__init__(parent)
self._include_substituents = include_substituents
layout = QGridLayout(self)
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels(
['name', 'denticity', 'coordinating elements'])
self.add_ligands(maxDenticity)
for i in range(0, 3):
self.table.resizeColumnToContents(i)
self.table.horizontalHeader().setStretchLastSection(False)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.setSortingEnabled(True)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
if singleSelect:
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.filterEdit = QLineEdit()
self.filterEdit.textChanged.connect(self.apply_filter)
self.filterEdit.setClearButtonEnabled(True)
self.filter_columns = QComboBox()
self.filter_columns.addItem("name")
self.filter_columns.addItem("denticity")
self.filter_columns.addItem("coordinating elements")
self.filter_columns.currentTextChanged.connect(
self.change_filter_method)
self.name_regex_option = QComboBox()
self.name_regex_option.addItem("case-insensitive")
self.name_regex_option.addItem("case-sensitive")
self.name_regex_option.currentTextChanged.connect(self.apply_filter)
self.name_regex_option.setVisible(
self.filter_columns.currentText() == "name")
self.coordinating_elements_method = QComboBox()
self.coordinating_elements_method.addItem("exactly")
self.coordinating_elements_method.addItem("at least")
self.coordinating_elements_method.currentTextChanged.connect(
self.apply_filter)
self.coordinating_elements_method.setVisible(
self.filter_columns.currentText() == "coordinating elements")
layout.addWidget(self.table, 0, 0, 1, 4)
layout.addWidget(QLabel("filter based on"), 1, 0)
layout.addWidget(self.filter_columns, 1, 1)
layout.addWidget(self.coordinating_elements_method, 1, 2)
layout.addWidget(self.name_regex_option, 1, 2)
layout.addWidget(self.filterEdit, 1, 3)
self.change_filter_method("name")
def add_ligands(self, maxDenticity=None):
from AaronTools.component import Component
names = []
for lib in [Component.AARON_LIBS, Component.BUILTIN]:
if not os.path.exists(lib):
continue
for lig in os.listdir(lib):
name, ext = os.path.splitext(lig)
if not any(".%s" % x == ext for x in read_types):
continue
if name in names:
continue
names.append(name)
geom = Geometry(
os.path.join(lib, lig),
refresh_connected=False,
refresh_ranks=False,
)
key_atoms = [geom.atoms[i] for i in geom.other["key_atoms"]]
if maxDenticity and len(key_atoms) > maxDenticity:
continue
row = self.table.rowCount()
self.table.insertRow(row)
self.table.setItem(row, 0, QTableWidgetItem(name))
#this is an integer, so I need to initialize it then set the data
denticity = QTableWidgetItem()
denticity.setData(Qt.DisplayRole, len(key_atoms))
self.table.setItem(row, 1, denticity)
self.table.setItem(
row, 2,
QTableWidgetItem(", ".join(
sorted([atom.element for atom in key_atoms]))))
if self._include_substituents:
from AaronTools.substituent import Substituent
for lib in [Substituent.AARON_LIBS, Substituent.BUILTIN]:
if not os.path.exists(lib):
continue
for sub in os.listdir(lib):
name, ext = os.path.splitext(sub)
if not any(".%s" % x == ext for x in read_types):
continue
if name in names:
continue
names.append(name)
geom = Geometry(
os.path.join(lib, sub),
refresh_connected=False,
refresh_ranks=False,
)
key_atoms = [geom.atoms[0]]
if maxDenticity and len(key_atoms) > maxDenticity:
continue
row = self.table.rowCount()
self.table.insertRow(row)
self.table.setItem(row, 0, QTableWidgetItem(name))
#this is an integer, so I need to initialize it then set the data
denticity = QTableWidgetItem()
denticity.setData(Qt.DisplayRole, len(key_atoms))
self.table.setItem(row, 1, denticity)
self.table.setItem(
row, 2,
QTableWidgetItem(", ".join(
sorted([atom.element for atom in key_atoms]))))
self.ligand_list = names
def change_filter_method(self, text):
if text == "coordinating elements":
self.filterEdit.setToolTip("comma and/or space delimited elements")
self.coordinating_elements_method.setVisible(True)
self.name_regex_option.setVisible(False)
elif text == "name":
self.filterEdit.setToolTip("name regex")
self.coordinating_elements_method.setVisible(False)
self.name_regex_option.setVisible(True)
elif text == "denticity":
self.filterEdit.setToolTip("number of key atoms")
self.coordinating_elements_method.setVisible(False)
self.name_regex_option.setVisible(False)
self.apply_filter()
def apply_filter(self, *args):
text = self.filterEdit.text()
if text:
if self.filter_columns.currentText() == "name":
m = QRegularExpression(text)
if m.isValid():
if self.name_regex_option.currentText(
) == "case-insensitive":
m.setPatternOptions(
QRegularExpression.CaseInsensitiveOption)
m.optimize()
filter = lambda row_num: m.match(
self.table.item(row_num, 0).text()).hasMatch()
else:
return
elif self.filter_columns.currentText() == "denticity":
if text.isdigit():
filter = lambda row_num: int(
self.table.item(row_num, 1).text()) == int(text)
else:
filter = lambda row: True
elif self.filter_columns.currentText() == "coordinating elements":
method = self.coordinating_elements_method.currentText()
def filter(row_num):
row_key_atoms = [
item.strip() for item in self.table.item(
row_num, 2).text().split(',')
]
search_atoms = []
for item in text.split():
for ele in item.split(','):
if ele.strip() != "":
search_atoms.append(ele)
if method == "exactly":
if all([row_key_atoms.count(element) == search_atoms.count(element) for element in set(search_atoms)]) and \
all([row_key_atoms.count(element) == search_atoms.count(element) for element in set(row_key_atoms)]):
return True
else:
return False
elif method == "at least":
if all([
row_key_atoms.count(element) >=
search_atoms.count(element)
for element in set(search_atoms)
]):
return True
else:
return False
else:
filter = lambda row: True
for i in range(0, self.table.rowCount()):
self.table.setRowHidden(i, not filter(i))
class Client(QDialog):
def __init__(self, parent: QWidget = None):
super().__init__(parent)
self._in = QDataStream()
self.blockSize = 0
self.currentFortune = ""
self.hostLineEdit = QLineEdit("fortune")
self.getFortuneButton = QPushButton(self.tr("Get Fortune"))
self.statusLabel = QLabel(
self.tr(
"This examples requires that you run the Local Fortune Server example as well."
)
)
self.socket = QLocalSocket()
self.setWindowFlags(self.windowFlags() & ~Qt.WindowContextHelpButtonHint)
hostLabel = QLabel(self.tr("&Server name:"))
hostLabel.setBuddy(self.hostLineEdit)
self.statusLabel.setWordWrap(True)
self.getFortuneButton.setDefault(True)
quitButton = QPushButton(self.tr("Quit"))
buttonBox = QDialogButtonBox()
buttonBox.addButton(self.getFortuneButton, QDialogButtonBox.ActionRole)
buttonBox.addButton(quitButton, QDialogButtonBox.RejectRole)
self._in.setDevice(self.socket)
self._in.setVersion(QDataStream.Qt_5_10)
self.hostLineEdit.textChanged.connect(self.enableGetFortuneButton)
self.getFortuneButton.clicked.connect(self.requestNewFortune)
quitButton.clicked.connect(self.close)
self.socket.readyRead.connect(self.readFortune)
self.socket.errorOccurred.connect(self.displayError)
mainLayout = QGridLayout(self)
mainLayout.addWidget(hostLabel, 0, 0)
mainLayout.addWidget(self.hostLineEdit, 0, 1)
mainLayout.addWidget(self.statusLabel, 2, 0, 1, 2)
mainLayout.addWidget(buttonBox, 3, 0, 1, 2)
self.setWindowTitle(QGuiApplication.applicationDisplayName())
self.hostLineEdit.setFocus()
@Slot()
def requestNewFortune(self):
self.getFortuneButton.setEnabled(False)
self.blockSize = 0
self.socket.abort()
self.socket.connectToServer(self.hostLineEdit.text())
@Slot()
def readFortune(self):
if self.blockSize == 0:
# Relies on the fact that QDataStream serializes a quint32 into
# sizeof(quint32) bytes
if self.socket.bytesAvailable() < 4: # (int)sizeof(quint32))
return
self.blockSize = self._in.readUInt32()
if self.socket.bytesAvailable() < self.blockSize or self._in.atEnd():
return
nextFortune = ""
nextFortune = self._in.readQString()
if nextFortune == self.currentFortune:
QTimer.singleShot(0, self.requestNewFortune)
return
currentFortune = nextFortune
self.statusLabel.setText(currentFortune)
self.getFortuneButton.setEnabled(True)
@Slot(QLocalSocket.LocalSocketError)
def displayError(self, socketError):
if socketError == QLocalSocket.ServerNotFoundError:
QMessageBox.information(
self,
self.tr("Local Fortune Client"),
self.tr(
"The host was not found. Please make sure "
"that the server is running and that the "
"server name is correct."
),
)
elif socketError == QLocalSocket.ConnectionRefusedError:
QMessageBox.information(
self,
self.tr("Local Fortune Client"),
self.tr(
"The connection was refused by the peer. "
"Make sure the fortune server is running, "
"and check that the server name is correct."
),
)
elif socketError == QLocalSocket.PeerClosedError:
return
else:
QMessageBox.information(
self,
self.tr("Local Fortune Client"),
self.tr(
"The following error occurred: %s." % (self.socket.errorString())
),
)
self.getFortuneButton.setEnabled(True)
@Slot()
def enableGetFortuneButton(self):
self.getFortuneButton.setEnabled(bool(self.hostLineEdit.ext()))
class CSSEditor:
"""
Make sure to instanciate *after* creating the top level widgets of your QApplication
"""
def __init__(self, project_name):
self.project_name = project_name
self._app = QApplication.instance()
self._css_filepath = None
self.main_window = QWidget()
self.main_window.setWindowFlags(Qt.Tool)
self.main_window.setWindowTitle("CSS Editor - " + self.project_name)
self.variables = Variables()
self.variables.changed.connect(self._variables_changed)
self.variables.changed.connect(self._render_and_apply)
self.template = CSSTextEdit()
self.template.changed.connect(self._template_changed)
self.template.changed.connect(self._render_and_apply)
self.save = QPushButton('Save stylesheet to')
self.save.clicked.connect(self._save_stylesheet)
self.save_destination = QLineEdit()
self.save_destination.textChanged.connect(self._destination_changed)
self.splitter = QSplitter()
self.splitter.setOrientation(Qt.Vertical)
self.splitter.addWidget(self.variables)
self.splitter.addWidget(self.template)
layout = QGridLayout(self.main_window)
layout.addWidget(self.splitter, 0, 0, 1, 2)
layout.addWidget(self.save, 1, 0)
layout.addWidget(self.save_destination, 1, 1)
self.main_window.resize(800, 600)
self._project_dir = self._ensure_project_dir()
self._top_level_widgets = [
widget for widget in QApplication.topLevelWidgets() if
widget.windowTitle() != self.main_window.windowTitle()
]
self._variables = dict()
self._template = None
self._stylesheet = ""
self._app.aboutToQuit.connect(self._save_editor_state)
self._open()
self.save_destination.setText(self.css_filepath)
self.main_window.show()
@property
def css_filepath(self):
if self._css_filepath is None:
return self._project_dir + self.project_name + '.css'
return self._css_filepath
def _ensure_project_dir(self):
dir_ = os.path.expanduser('~/CSSEditor/' + self.project_name + '/')
if not os.path.isdir(dir_):
os.makedirs(dir_)
return dir_
def _open(self):
self.variables.blockSignals(True)
self.template.blockSignals(True)
try:
with open(self._project_dir + EDITOR_STATE, 'r') as qsseditor_file:
qsseditor = json.load(qsseditor_file)
WindowPosition.restore(self.main_window, qsseditor['window'])
self.splitter.setSizes(qsseditor['splitter'])
self._css_filepath = qsseditor.get('save_destination', self.css_filepath)
self.save_destination.setText(self._css_filepath)
with open(self._project_dir + THEME_VARIABLES, 'r') as f_variables:
self.variables.variables = json.load(f_variables)
with open(self._project_dir + THEME_TEMPLATE, 'r') as f_template:
self.template.set_plain_text(f_template.read())
except Exception as e:
pass
self.variables.blockSignals(False)
self.template.blockSignals(False)
self._template_changed()
self._variables_changed()
self._render_and_apply()
def _destination_changed(self):
self._css_filepath = self.save_destination.text()
self._save_editor_state()
def _save_editor_state(self):
with open(self._project_dir + EDITOR_STATE, 'w+') as f_qsseditor:
json.dump({
'window': WindowPosition.save(self.main_window),
'splitter': self.splitter.sizes(),
'save_destination': self.css_filepath
}, f_qsseditor)
def _template_changed(self):
template = self.template.plain_text()
with open(self._project_dir + THEME_TEMPLATE, 'w+') as f_template:
f_template.write(template)
try:
self._template = jinja2.Template(template)
except TemplateSyntaxError:
pass
def _variables_changed(self):
with open(self._project_dir + THEME_VARIABLES, 'w+') as f_variables:
f_variables.write(json.dumps(self.variables.variables, indent=2))
self._variables = dict()
for variable_name, variable_value in self.variables.variables.items():
if isinstance(variable_value, list) and len(variable_value) == 3:
self._variables[variable_name] = 'rgb({})'.format(', '.join([str(channel) for channel in variable_value]))
for variant in COLOR_VARIANTS:
channels = [str(int(channel * variant * 0.01)) for channel in variable_value]
self._variables['{}{:02d}'.format(variable_name, variant)] = 'rgb({})'.format(', '.join(channels))
else:
self._variables[variable_name] = variable_value
def _apply_style(self, style):
for widget in self._top_level_widgets:
widget.setStyleSheet(style)
def _render_and_apply(self):
self._apply_style("")
if self._template is None:
return
self._stylesheet = self._template.render(**self._variables)
self._apply_style(self._stylesheet)
def _save_stylesheet(self):
stylesheet = [
"/* GUI Bedos - CSS Template */",
"/****************************/",
"",
"/* VARIABLES",
json.dumps(self.variables.variables, indent=2),
"/****************************/",
"",
"/* TEMPLATE",
self.template.plain_text().replace('*/', '*|'),
"/****************************/",
"",
"/* ACTUAL CSS */",
"",
self._stylesheet
]
with open(self.css_filepath, 'w+') as f_stylesheet:
f_stylesheet.write('\n'.join(stylesheet))
def addAttributeSlot(self):
""" Adds a new attribute (column) to the table """
dialog = QDialog(self)
dialog.setModal(True)
dialog.setWindowTitle('Add Attribute')
layout = QVBoxLayout()
dialog.setLayout(layout)
form = QFormLayout()
nameBox = QLineEdit()
typeCombo = QComboBox()
for attrType in _attrTypes:
typeName = partio.TypeName(attrType)
typeCombo.addItem(typeName)
typeCombo.setCurrentIndex(partio.FLOAT)
countBox = QLineEdit()
countBox.setValidator(QIntValidator())
countBox.setText('1')
fixedCheckbox = QCheckBox()
valueBox = QLineEdit()
valueBox.setText('0')
form.addRow('Name:', nameBox)
form.addRow('Type:', typeCombo)
form.addRow('Count:', countBox)
form.addRow('Fixed:', fixedCheckbox)
form.addRow('Default Value:', valueBox)
layout.addLayout(form)
buttons = QHBoxLayout()
layout.addLayout(buttons)
add = QPushButton('Add')
add.clicked.connect(dialog.accept)
buttons.addWidget(add)
cancel = QPushButton('Cancel')
cancel.clicked.connect(dialog.reject)
buttons.addWidget(cancel)
if not dialog.exec_():
return
name = str(nameBox.text())
if not name:
print 'Please supply a name for the new attribute' # TODO: prompt
return
attrType = typeCombo.currentIndex()
count = int(countBox.text())
fixed = fixedCheckbox.isChecked()
values = list(str(valueBox.text()).strip().split())
for i in range(count):
if i < len(values):
value = values[i]
else:
value = values[-1]
if attrType == partio.INT or attrType == partio.INDEXEDSTR:
values[i] = int(value)
elif attrType == partio.FLOAT or attrType == partio.VECTOR:
values[i] = float(value) # pylint:disable=R0204
else:
values[i] = 0.0 # pylint:disable=R0204
value = tuple(values)
self.data.addAttribute(name, attrType, count, fixed, value)
def addAttributeSlot(self):
""" Adds a new attribute (column) to the table """
dialog = QDialog(self)
dialog.setModal(True)
dialog.setWindowTitle('Add Attribute')
layout = QVBoxLayout()
dialog.setLayout(layout)
form = QFormLayout()
nameBox = QLineEdit()
typeCombo = QComboBox()
for attrType in _attrTypes:
typeName = partio.TypeName(attrType)
typeCombo.addItem(typeName)
typeCombo.setCurrentIndex(partio.FLOAT)
countBox = QLineEdit()
countBox.setValidator(QIntValidator())
countBox.setText('1')
fixedCheckbox = QCheckBox()
valueBox = QLineEdit()
valueBox.setText('0')
form.addRow('Name:', nameBox)
form.addRow('Type:', typeCombo)
form.addRow('Count:', countBox)
form.addRow('Fixed:', fixedCheckbox)
form.addRow('Default Value:', valueBox)
layout.addLayout(form)
buttons = QHBoxLayout()
layout.addLayout(buttons)
add = QPushButton('Add')
add.clicked.connect(dialog.accept)
buttons.addWidget(add)
cancel = QPushButton('Cancel')
cancel.clicked.connect(dialog.reject)
buttons.addWidget(cancel)
if not dialog.exec_():
return
name = str(nameBox.text())
if not name:
print('Please supply a name for the new attribute') # TODO: prompt
return
attrType = typeCombo.currentIndex()
count = int(countBox.text())
fixed = fixedCheckbox.isChecked()
values = list(str(valueBox.text()).strip().split())
for i in range(count):
if i < len(values):
value = values[i]
else:
value = values[-1]
if attrType == partio.INT or attrType == partio.INDEXEDSTR:
values[i] = int(value)
elif attrType == partio.FLOAT or attrType == partio.VECTOR:
values[i] = float(value) # pylint:disable=R0204
else:
values[i] = 0.0 # pylint:disable=R0204
value = tuple(values)
self.data.addAttribute(name, attrType, count, fixed, value)
class EditStructure(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Structure-Modification-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
self.settings = _EditStructureSettings(session, "Structure Modification")
self.tool_window = MainToolWindow(self)
self.close_previous_bool = self.settings.modify
self._build_ui()
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)
def close_previous_change(self, state):
if state == Qt.Checked:
self.settings.modify = True
for checkbox in [self.close_previous_lig, self.close_previous_sub, self.close_previous_ring]:
checkbox.setChecked(True)
self.close_previous_bool = True
else:
self.settings.modify = False
for checkbox in [self.close_previous_lig, self.close_previous_sub, self.close_previous_ring]:
checkbox.setChecked(False)
self.close_previous_bool = False
def do_substitute(self):
subnames = self.subname.text()
new_name = self.new_sub_name.text()
use_attached = not self.guess_old.isChecked()
minimize = self.minimize.isChecked()
new_residue = self.new_residue.isChecked()
use_greek = self.use_greek.isChecked()
self.settings.minimize = minimize
self.settings.use_greek = use_greek
if len(new_name.strip()) > 0:
run(
self.session,
"substitute sel substituents %s newName %s guessAttachment %s modify %s minimize %s useRemoteness %s newResidue %s" %
(
subnames,
new_name,
not use_attached,
self.close_previous_bool,
minimize,
use_greek,
new_residue,
)
)
else:
run(
self.session,
"substitute sel substituents %s guessAttachment %s modify %s minimize %s useRemoteness %s newResidue %s" %
(
subnames,
not use_attached,
self.close_previous_bool,
minimize,
use_greek,
new_residue,
)
)
def open_sub_selector(self):
self.tool_window.create_child_window("select substituents", window_class=SubstituentSelection, textBox=self.subname)
def do_maplig(self):
lignames = self.ligname.text()
selection = selected_atoms(self.session)
if len(selection) < 1:
raise RuntimeWarning("nothing selected")
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [AtomSpec(atom.atomspec)]
else:
models[atom.structure].append(AtomSpec(atom.atomspec))
first_pass = True
new_structures = []
for ligname in lignames.split(','):
ligname = ligname.strip()
lig = Component(ligname)
for model in models:
if self.close_previous_bool and first_pass:
rescol = ResidueCollection(model)
elif self.close_previous_bool and not first_pass:
raise RuntimeError("only the first model can be replaced")
else:
model_copy = model.copy()
rescol = ResidueCollection(model_copy)
for i, atom in enumerate(model.atoms):
rescol.atoms[i].atomspec = atom.atomspec
rescol.atoms[i].add_tag(atom.atomspec)
rescol.atoms[i].chix_atom = atom
target = rescol.find(models[model])
if len(target) % len(lig.key_atoms) == 0:
k = 0
ligands = []
while k != len(target):
res_lig = ResidueCollection(lig.copy(), comment=lig.comment)
res_lig.parse_comment()
res_lig = Component(res_lig, key_atoms = ",".join([str(k + 1) for k in res_lig.other["key_atoms"]]))
ligands.append(res_lig)
k += len(lig.key_atoms)
else:
raise RuntimeError("number of key atoms no not match: %i now, new ligand has %i" % (len(target), len(lig.key_atoms)))
rescol.map_ligand(ligands, target)
for center_atom in rescol.center:
center_atom.connected = set([])
for atom in rescol.atoms:
if atom not in rescol.center:
if center_atom.is_connected(atom):
atom.connected.add(center_atom)
center_atom.connected.add(atom)
if self.close_previous_bool:
rescol.update_chix(model)
else:
struc = rescol.get_chimera(self.session)
new_structures.append(struc)
first_pass = False
if not self.close_previous_bool:
self.session.models.add(new_structures)
def open_lig_selector(self):
self.tool_window.create_child_window("select ligands", window_class=LigandSelection, textBox=self.ligname)
def do_fusering(self):
ring_names = self.ringname.text()
new_name = self.new_ring_name.text()
minimize_ring = self.minimize_ring.isChecked()
self.settings.minimize_ring = minimize_ring
if len(new_name.strip()) > 0:
run(
self.session,
"fuseRing sel rings %s newName %s modify %s minimize %s" % (
ring_names,
new_name,
self.close_previous_bool,
minimize_ring,
)
)
else:
run(
self.session,
"fuseRing sel rings %s modify %s minimize %s" % (
ring_names,
self.close_previous_bool,
minimize_ring,
)
)
def open_ring_selector(self):
self.tool_window.create_child_window("select rings", window_class=RingSelection, textBox=self.ringname)
def open_ptable(self):
self.tool_window.create_child_window("select element", window_class=_PTable, button=self.element)
def display_help(self):
"""Show the help for this tool in the help viewer."""
from chimerax.core.commands import run
run(self.session,
'open %s' % self.help if self.help is not None else "")
def do_change_element(self):
element = self.element.text()
adjust_bonds = self.change_bonds.isChecked()
self.settings.change_bonds = adjust_bonds
vsepr = self.vsepr.currentText()
if vsepr == "do not change":
vsepr = False
elif vsepr == "linear (1 bond)":
vsepr = "linear 1"
goal = 1
elif vsepr == "linear (2 bonds)":
vsepr = "linear 2"
goal = 2
elif vsepr == "trigonal planar (2 bonds)":
vsepr = "bent 2 planar"
goal = 2
elif vsepr == "tetrahedral (2 bonds)":
vsepr = "bent 2 tetrahedral"
goal = 2
elif vsepr == "trigonal planar":
goal = 3
elif vsepr == "tetrahedral (3 bonds)":
vsepr = "bent 3 tetrahedral"
goal = 3
else:
goal = len(Atom.get_shape(vsepr)) - 1
sel = selected_atoms(self.session)
models, _ = guessAttachmentTargets(sel, self.session, allow_adjacent=False)
for model in models:
conv_res = list(models[model].keys())
for res in models[model]:
for target in models[model][res]:
for neighbor in target.neighbors:
if neighbor.residue not in conv_res:
conv_res.append(neighbor.residue)
for pbg in self.session.models.list(type=PseudobondGroup):
for pbond in pbg.pseudobonds:
if target in pbond.atoms and all(atom.structure is model for atom in pbond.atoms):
other_atom = pbond.other_atom(target)
if other_atom.residue not in conv_res:
conv_res.append(other_atom.residue)
rescol = ResidueCollection(model, convert_residues=conv_res)
for res in models[model]:
residue = [resi for resi in rescol.residues if resi.chix_residue is res][0]
for target in models[model][res]:
targ = rescol.find_exact(AtomSpec(target.atomspec))[0]
adjust_hydrogens = vsepr
if vsepr is not False:
cur_bonds = len(targ.connected)
change_Hs = goal - cur_bonds
adjust_hydrogens = (change_Hs, vsepr)
residue.change_element(targ,
element,
adjust_bonds=adjust_bonds,
adjust_hydrogens=adjust_hydrogens,
)
residue.update_chix(res)
def do_new_ring(self):
rings = self.ringname.text()
for ring in rings.split(","):
ring = ring.strip()
rescol = ResidueCollection(Ring(ring))
model = self.ring_model_selector.currentData()
if model is None:
chix = rescol.get_chimera(self.session)
self.session.models.add([chix])
apply_seqcrow_preset(chix, fallback="Ball-Stick-Endcap")
self.ring_model_selector.setCurrentIndex(self.ring_model_selector.count()-1)
else:
res = model.new_residue("new", "a", len(model.residues)+1)
rescol.residues[0].update_chix(res)
run(self.session, "select add %s" % " ".join([atom.atomspec for atom in res.atoms]))
def do_new_lig(self):
ligands = self.ligname.text()
for lig in ligands.split(","):
lig = lig.strip()
rescol = ResidueCollection(Component(lig))
model = self.lig_model_selector.currentData()
if model is None:
chix = rescol.get_chimera(self.session)
self.session.models.add([chix])
apply_seqcrow_preset(chix, fallback="Ball-Stick-Endcap")
self.lig_model_selector.setCurrentIndex(self.lig_model_selector.count()-1)
else:
res = model.new_residue("new", "a", len(model.residues)+1)
rescol.residues[0].update_chix(res)
run(self.session, "select add %s" % " ".join([atom.atomspec for atom in res.atoms]))
def do_new_atom(self):
element = self.element.text()
adjust_bonds = self.change_bonds.isChecked()
self.settings.change_bonds = adjust_bonds
vsepr = self.vsepr.currentText()
if vsepr == "do not change":
vsepr = False
elif vsepr == "linear (1 bond)":
vsepr = "linear 1"
elif vsepr == "linear (2 bonds)":
vsepr = "linear 2"
elif vsepr == "trigonal planar (2 bonds)":
vsepr = "bent 2 planar"
elif vsepr == "tetrahedral (2 bonds)":
vsepr = "bent 2 tetrahedral"
elif vsepr == "tetrahedral (3 bonds)":
vsepr = "bent 3 tetrahedral"
if vsepr:
atoms = Atom.get_shape(vsepr)
atoms[0].element = element
for atom in atoms[1:]:
atom.element = "H"
if adjust_bonds:
# this works b/c all atoms are 1 angstrom from the center
# just multiply by the distance we want
expected_dist = RADII[element] + RADII["H"]
for atom in atoms[1:]:
atom.coords *= expected_dist
for atom in atoms[1:]:
atoms[0].connected.add(atom)
atom.connected.add(atoms[0])
else:
atoms = [Atom(element=element, coords=np.zeros(3))]
rescol = ResidueCollection(atoms, name="new", refresh_connected=False)
model = self.model_selector.currentData()
if model is None:
chix = rescol.get_chimera(self.session)
self.session.models.add([chix])
apply_seqcrow_preset(chix, fallback="Ball-Stick-Endcap")
self.model_selector.setCurrentIndex(self.model_selector.count()-1)
else:
res = model.new_residue("new", "a", len(model.residues)+1)
rescol.residues[0].update_chix(res)
run(self.session, "select add %s" % " ".join([atom.atomspec for atom in res.atoms]))
def delete_atoms(self, *args):
atoms = selected_atoms(self.session)
for atom in atoms:
atom.delete()
def delete(self):
self.ring_model_selector.deleteLater()
self.lig_model_selector.deleteLater()
self.model_selector.deleteLater()
return super().delete()
def close(self):
self.ring_model_selector.deleteLater()
self.lig_model_selector.deleteLater()
self.model_selector.deleteLater()
return super().close()
class TestRunner(ToolInstance):
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self._build_ui()
def _build_ui(self):
"""
ui should have:
* table with a list of available tests and show results after they are done
* way to filter tests
* button to run tests
"""
layout = QFormLayout()
# table to list test classes and the results
self.table = QTableWidget()
self.table.setColumnCount(2)
self.table.setHorizontalHeaderLabels(["test", "result"])
self.table.horizontalHeader().setSectionResizeMode(
0,
self.table.horizontalHeader().Interactive)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.horizontalHeader().setSectionResizeMode(
1,
self.table.horizontalHeader().Stretch)
self.table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
self.table.setSelectionBehavior(self.table.SelectRows)
layout.addRow(self.table)
self.filter = QLineEdit()
self.filter.setPlaceholderText("filter test names")
self.filter.setClearButtonEnabled(True)
self.filter.textChanged.connect(self.apply_filter)
layout.addRow(self.filter)
self.profile = QCheckBox()
self.profile.setToolTip("profile functions called during testing "
"using cProfile")
layout.addRow("profile calls:", self.profile)
self.run_button = QPushButton("run tests")
self.run_button.clicked.connect(self.run_tests)
self.run_button.setToolTip(
"if no tests are selected on the table, run all tests\n" +
"otherwise, run selected tests")
layout.addRow(self.run_button)
self.fill_table()
self.table.resizeColumnToContents(0)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def apply_filter(self, text=None):
"""filter table to only show tests matching text"""
if text is None:
text = self.filter.text()
if text:
text = text.replace("(", "\(")
text = text.replace(")", "\)")
m = QRegularExpression(text)
m.setPatternOptions(QRegularExpression.CaseInsensitiveOption)
if m.isValid():
m.optimize()
filter = lambda row_num: m.match(
self.table.item(row_num, 0).text()).hasMatch()
else:
return
else:
filter = lambda row: True
for i in range(0, self.table.rowCount()):
self.table.setRowHidden(i, not filter(i))
def fill_table(self):
"""adds test names to the table"""
mgr = self.session.test_manager
for name in mgr.tests.keys():
row = self.table.rowCount()
self.table.insertRow(row)
test_name = QTableWidgetItem()
test_name.setData(Qt.DisplayRole, name)
self.table.setItem(row, 0, test_name)
def run_tests(self):
"""run the tests selected on the table and show the results"""
from TestManager.commands.test import test
test_list = []
use_selected = True
for row in self.table.selectionModel().selectedRows():
if self.table.isRowHidden(row.row()):
continue
test_name = self.table.item(row.row(), 0).text()
test_list.append(test_name)
if not test_list:
use_selected = False
for i in range(0, self.table.rowCount()):
if self.table.isRowHidden(i):
continue
test_name = self.table.item(i, 0).text()
test_list.append(test_name)
if not test_list:
test_list = ["all"]
results, stats = test(self.session,
test_list,
profile=self.profile.checkState() == Qt.Checked)
cell_widgets = []
for name in results:
widget = QWidget()
widget_layout = QHBoxLayout(widget)
widget_layout.setContentsMargins(0, 0, 0, 0)
success_button = get_button("success")
fail_button = get_button("fail")
skip_button = get_button("skip")
error_button = get_button("error")
expected_fail_button = get_button("expected fail")
unexpected_success_button = get_button("unexpected success")
success_count = 0
fail_count = 0
error_count = 0
unexpected_success_count = 0
expected_fail_count = 0
skip_count = 0
success_tooltip = "Successes:\n"
fail_tooltip = "Failed tests:\n"
error_tooltip = "Errors during test:\n"
unexpected_success_tooltip = "Unexpected successes:\n"
expected_fail_tooltip = "Expected fails:\n"
skip_tooltip = "Skipped tests:\n"
for case in results[name]:
result, msg = results[name][case]
if result == "success":
success_count += 1
success_tooltip += "%s.%s: %s\n" % (
case.__class__.__qualname__, case._testMethodName, msg)
elif result == "fail":
fail_count += 1
fail_tooltip += "%s.%s failed: %s\n" % (
case.__class__.__qualname__, case._testMethodName, msg)
elif result == "error":
error_count += 1
error_tooltip += "error during %s.%s: %s\n" % (
case.__class__.__qualname__, case._testMethodName, msg)
elif result == "expected_failure":
expected_fail_count += 1
expected_fail_tooltip += "intended failure during %s.%s: %s\n" % (
case.__class__.__qualname__, case._testMethodName, msg)
elif result == "skip":
skip_count += 1
skip_tooltip += "%s.%s\n" % (case.__class__.__qualname__,
case._testMethodName)
elif result == "unexpected_success":
unexpected_success_count += 1
unexpected_success_tooltip += "%s.%s should not have worked, but did\n" % (
case.__class__.__qualname__, case._testMethodName)
success_tooltip = success_tooltip.strip()
fail_tooltip = fail_tooltip.strip()
error_tooltip = error_tooltip.strip()
expected_fail_tooltip = expected_fail_tooltip.strip()
skip_tooltip = skip_tooltip.strip()
unexpected_success_tooltip = unexpected_success_tooltip.strip()
icon_count = 0
if success_count:
success_button.setText("%i" % success_count)
success_button.setToolTip(success_tooltip)
success_button.clicked.connect(
lambda *args, t_name=name, res=success_tooltip: self.
tool_window.create_child_window(
"successes for %s" % t_name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, success_button, 1)
icon_count += 1
if fail_count:
fail_button.setText("%i" % fail_count)
fail_button.setToolTip(fail_tooltip)
fail_button.clicked.connect(
lambda *args, res=fail_tooltip: self.tool_window.
create_child_window(
"failures for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, fail_button, 1)
icon_count += 1
if error_count:
error_button.setText("%i" % error_count)
error_button.setToolTip(error_tooltip)
error_button.clicked.connect(
lambda *args, res=error_tooltip: self.tool_window.
create_child_window(
"errors for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, error_button, 1)
icon_count += 1
if unexpected_success_count:
unexpected_success_button.setText("%i" %
unexpected_success_count)
unexpected_success_button.setToolTip(
unexpected_success_tooltip)
unexpected_success_button.clicked.connect(
lambda *args, res=unexpected_success_tooltip: self.
tool_window.create_child_window(
"unexpected successes for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count,
unexpected_success_button, 1)
icon_count += 1
if expected_fail_count:
expected_fail_button.setText("%i" % expected_fail_count)
expected_fail_button.setToolTip(expected_fail_tooltip)
expected_fail_button.clicked.connect(
lambda *args, res=expected_fail_tooltip: self.tool_window.
create_child_window(
"expected failures for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, expected_fail_button, 1)
icon_count += 1
if skip_count:
skip_button.setText("%i" % skip_count)
skip_button.setToolTip(skip_tooltip)
skip_button.clicked.connect(
lambda *args, res=skip_tooltip: self.tool_window.
create_child_window(
"skipped tests for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, skip_button, 1)
cell_widgets.append(widget)
widget_count = 0
if use_selected:
for row in self.table.selectionModel().selectedRows():
if self.table.isRowHidden(row.row()):
continue
self.table.setCellWidget(row.row(), 1,
cell_widgets[widget_count])
self.table.resizeRowToContents(row.row())
widget_count += 1
else:
for i in range(0, self.table.rowCount()):
if self.table.isRowHidden(i):
continue
self.table.setCellWidget(i, 1, cell_widgets[widget_count])
# self.table.resizeRowToContents(i)
widget_count += 1
if self.profile.checkState() == Qt.Checked:
self.tool_window.create_child_window("stats",
text=stats,
window_class=ResultsWindow)
class EditableTabBar(QTabBar, object):
"""
Basic implementation of an editable tab bar
"""
addTabClicked = Signal()
tabRenamed = Signal(object, object, object)
def __init__(self, parent=None):
super(EditableTabBar, self).__init__(parent=parent)
self._is_editable = True
self._editor = QLineEdit(self)
self._editor.setWindowFlags(Qt.Popup)
self._editor.setFocusProxy(self)
self._editor.editingFinished.connect(self.handle_editing_finished)
self._editor.installEventFilter(self)
self.add_tab_btn = EditableAddButton(parent=self)
self._move_add_tab_btn()
self.setDrawBase(False)
self.add_tab_btn.clicked.connect(self.addTabClicked.emit)
def is_editable(self):
"""
Returns whether the tab bar enables rename mode when the user double clicks on the tab
:return: bool
"""
return self._is_editable
def set_is_editable(self, flag):
"""
Sets whether the tabs are editable or not
:param flag: bool
"""
self._is_editable = bool(flag)
def edit_tab(self, index):
"""
Function that is called when the tab is going to be edited
:param index:
:return:
"""
if not self._is_editable:
return
rect = self.tabRect(index)
self._editor.setFixedSize(rect.size())
self._editor.move(self.parent().mapToGlobal(rect.topLeft()))
self._editor.setText(self.tabText(index))
self._editor.selectAll()
if not self._editor.isVisible():
self._editor.show()
def handle_editing_finished(self):
"""
Function that is called when the tab edit has been completed
"""
index = self.currentIndex()
if index >= 0:
self._editor.hide()
for i in range(self.count()):
if self.tabText(i) == self._editor.text():
LOGGER.warning(
'Impossible to rename category because exists a tab with the same name!'
)
return
old_name = self.tabText(index)
self.setTabText(index, self._editor.text())
self.tabRenamed.emit(index, self.tabText(index), old_name)
def sizeHint(self):
"""
Return the size of the tab bar with increased width for the add tab button
:return: QSize, size of the tab bar
"""
size_hint = super(EditableTabBar, self).sizeHint()
return QSize(size_hint.width() + 25, size_hint.height())
def resizeEvent(self, event):
"""
Resize the widget and make sure the add tab button is in the correct location
"""
super(EditableTabBar, self).resizeEvent(event)
self._move_add_tab_btn()
def tabLayoutChange(self):
"""
This virtual handler is called whenever the tab layout changes.
If anything changes make sure the add char btn is in the correct location
"""
super(EditableTabBar, self).tabLayoutChange()
self._move_add_tab_btn()
def eventFilter(self, widget, event):
if ((event.type() == QEvent.MouseButtonPress
and not self._editor.geometry().contains(event.globalPos()))
or (event.type() == QEvent.KeyPress
and event.key() == Qt.Key_Escape)):
self._editor.hide()
return True
return QTabBar.eventFilter(self, widget, event)
def mouseDoubleClickEvent(self, event):
index = self.tabAt(event.pos())
if index >= 0:
if not self._is_editable:
return
self.edit_tab(index)
def _move_add_tab_btn(self):
"""
Move the add tab button to the correct location
"""
# Find the width of all of the tabs
size = sum([self.tabRect(i).width() for i in range(self.count())])
# Set the add tab button location in a visible area
h = self.geometry().top()
w = self.width()
if size > w:
self.add_tab_btn.move(w - 50, h)
else:
self.add_tab_btn.move(size, h)
class LibAdd(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Add-to-Personal-Library-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.key_atomspec = []
self._build_ui()
def _build_ui(self):
layout = QGridLayout()
library_tabs = QTabWidget()
#ligand tab
ligand_tab = QWidget()
ligand_layout = QFormLayout(ligand_tab)
self.ligand_name = QLineEdit()
self.ligand_name.setText("")
self.ligand_name.setPlaceholderText("leave blank to preview")
self.ligand_name.setToolTip(
"name of ligand you are adding to your ligand library\nleave blank to open a new model with just the ligand"
)
ligand_layout.addRow("ligand name:", self.ligand_name)
ligand_key_atoms = QPushButton("set key atoms to current selection")
ligand_key_atoms.clicked.connect(self.update_key_atoms)
ligand_key_atoms.setToolTip(
"the current selection will be the key atoms for the ligand\nleave blank to automatically determine key atoms"
)
ligand_layout.addRow(ligand_key_atoms)
libadd_ligand = QPushButton("add current selection to library")
libadd_ligand.clicked.connect(self.libadd_ligand)
ligand_layout.addRow(libadd_ligand)
#substituent tab
sub_tab = QWidget()
sub_layout = QFormLayout(sub_tab)
self.sub_name = QLineEdit()
self.sub_name.setText("")
self.sub_name.setPlaceholderText("leave blank to preview")
self.sub_name.setToolTip(
"name of substituent you are adding to your substituent library\nleave blank to open a new model with just the substituent"
)
sub_layout.addRow("substituent name:", self.sub_name)
self.sub_confs = QSpinBox()
self.sub_confs.setMinimum(1)
sub_layout.addRow("number of conformers:", self.sub_confs)
self.sub_angle = QSpinBox()
self.sub_angle.setRange(0, 180)
self.sub_angle.setSingleStep(30)
sub_layout.addRow("angle between conformers:", self.sub_angle)
libadd_sub = QPushButton("add current selection to library")
libadd_sub.clicked.connect(self.libadd_substituent)
sub_layout.addRow(libadd_sub)
#ring tab
ring_tab = QWidget()
ring_layout = QFormLayout(ring_tab)
self.ring_name = QLineEdit()
self.ring_name.setText("")
self.ring_name.setPlaceholderText("leave blank to preview")
self.ring_name.setToolTip(
"name of ring you are adding to your ring library\nleave blank to open a new model with just the ring"
)
ring_layout.addRow("ring name:", self.ring_name)
libadd_ring = QPushButton("add ring with selected walk to library")
libadd_ring.clicked.connect(self.libadd_ring)
ring_layout.addRow(libadd_ring)
library_tabs.addTab(sub_tab, "substituent")
library_tabs.addTab(ring_tab, "ring")
library_tabs.addTab(ligand_tab, "ligand")
self.library_tabs = library_tabs
layout.addWidget(library_tabs)
whats_this = QLabel()
whats_this.setText(
"<a href=\"req\" style=\"text-decoration: none;\">what's this?</a>"
)
whats_this.setTextFormat(Qt.RichText)
whats_this.setTextInteractionFlags(Qt.TextBrowserInteraction)
whats_this.linkActivated.connect(self.open_link)
whats_this.setToolTip(
"click for more information about AaronTools libraries")
layout.addWidget(whats_this)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def update_key_atoms(self):
selection = selected_atoms(self.session)
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
else:
self.key_atomspec = selection
self.tool_window.status("key atoms set to %s" %
" ".join(atom.atomspec for atom in selection))
def libadd_ligand(self):
"""add ligand to library or open it in a new model"""
selection = selected_atoms(self.session)
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
rescol = ResidueCollection(selection[0].structure)
ligand_atoms = [
atom for atom in rescol.atoms if atom.chix_atom in selection
]
key_chix_atoms = [
atom for atom in self.key_atomspec if not atom.deleted
]
if len(key_chix_atoms) < 1:
key_atoms = set([])
for atom in ligand_atoms:
for atom2 in atom.connected:
if atom2 not in ligand_atoms:
key_atoms.add(atom)
else:
key_atoms = rescol.find(
[AtomSpec(atom.atomspec) for atom in key_chix_atoms])
if len(key_atoms) < 1:
raise RuntimeError("no key atoms could be determined")
lig_name = self.ligand_name.text()
ligand = Component(ligand_atoms, name=lig_name, key_atoms=key_atoms)
ligand.comment = "K:%s" % ",".join(
[str(ligand.atoms.index(atom) + 1) for atom in key_atoms])
if len(lig_name) == 0:
chimerax_ligand = ResidueCollection(ligand).get_chimera(
self.session)
chimerax_ligand.name = "ligand preview"
self.session.models.add([chimerax_ligand])
bild_obj = key_atom_highlight(ligand, [0.2, 0.5, 0.8, 0.5],
self.session)
self.session.models.add(bild_obj, parent=chimerax_ligand)
else:
check_aaronlib_dir()
filename = os.path.join(AARONLIB, "Ligands", lig_name + ".xyz")
if os.path.exists(filename):
exists_warning = QMessageBox()
exists_warning.setIcon(QMessageBox.Warning)
exists_warning.setText(
"%s already exists.\nWould you like to overwrite?" %
filename)
exists_warning.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
rv = exists_warning.exec_()
if rv == QMessageBox.Yes:
ligand.write(outfile=filename)
self.tool_window.status("%s added to ligand library" %
lig_name)
else:
self.tool_window.status(
"%s has not been added to ligand library" % lig_name)
else:
ligand.write(outfile=filename)
self.tool_window.status("%s added to ligand library" %
lig_name)
def libadd_ring(self):
"""add ring to library or open it in a new model"""
selection = self.session.seqcrow_ordered_selection_manager.selection
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
rescol = ResidueCollection(selection[0].structure)
walk_atoms = rescol.find(
[AtomSpec(atom.atomspec) for atom in selection])
if len(walk_atoms) < 1:
raise RuntimeError("no walk direction could be determined")
ring_name = self.ring_name.text()
ring = Ring(rescol, name=ring_name, end=walk_atoms)
ring.comment = "E:%s" % ",".join(
[str(rescol.atoms.index(atom) + 1) for atom in walk_atoms])
if len(ring_name) == 0:
chimerax_ring = ResidueCollection(ring).get_chimera(self.session)
chimerax_ring.name = "ring preview"
self.session.models.add([chimerax_ring])
bild_obj = show_walk_highlight(ring, chimerax_ring,
[0.9, 0.4, 0.3, 0.9], self.session)
self.session.models.add(bild_obj, parent=chimerax_ring)
else:
check_aaronlib_dir()
filename = os.path.join(AARONLIB, "Rings", ring_name + ".xyz")
if os.path.exists(filename):
exists_warning = QMessageBox()
exists_warning.setIcon(QMessageBox.Warning)
exists_warning.setText(
"%s already exists.\nWould you like to overwrite?" %
filename)
exists_warning.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
rv = exists_warning.exec_()
if rv == QMessageBox.Yes:
ring.write(outfile=filename)
self.tool_window.status("%s added to ring library" %
ring_name)
else:
self.tool_window.status(
"%s has not been added to ring library" % ring_name)
else:
ring.write(outfile=filename)
self.tool_window.status("%s added to ring library" % ring_name)
def libadd_substituent(self):
"""add ligand to library or open it in a new model"""
selection = selected_atoms(self.session)
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
residues = []
for atom in selection:
if atom.residue not in residues:
residues.append(atom.residue)
rescol = ResidueCollection(selection[0].structure,
convert_residues=residues)
substituent_atoms = [
atom for atom in rescol.atoms if atom.chix_atom in selection
]
start = None
avoid = None
for atom in substituent_atoms:
for atom2 in atom.connected:
if atom2 not in substituent_atoms:
if start is None:
start = atom
avoid = atom2
else:
raise RuntimeError(
"substituent must only have one connection to the molecule"
)
if start is None:
raise RuntimeError(
"substituent is not connected to a larger molecule")
substituent_atoms.remove(start)
substituent_atoms.insert(0, start)
sub_name = self.sub_name.text()
confs = self.sub_confs.value()
angle = self.sub_angle.value()
comment = "CF:%i,%i" % (confs, angle)
if len(sub_name) == 0:
sub = Substituent(substituent_atoms,
name="test",
conf_num=confs,
conf_angle=angle)
else:
sub = Substituent(substituent_atoms,
name=sub_name,
conf_num=confs,
conf_angle=angle)
sub.comment = comment
#align substituent bond to x axis
sub.coord_shift(-avoid.coords)
x_axis = np.array([1., 0., 0.])
n = np.linalg.norm(start.coords)
vb = start.coords / n
d = np.linalg.norm(vb - x_axis)
theta = np.arccos((d**2 - 2) / -2)
vx = np.cross(vb, x_axis)
sub.rotate(vx, theta)
add = False
if len(sub_name) == 0:
chimerax_sub = ResidueCollection(sub).get_chimera(self.session)
chimerax_sub.name = "substituent preview"
self.session.models.add([chimerax_sub])
bild_obj = ghost_connection_highlight(
sub, [0.60784, 0.145098, 0.70196, 0.5], self.session)
self.session.models.add(bild_obj, parent=chimerax_sub)
else:
check_aaronlib_dir()
filename = os.path.join(AARONLIB, "Subs", sub_name + ".xyz")
if os.path.exists(filename):
exists_warning = QMessageBox()
exists_warning.setIcon(QMessageBox.Warning)
exists_warning.setText(
"%s already exists.\nWould you like to overwrite?" %
filename)
exists_warning.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
rv = exists_warning.exec_()
if rv == QMessageBox.Yes:
add = True
else:
self.tool_window.status(
"%s has not been added to substituent library" %
sub_name)
else:
add = True
if add:
sub.write(outfile=filename)
self.tool_window.status("%s added to substituent library" %
sub_name)
register_selectors(self.session.logger, sub_name)
if self.session.ui.is_gui:
if (sub_name not in ELEMENTS and sub_name[0].isalpha()
and (len(sub_name) > 1
and not any(not (c.isalnum() or c in "+-")
for c in sub_name[1:]))):
add_submenu = self.session.ui.main_window.add_select_submenu
add_selector = self.session.ui.main_window.add_menu_selector
substituent_menu = add_submenu(['Che&mistry'],
'Substituents')
add_selector(substituent_menu, sub_name, sub_name)
def display_help(self):
"""Show the help for this tool in the help viewer."""
from chimerax.core.commands import run
run(self.session,
'open %s' % self.help if self.help is not None else "")
def open_link(self, *args):
if self.library_tabs.currentIndex() == 0:
link = "https://github.com/QChASM/AaronTools.py/wiki/AaronTools-Libraries#substituents"
elif self.library_tabs.currentIndex() == 1:
link = "https://github.com/QChASM/AaronTools.py/wiki/AaronTools-Libraries#rings"
elif self.library_tabs.currentIndex() == 2:
link = "https://github.com/QChASM/AaronTools.py/wiki/AaronTools-Libraries#ligands"
run(self.session, "open %s" % link)
class DockTitleBar(QWidget, object):
def __init__(self, dock_widget, renamable=False):
super(DockTitleBar, self).__init__(dock_widget)
self._renamable = renamable
main_layout = QHBoxLayout()
main_layout.setContentsMargins(0, 0, 0, 1)
self.setLayout(main_layout)
self._buttons_box = QGroupBox('')
self._buttons_box.setObjectName('Docked')
self._buttons_layout = QHBoxLayout()
self._buttons_layout.setSpacing(1)
self._buttons_layout.setMargin(2)
self._buttons_box.setLayout(self._buttons_layout)
main_layout.addWidget(self._buttons_box)
self._title_label = QLabel(self)
self._title_label.setStyleSheet('background: transparent')
self._title_edit = QLineEdit(self)
self._title_edit.setVisible(False)
self._button_size = QSize(14, 14)
self._dock_btn = QToolButton(self)
self._dock_btn.setIcon(resources.icon('restore_window', theme='color'))
self._dock_btn.setMaximumSize(self._button_size)
self._dock_btn.setAutoRaise(True)
self._close_btn = QToolButton(self)
self._close_btn.setIcon(resources.icon('close_window', theme='color'))
self._close_btn.setMaximumSize(self._button_size)
self._close_btn.setAutoRaise(True)
self._buttons_layout.addSpacing(2)
self._buttons_layout.addWidget(self._title_label)
self._buttons_layout.addWidget(self._title_edit)
self._buttons_layout.addStretch()
self._buttons_layout.addSpacing(5)
self._buttons_layout.addWidget(self._dock_btn)
self._buttons_layout.addWidget(self._close_btn)
self._buttons_box.mouseDoubleClickEvent = self.mouseDoubleClickEvent
self._buttons_box.mousePressEvent = self.mousePressEvent
self._buttons_box.mouseMoveEvent = self.mouseMoveEvent
self._buttons_box.mouseReleaseEvent = self.mouseReleaseEvent
dock_widget.featuresChanged.connect(self._on_dock_features_changed)
self._title_edit.editingFinished.connect(self._on_finish_edit)
self._dock_btn.clicked.connect(self._on_dock_btn_clicked)
self._close_btn.clicked.connect(self._on_close_btn_clicked)
self._on_dock_features_changed(dock_widget.features())
self.set_title(dock_widget.windowTitle())
dock_widget.installEventFilter(self)
dock_widget.topLevelChanged.connect(self._on_change_floating_style)
@property
def renamable(self):
return self._renamable
@renamable.setter
def renamable(self, flag):
self._renamable = flag
def eventFilter(self, obj, event):
if event.type() == QEvent.WindowTitleChange:
self.set_title(obj.windowTitle())
return super(DockTitleBar, self).eventFilter(obj, event)
def mouseMoveEvent(self, event):
event.ignore()
def mousePressEvent(self, event):
event.ignore()
def mouseReleaseEvent(self, event):
event.ignore()
def mouseDoubleClickEvent(self, event):
if event.pos().x() <= self._title_label.width() and self._renamable:
self._start_edit()
else:
super(DockTitleBar, self).mouseDoubleClickEvent(event)
def update(self, *args, **kwargs):
self._on_change_floating_style(self.parent().isFloating())
super(DockTitleBar, self).update(*args, **kwargs)
def set_title(self, title):
self._title_label.setText(title)
self._title_edit.setText(title)
def add_button(self, button):
button.setAutoRaise(True)
button.setMaximumSize(self._button_size)
self._buttons_layout.insertWidget(5, button)
def _start_edit(self):
self._title_label.hide()
self._title_edit.show()
self._title_edit.setFocus()
def _finish_edit(self):
self._title_edit.hide()
self._title_label.show()
self.parent().setWindowTitle(self._title_edit.text())
def _on_dock_features_changed(self, features):
if not features & QDockWidget.DockWidgetVerticalTitleBar:
self._close_btn.setVisible(features
& QDockWidget.DockWidgetClosable)
self._dock_btn.setVisible(features
& QDockWidget.DockWidgetFloatable)
else:
raise ValueError('Vertical title bar is not supported!')
def _on_finish_edit(self):
self._finish_edit()
def _on_dock_btn_clicked(self):
self.parent().setFloating(not self.parent().isFloating())
def _on_close_btn_clicked(self):
self.parent().toggleViewAction().setChecked(False)
self.parent().close()
def _on_change_floating_style(self, state):
pass
class SubstituentTable(QWidget):
def __init__(self, parent=None, singleSelect=False):
super().__init__(parent)
layout = QGridLayout(self)
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels(
['name', 'conformers', 'conf. angle'])
self.add_subs()
for i in range(0, 3):
self.table.resizeColumnToContents(i)
self.table.horizontalHeader().setStretchLastSection(False)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.setSortingEnabled(True)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
if singleSelect:
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.filterEdit = QLineEdit()
self.filterEdit.textChanged.connect(self.apply_filter)
self.filterEdit.setClearButtonEnabled(True)
self.filter_columns = QComboBox()
self.filter_columns.addItem("name")
self.filter_columns.addItem("conformers")
self.filter_columns.addItem("conf. angle")
self.filter_columns.currentTextChanged.connect(
self.change_filter_method)
self.name_regex_option = QComboBox()
self.name_regex_option.addItem("case-insensitive")
self.name_regex_option.addItem("case-sensitive")
self.name_regex_option.currentTextChanged.connect(self.apply_filter)
self.name_regex_option.setVisible(
self.filter_columns.currentText() == "name")
layout.addWidget(self.table, 0, 0, 1, 4)
layout.addWidget(QLabel("filter based on"), 1, 0)
layout.addWidget(self.filter_columns, 1, 1)
layout.addWidget(self.name_regex_option, 1, 2)
layout.addWidget(self.filterEdit, 1, 3)
self.change_filter_method("name")
def change_filter_method(self, text):
if text == "name":
self.filterEdit.setToolTip("name regex")
self.name_regex_option.setVisible(True)
elif text == "conformers":
self.filterEdit.setToolTip("number of conformers")
self.name_regex_option.setVisible(False)
elif text == "conf. angle":
self.filterEdit.setToolTip("angle between conformers")
self.name_regex_option.setVisible(False)
self.apply_filter()
def apply_filter(self, *args):
text = self.filterEdit.text()
if text:
if self.filter_columns.currentText() == "name":
m = QRegularExpression(text)
if m.isValid():
if self.name_regex_option.currentText(
) == "case-insensitive":
m.setPatternOptions(
QRegularExpression.CaseInsensitiveOption)
m.optimize()
filter = lambda row_num: m.match(
self.table.item(row_num, 0).text()).hasMatch()
else:
return
elif self.filter_columns.currentText() == "conformers":
if text.isdigit():
filter = lambda row_num: int(
self.table.item(row_num, 1).text()) == int(text)
else:
filter = lambda row: True
elif self.filter_columns.currentText() == "conf. angle":
if text.isdigit():
filter = lambda row_num: int(
self.table.item(row_num, 2).text()) == int(text)
else:
filter = lambda row: True
else:
filter = lambda row: True
for i in range(0, self.table.rowCount()):
self.table.setRowHidden(i, not filter(i))
def add_subs(self):
from AaronTools.substituent import Substituent
names = []
for lib in [Substituent.AARON_LIBS, Substituent.BUILTIN]:
if not os.path.exists(lib):
continue
for ring in os.listdir(lib):
name, ext = os.path.splitext(ring)
if not any(".%s" % x == ext for x in read_types):
continue
if name in names:
continue
names.append(name)
geom = Geometry(
os.path.join(lib, ring),
refresh_connected=False,
refresh_ranks=False,
)
conf_info = re.search(r"CF:(\d+),(\d+)", geom.comment)
row = self.table.rowCount()
self.table.insertRow(row)
self.table.setItem(row, 0, QTableWidgetItem(name))
#the next two items are integers - need to initialize then setData so they sort and display correctly
conf_num = QTableWidgetItem()
conf_num.setData(Qt.DisplayRole, conf_info.group(1))
self.table.setItem(row, 1, conf_num)
conf_angle = QTableWidgetItem()
conf_angle.setData(Qt.DisplayRole, conf_info.group(2))
self.table.setItem(row, 2, conf_angle)
self.substituent_list = names
class RowTableWidget(QFrame):
double_clicked = Signal(object)
def __init__(self,
auto_resize=False,
single_row_select=True,
context_menu_callback=None,
last_column_stretch=True,
has_counters=False,
parent=None
):
QFrame.__init__(self, parent)
self._has_counters = has_counters
self.model = None
self.table_view = RowTableView(auto_resize, single_row_select, context_menu_callback, last_column_stretch)
self.table_view.doubleClicked.connect(self._double_clicked)
if has_counters:
self.counters = Counters()
self.counters.button_clicked.connect(self._counter_clicked)
self.search_bar = QLineEdit()
self.search_bar.setFixedHeight(SEARCHBAR_HEIGHT)
self.search_bar.textChanged.connect(self.set_search_text)
self.search_bar.setToolTip("Search bar")
self.auto_size_button = QPushButton('<>')
self.auto_size_button.setFixedSize(SEARCHBAR_HEIGHT, SEARCHBAR_HEIGHT)
self.auto_size_button.clicked.connect(self._auto_size_clicked)
self.auto_size_button.setToolTip("Auto size")
self.status_label = QLabel(STATUS_LABEL_MESSAGE.format(0, 0))
self.status_label.setFixedWidth(STATUS_LABEL_WIDTH)
self.progress_bar = QProgressBar()
self.progress_bar.setFormat('')
layout = QGridLayout()
layout.addWidget(self.search_bar, 0, 0, 1, 3)
layout.addWidget(self.auto_size_button, 0, 3)
if has_counters:
layout.addWidget(self.counters, 1, 0, 1, 2)
layout.addWidget(self.table_view, 1, 2, 1, 2)
else:
layout.addWidget(self.table_view, 1, 0, 1, 4)
layout.addWidget(self.status_label, 2, 0)
layout.addWidget(self.progress_bar, 2, 1, 1, 3)
layout.setColumnStretch(2, 100)
self.setLayout(layout)
def set_model(self, model):
self.model = model
self.table_view.setModel(model)
model.modelReset.connect(self._set_progress_maximum)
model.modelReset.connect(self._update_status)
if self._has_counters:
model.modelReset.connect(self._update_counters)
self._update_counters()
model.progress_updated.connect(self._update_progress)
self._set_progress_maximum()
self._update_status()
self.progress_bar.setVisible(model.has_background_callback)
@property
def selected_rows(self):
return [self.model.data(index, Qt.UserRole) for index
in self.table_view.selectionModel().selectedIndexes() if index.column() == 0]
@property
def search_text(self):
return self.search_bar.text()
def set_search_text(self, text):
self.search_bar.blockSignals(True)
self.search_bar.setText(text)
self.search_bar.blockSignals(False)
self.model.set_search_text(text)
def _set_progress_maximum(self):
self.progress_bar.setMaximum(self.model.progress_max) # do better ?
def _update_progress(self, value):
self.progress_bar.setValue(value)
def _update_status(self):
self.status_label.setText(STATUS_LABEL_MESSAGE.format(
self.model.rowCount(), self.model.total_row_count
))
def _counter_clicked(self, entry, checked_buttons):
entries = [entry for entry, active in checked_buttons.items() if active]
self.model.set_search_counters(entries)
def _update_counters(self):
self.counters.set(self.model.counters)
def _auto_size_clicked(self):
with Hourglass():
self.table_view.resizeColumnsToContents()
def _double_clicked(self, index):
row = self.model.data(index, Qt.UserRole)
self.double_clicked.emit(row)
def state(self):
header_sizes = list()
header = self.table_view.horizontalHeader()
for section_index in range(header.count()):
header_sizes.append(header.sectionSize(section_index))
return {
'header_sizes': header_sizes,
'search_text': self.search_bar.text()
}
def load_state(self, state):
header = self.table_view.horizontalHeader()
for section_index, size in enumerate(state['header_sizes']):
header.resizeSection(section_index, size)
self.search_bar.setText(state['search_text'])
class MainWindow(QMainWindow):
def __init__(self, url):
super().__init__()
self.setAttribute(Qt.WA_DeleteOnClose, True)
self.progress = 0
f = QFile()
f.setFileName(":/jquery.min.js")
f.open(QIODevice.ReadOnly)
self.jQuery = f.readAll().data().decode()
self.jQuery += "\nvar qt = { 'jQuery': jQuery.noConflict(true) };"
f.close()
self.view = QWebEngineView(self)
self.view.load(url)
self.view.loadFinished.connect(self.adjustLocation)
self.view.titleChanged.connect(self.adjustTitle)
self.view.loadProgress.connect(self.setProgress)
self.view.loadFinished.connect(self.finishLoading)
self.locationEdit = QLineEdit(self)
self.locationEdit.setSizePolicy(
QSizePolicy.Expanding,
self.locationEdit.sizePolicy().verticalPolicy())
self.locationEdit.returnPressed.connect(self.changeLocation)
toolBar = self.addToolBar(self.tr("Navigation"))
toolBar.addAction(self.view.pageAction(QWebEnginePage.Back))
toolBar.addAction(self.view.pageAction(QWebEnginePage.Forward))
toolBar.addAction(self.view.pageAction(QWebEnginePage.Reload))
toolBar.addAction(self.view.pageAction(QWebEnginePage.Stop))
toolBar.addWidget(self.locationEdit)
viewMenu = self.menuBar().addMenu(self.tr("&View"))
viewSourceAction = QAction(self.tr("Page Source"), self)
viewSourceAction.triggered.connect(self.viewSource)
viewMenu.addAction(viewSourceAction)
effectMenu = self.menuBar().addMenu(self.tr("&Effect"))
effectMenu.addAction(self.tr("Highlight all links"),
self.highlightAllLinks)
self.rotateAction = QAction(self)
self.rotateAction.setIcon(self.style().standardIcon(
QStyle.SP_FileDialogDetailedView))
self.rotateAction.setCheckable(True)
self.rotateAction.setText(self.tr("Turn images upside down"))
self.rotateAction.toggled.connect(self.rotateImages)
effectMenu.addAction(self.rotateAction)
toolsMenu = self.menuBar().addMenu(self.tr("&Tools"))
toolsMenu.addAction(self.tr("Remove GIF images"), self.removeGifImages)
toolsMenu.addAction(self.tr("Remove all inline frames"),
self.removeInlineFrames)
toolsMenu.addAction(self.tr("Remove all object elements"),
self.removeObjectElements)
toolsMenu.addAction(self.tr("Remove all embedded elements"),
self.removeEmbeddedElements)
self.setCentralWidget(self.view)
@Slot()
def adjustLocation(self):
self.locationEdit.setText(self.view.url().toString())
@Slot()
def changeLocation(self):
url = QUrl.fromUserInput(self.locationEdit.text())
self.view.load(url)
self.view.setFocus()
@Slot()
def adjustTitle(self):
if self.progress <= 0 or self.progress >= 100:
self.setWindowTitle(self.view.title())
else:
self.setWindowTitle("%s (%2d)" %
(self.view.title(), self.progress))
@Slot(int)
def setProgress(self, p):
self.progress = p
self.adjustTitle()
@Slot()
def finishLoading(self):
self.progress = 100
self.adjustTitle()
self.view.page().runJavaScript(self.jQuery)
self.rotateImages(self.rotateAction.isChecked())
@Slot()
def viewSource(self):
self.textEdit = QTextEdit()
self.textEdit.setAttribute(Qt.WA_DeleteOnClose)
self.textEdit.adjustSize()
self.textEdit.move(self.geometry().center() -
self.textEdit.rect().center())
self.textEdit.show()
self.view.page().toHtml(self.textEdit.setPlainText)
@Slot()
def highlightAllLinks(self):
code = "qt.jQuery('a').each( function () { qt.jQuery(this).css('background-color', 'yellow') } )"
self.view.page().runJavaScript(code)
@Slot(bool)
def rotateImages(self, invert):
code = ""
if invert:
code = "qt.jQuery('img').each( function () { qt.jQuery(this).css('transition', 'transform 2s'); qt.jQuery(this).css('transform', 'rotate(180deg)') } )" # noqa: E501
else:
code = "qt.jQuery('img').each( function () { qt.jQuery(this).css('transition', 'transform 2s'); qt.jQuery(this).css('transform', 'rotate(0deg)') } )" # noqa: E501
self.view.page().runJavaScript(code)
@Slot()
def removeGifImages(self):
code = "qt.jQuery('[src*=gif]').remove()"
self.view.page().runJavaScript(code)
@Slot()
def removeInlineFrames(self):
code = "qt.jQuery('iframe').remove()"
self.view.page().runJavaScript(code)
@Slot()
def removeObjectElements(self):
code = "qt.jQuery('object').remove()"
self.view.page().runJavaScript(code)
@Slot()
def removeEmbeddedElements(self):
code = "qt.jQuery('embed').remove()"
self.view.page().runJavaScript(code)
class Info(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/File-Info-Tool"
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _InfoSettings(self.session, name)
self._build_ui()
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 header_check(self, state):
"""user has [un]checked the 'include header' option on the menu"""
if state:
self.settings.include_header = True
else:
self.settings.include_header = False
def get_csv(self):
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
if self.tabs.currentIndex() == 0:
if self.settings.include_header:
s = delim.join(["Data", "Value"])
s += "\n"
else:
s = ""
for i in range(0, self.table.rowCount()):
if self.table.isRowHidden(i):
continue
s += delim.join([
item.text().replace("<sub>", "").replace("</sub>", "")
for item in [
self.table.item(i, j) if self.table.item(i, j)
is not None else self.table.cellWidget(i, j)
for j in range(0, 2)
]
])
s += "\n"
elif self.tabs.currentIndex() == 1:
if self.settings.include_header:
s = delim.join([
"Frequency (cm\u207b\u00b9)", "symmetry", "IR intensity",
"force constant"
])
s += "\n"
else:
s = ""
for i in range(0, self.freq_table.rowCount()):
if self.freq_table.isRowHidden(i):
continue
s += delim.join([
item.text().replace("<sub>", "").replace("</sub>", "")
for item in [
self.freq_table.item(i, j) if self.freq_table.
item(i, j) is not None else self.freq_table.
cellWidget(i, j) for j in range(0, 4)
]
])
s += "\n"
else:
if self.settings.include_header:
s = delim.join(
["Fundamental (cm\u207b\u00b9)", "Δanh", "IR intensity"])
s += "\n"
else:
s = ""
for i in range(0, self.fundamental_table.rowCount()):
if self.fundamental_table.isRowHidden(i):
continue
s += delim.join([
item.text().replace("<sub>", "").replace("</sub>", "")
for item in [
self.fundamental_table.item(i, j) if self.
fundamental_table.item(i, j) is not None else self.
fundamental_table.cellWidget(i, j)
for j in range(0, 3)
]
])
s += "\n"
if self.settings.include_header:
s += delim.join([
"Fundamental (cm\u207b\u00b9)",
"Fundamental (cm\u207b\u00b9)",
"Combination (cm\u207b\u00b9)", "IR intensity"
])
s += "\n"
else:
s += "\n"
for i in range(0, self.combo_table.rowCount()):
if self.combo_table.isRowHidden(i):
continue
s += delim.join([
item.text().replace("<sub>", "").replace("</sub>", "")
for item in [
self.combo_table.item(i, j) if self.combo_table.
item(i, j) is not None else self.combo_table.
cellWidget(i, j) for j in range(0, 4)
]
])
s += "\n"
return s
def copy_csv(self):
app = QApplication.instance()
clipboard = app.clipboard()
csv = self.get_csv()
clipboard.setText(csv)
self.session.logger.status("copied to clipboard")
def save_csv(self):
"""save data on current tab to CSV file"""
filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)")
if filename:
s = self.get_csv()
with open(filename, 'w') as f:
f.write(s.strip())
self.session.logger.status("saved to %s" % filename)
def fill_table(self, ndx):
self.table.setRowCount(0)
self.freq_table.setRowCount(0)
self.fundamental_table.setRowCount(0)
# self.overtone_table.setRowCount(0)
self.combo_table.setRowCount(0)
if ndx < 0:
self.fundamental_table.setVisible(False)
self.combo_table.setVisible(False)
return
fr = self.file_selector.currentData()
item = QTableWidgetItem()
item.setData(Qt.DisplayRole, "name")
val = QTableWidgetItem()
val.setData(Qt.DisplayRole, fr.name)
self.table.insertRow(0)
self.table.setItem(0, 0, item)
self.table.setItem(0, 1, val)
for info in fr.other.keys():
if info == "archive" and not self.settings.archive:
continue
if any(
isinstance(fr.other[info], obj)
for obj in [str, float, int]):
row = self.table.rowCount()
self.table.insertRow(row)
item = QTableWidgetItem()
info_name = info.replace("_", " ")
val = fr.other[info]
if info == "mass":
info_name += " (%s)" % self.settings.mass
if self.settings.mass == "Da":
val /= UNIT.AMU_TO_KG
elif info == "temperature":
info_name += " (K)"
elif (any(info == s for s in nrg_infos)
or info.lower().endswith("energy")
or info.startswith("E(")):
if self.settings.energy == "Hartree":
info_name += " (E<sub>h</sub>)"
else:
info_name += " (%s)" % self.settings.energy
info_name = info_name.replace("orrelation", "orr.")
info_name = info_name.replace("Same-spin", "SS")
info_name = info_name.replace("Opposite-spin", "OS")
if self.settings.energy == "kcal/mol":
val *= UNIT.HART_TO_KCAL
elif self.settings.energy == "kJ/mol":
val *= 4.184 * UNIT.HART_TO_KCAL
val = "%.6f" % val
elif info.startswith("optical rotation"):
info_name += " (°)"
elif any(info == x for x in pg_infos):
info_name = info.replace("_", " ")
if re.search("\d", val):
val = re.sub(r"(\d+)", r"<sub>\1</sub>", val)
# gaussian uses * for infinity
val = val.replace("*", "<sub>∞</sub>")
# psi4 uses _inf_
val = val.replace("_inf_", "<sub>∞</sub>")
if any(val.endswith(char) for char in "vhdsiVHDSI"):
val = val[:-1] + "<sub>" + val[-1].lower() + "</sub>"
if "<sub>" in info_name:
self.table.setCellWidget(row, 0, QLabel(info_name))
else:
item = QTableWidgetItem()
item.setData(Qt.DisplayRole, info_name)
self.table.setItem(row, 0, item)
value = QTableWidgetItem()
val = str(val)
if "<sub>" in val:
self.table.setCellWidget(row, 1, QLabel(val))
else:
value.setData(Qt.DisplayRole, val)
self.table.setItem(row, 1, value)
elif isinstance(fr.other[info], Theory):
theory = fr.other[info]
if theory.method is not None:
row = self.table.rowCount()
self.table.insertRow(row)
item = QTableWidgetItem()
item.setData(Qt.DisplayRole, "method")
self.table.setItem(row, 0, item)
value = QTableWidgetItem()
value.setData(Qt.DisplayRole, theory.method.name)
self.table.setItem(row, 1, value)
if theory.basis is not None:
if theory.basis.basis:
for basis in theory.basis.basis:
row = self.table.rowCount()
self.table.insertRow(row)
item = QTableWidgetItem()
if not basis.elements:
item.setData(Qt.DisplayRole, "basis set")
else:
item.setData(
Qt.DisplayRole,
"basis for %s" % ", ".join(basis.elements))
self.table.setItem(row, 0, item)
value = QTableWidgetItem()
value.setData(Qt.DisplayRole, basis.name)
self.table.setItem(row, 1, value)
if theory.basis.ecp:
for ecp in theory.basis.ecp:
row = self.table.rowCount()
self.table.insertRow(row)
item = QTableWidgetItem()
if ecp.elements is None:
item.setData(Qt.DisplayRole, "ECP")
else:
item.setData(Qt.DisplayRole,
"ECP %s" % " ".join(ecp.elements))
self.table.setItem(row, 0, item)
value = QTableWidgetItem()
value.setData(Qt.DisplayRole, ecp.name)
self.table.setItem(row, 1, value)
elif (hasattr(fr.other[info], "__iter__")
and all(isinstance(x, float) for x in fr.other[info])
and len(fr.other[info]) > 1):
row = self.table.rowCount()
self.table.insertRow(row)
item = QTableWidgetItem()
info_name = info.replace("_", " ")
vals = fr.other[info]
if "rotational_temperature" in info:
info_name = info_name.replace(
"temperature",
"constants (%s)" % self.settings.rot_const)
if self.settings.rot_const == "GHz":
vals = [
x * PHYSICAL.KB / (PHYSICAL.PLANCK * (10**9))
for x in vals
]
item.setData(Qt.DisplayRole, info_name)
self.table.setItem(row, 0, item)
value = QTableWidgetItem()
value.setData(Qt.DisplayRole,
", ".join(["%.4f" % x for x in vals]))
self.table.setItem(row, 1, value)
if "frequency" in fr.other:
self.tabs.setTabEnabled(1, True)
freq_data = fr.other['frequency'].data
for i, mode in enumerate(freq_data):
row = self.freq_table.rowCount()
self.freq_table.insertRow(row)
freq = FreqTableWidgetItem()
freq.setData(
Qt.DisplayRole, "%.2f%s" %
(abs(mode.frequency), "i" if mode.frequency < 0 else ""))
freq.setData(Qt.UserRole, i)
self.freq_table.setItem(row, 0, freq)
if mode.symmetry:
text = mode.symmetry
if re.search("\d", text):
text = re.sub(r"(\d+)", r"<sub>\1</sub>", text)
if text.startswith("SG"):
text = "Σ" + text[2:]
elif text.startswith("PI"):
text = "Π" + text[2:]
elif text.startswith("DLT"):
text = "Δ" + text[3:]
if any(text.endswith(char) for char in "vhdugVHDUG"):
text = text[:-1] + "<sub>" + text[-1].lower(
) + "</sub>"
label = QLabel(text)
label.setAlignment(Qt.AlignCenter)
self.freq_table.setCellWidget(row, 1, label)
intensity = QTableWidgetItem()
if mode.intensity is not None:
intensity.setData(Qt.DisplayRole, round(mode.intensity, 2))
self.freq_table.setItem(row, 2, intensity)
forcek = QTableWidgetItem()
if mode.forcek is not None:
forcek.setData(Qt.DisplayRole, round(mode.forcek, 2))
self.freq_table.setItem(row, 3, forcek)
if fr.other["frequency"].anharm_data:
self.fundamental_table.setVisible(True)
self.combo_table.setVisible(True)
freq = fr.other["frequency"]
self.tabs.setTabEnabled(2, True)
anharm_data = sorted(
freq.anharm_data,
key=lambda x: x.harmonic_frequency,
)
for i, mode in enumerate(anharm_data):
row = self.fundamental_table.rowCount()
self.fundamental_table.insertRow(row)
fund = FreqTableWidgetItem()
fund.setData(
Qt.DisplayRole,
"%.2f%s" % (abs(mode.frequency),
"i" if mode.frequency < 0 else ""))
fund.setData(Qt.UserRole, i)
self.fundamental_table.setItem(row, 0, fund)
delta_anh = QTableWidgetItem()
delta_anh.setData(Qt.DisplayRole, round(mode.delta_anh, 2))
self.fundamental_table.setItem(row, 1, delta_anh)
intensity = QTableWidgetItem()
if mode.intensity is not None:
intensity.setData(Qt.DisplayRole,
round(mode.intensity, 2))
self.fundamental_table.setItem(row, 2, intensity)
for overtone in mode.overtones:
row = self.combo_table.rowCount()
self.combo_table.insertRow(row)
fund = FreqTableWidgetItem()
fund.setData(
Qt.DisplayRole,
"%.2f%s" % (abs(mode.frequency),
"i" if mode.frequency < 0 else ""))
fund.setData(Qt.UserRole, i)
self.combo_table.setItem(row, 0, fund)
fund = FreqTableWidgetItem()
fund.setData(Qt.UserRole, i)
self.combo_table.setItem(row, 1, fund)
ot = FreqTableWidgetItem()
ot.setData(
Qt.DisplayRole,
"%.2f%s" % (abs(overtone.frequency),
"i" if overtone.frequency < 0 else ""))
ot.setData(Qt.UserRole, i)
self.combo_table.setItem(row, 2, ot)
intensity = QTableWidgetItem()
if overtone.intensity is not None:
intensity.setData(Qt.DisplayRole,
round(overtone.intensity, 2))
self.combo_table.setItem(row, 3, intensity)
for key in mode.combinations:
for combination in mode.combinations[key]:
row = self.combo_table.rowCount()
self.combo_table.insertRow(row)
fund = FreqTableWidgetItem()
fund.setData(
Qt.DisplayRole,
"%.2f%s" % (abs(mode.frequency),
"i" if mode.frequency < 0 else ""))
fund.setData(Qt.UserRole, i)
self.combo_table.setItem(row, 0, fund)
other_freq = freq.anharm_data[key].frequency
fund = FreqTableWidgetItem()
fund.setData(
Qt.DisplayRole,
"%.2f%s" % (abs(other_freq),
"i" if other_freq < 0 else ""))
fund.setData(Qt.UserRole,
i + len(freq.anharm_data) * key)
self.combo_table.setItem(row, 1, fund)
combo = FreqTableWidgetItem()
combo.setData(
Qt.DisplayRole, "%.2f%s" %
(abs(combination.frequency),
"i" if combination.frequency < 0 else ""))
combo.setData(Qt.UserRole, i)
self.combo_table.setItem(row, 2, combo)
intensity = QTableWidgetItem()
if combination.intensity is not None:
intensity.setData(
Qt.DisplayRole,
round(combination.intensity, 2))
self.combo_table.setItem(row, 3, intensity)
else:
self.fundamental_table.setVisible(False)
self.combo_table.setVisible(False)
self.tabs.setTabEnabled(2, False)
else:
self.fundamental_table.setVisible(False)
self.combo_table.setVisible(False)
self.tabs.setTabEnabled(1, False)
self.tabs.setTabEnabled(2, False)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.freq_table.resizeColumnToContents(0)
self.freq_table.resizeColumnToContents(1)
self.freq_table.resizeColumnToContents(2)
self.apply_filter()
def apply_filter(self, text=None):
if text is None:
text = self.filter.text()
if text:
text = text.replace("(", "\(")
text = text.replace(")", "\)")
m = QRegularExpression(text)
m.setPatternOptions(QRegularExpression.CaseInsensitiveOption)
if m.isValid():
m.optimize()
filter = lambda row_num: m.match(
self.table.item(row_num, 0).text()
if self.table.item(row_num, 0) is not None else self.table.
cellWidget(row_num, 0).text().replace("<sub>", "").replace(
"</sub>", "")).hasMatch()
else:
return
else:
filter = lambda row: True
for i in range(0, self.table.rowCount()):
self.table.setRowHidden(i, not filter(i))
def delete(self):
self.file_selector.deleteLater()
return super().delete()
def close(self):
self.file_selector.deleteLater()
return super().close()
class RingTable(QWidget):
def __init__(self, parent=None):
super().__init__(parent)
layout = QGridLayout(self)
self.table = QTableWidget()
self.table.setColumnCount(1)
self.table.setHorizontalHeaderLabels(['name'])
self.add_rings()
for i in range(0, 1):
self.table.resizeColumnToContents(i)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Stretch)
self.table.setSortingEnabled(True)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.filterEdit = QLineEdit()
self.filterEdit.textChanged.connect(self.apply_filter)
self.filterEdit.setClearButtonEnabled(True)
self.filter_columns = QComboBox()
self.filter_columns.addItem("name")
self.filter_columns.currentTextChanged.connect(
self.change_filter_method)
self.name_regex_option = QComboBox()
self.name_regex_option.addItem("case-insensitive")
self.name_regex_option.addItem("case-sensitive")
self.name_regex_option.currentTextChanged.connect(self.apply_filter)
self.name_regex_option.setVisible(
self.filter_columns.currentText() == "name")
layout.addWidget(self.table, 0, 0, 1, 4)
layout.addWidget(QLabel("filter based on"), 1, 0)
layout.addWidget(self.filter_columns, 1, 1)
layout.addWidget(self.name_regex_option, 1, 2)
layout.addWidget(self.filterEdit, 1, 3)
self.change_filter_method("name")
def change_filter_method(self, text):
if text == "name":
self.filterEdit.setToolTip("name regex")
self.name_regex_option.setVisible(True)
self.apply_filter()
def apply_filter(self, *args):
text = self.filterEdit.text()
if text:
if self.filter_columns.currentText() == "name":
m = QRegularExpression(text)
if m.isValid():
if self.name_regex_option.currentText(
) == "case-insensitive":
m.setPatternOptions(
QRegularExpression.CaseInsensitiveOption)
m.optimize()
filter = lambda row_num: m.match(
self.table.item(row_num, 0).text()).hasMatch()
else:
return
else:
filter = lambda row: True
for i in range(0, self.table.rowCount()):
self.table.setRowHidden(i, not filter(i))
def add_rings(self):
from AaronTools.ring import Ring
names = []
for lib in [Ring.AARON_LIBS, Ring.BUILTIN]:
if not os.path.exists(lib):
continue
for ring in os.listdir(lib):
name, ext = os.path.splitext(ring)
if not any(".%s" % x == ext for x in read_types):
continue
if name in names:
continue
names.append(name)
row = self.table.rowCount()
self.table.insertRow(row)
self.table.setItem(row, 0, QTableWidgetItem(name))
self.ring_list = names
class _SubstituentSelector(ToolInstance):
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self._build_ui()
def _build_ui(self):
layout = QFormLayout()
self.substituent_table = SubstituentTable(singleSelect=True)
layout.addRow(self.substituent_table)
self.new_residue = QCheckBox()
self.new_residue.setCheckState(
Qt.Checked if SubstituteMouseMode.newRes else Qt.Unchecked)
layout.addRow("new residue:", self.new_residue)
self.res_name = QLineEdit()
self.res_name.setPlaceholderText("leave blank to keep current")
layout.addRow("set residue name:", self.res_name)
self.distance_names = QCheckBox()
self.distance_names.setCheckState(
Qt.Checked if SubstituteMouseMode.useRemoteness else Qt.Unchecked)
layout.addRow("distance atom names:", self.distance_names)
self.keep_open = QCheckBox()
layout.addRow("keep list open:", self.keep_open)
do_it = QPushButton("set substituent")
do_it.clicked.connect(self.set_sub)
layout.addRow(do_it)
self.keep_open.stateChanged.connect(
lambda state: do_it.setVisible(state != Qt.Checked))
self.keep_open.stateChanged.connect(self.sub_changed)
self.substituent_table.table.itemSelectionChanged.connect(
self.sub_changed)
self.new_residue.stateChanged.connect(self.sub_changed)
self.res_name.textChanged.connect(self.sub_changed)
self.distance_names.stateChanged.connect(self.sub_changed)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def sub_changed(self):
if self.keep_open.checkState() == Qt.Checked:
self.set_sub()
def set_sub(self):
sub_names = []
for row in self.substituent_table.table.selectionModel().selectedRows(
):
if self.substituent_table.table.isRowHidden(row.row()):
continue
sub_names.append(row.data())
if sub_names:
SubstituteMouseMode.substituent = sub_names[0]
SubstituteMouseMode.newRes = self.new_residue.checkState(
) == Qt.Checked
SubstituteMouseMode.useRemoteness = self.distance_names.checkState(
) == Qt.Checked
sub_name = self.res_name.text()
SubstituteMouseMode.resName = sub_name
if self.keep_open.checkState() != Qt.Checked:
self.delete()
def close(self):
sub_names = []
for row in self.substituent_table.table.selectionModel().selectedRows(
):
if self.substituent_table.table.isRowHidden(row.row()):
continue
sub_names.append(row.data())
if sub_names:
SubstituteMouseMode.substituent = sub_names[0]
SubstituteMouseMode.newRes = self.new_residue.checkState(
) == Qt.Checked
SubstituteMouseMode.useRemoteness = self.distance_names.checkState(
) == Qt.Checked
sub_name = self.res_name.text()
SubstituteMouseMode.resName = sub_name
super().close()
class Second(QMainWindow):
def __init__(self):
super(Second, self).__init__()
self.setWindowTitle("Add new device")
self.nameLabel = QLabel(self)
self.nameLabel.move(10, 10)
self.nameLabel.setText("Device name")
self.nameEntry = QLineEdit(self)
self.nameEntry.move(10, 40)
self.nameEntry.resize(100, 30)
self.colorLabel = QLabel(self)
self.colorLabel.move(120, 10)
self.colorLabel.setText("Color cameras")
self.colorEntry = QLineEdit(self)
self.colorEntry.move(140, 40)
self.colorEntry.resize(70, 30)
self.colorEntry.setValidator(QtGui.QIntValidator())
self.monoLabel = QLabel(self)
self.monoLabel.move(230, 10)
self.monoLabel.setText("Mono cameras")
self.monoEntry = QLineEdit(self)
self.monoEntry.move(250, 40)
self.monoEntry.resize(70, 30)
self.monoEntry.setValidator(QtGui.QIntValidator())
self.depthPresent = QCheckBox("Include depth", self)
self.depthPresent.move(10, 80)
self.depthPresent.resize(150, 30)
self.depthPresent.stateChanged.connect(self.toggle_depth)
self.leftfovLabel = QLabel(self)
self.leftfovLabel.move(10, 120)
self.leftfovLabel.setText("Left FOV deg.")
self.leftfovEntry = QLineEdit(self)
self.leftfovEntry.move(180, 120)
self.leftfovEntry.resize(140, 30)
self.leftfovEntry.setValidator(QtGui.QDoubleValidator())
self.rightfovLabel = QLabel(self)
self.rightfovLabel.move(10, 160)
self.rightfovLabel.setText("Right FOV deg.")
self.rightfovEntry = QLineEdit(self)
self.rightfovEntry.move(180, 160)
self.rightfovEntry.resize(140, 30)
self.rightfovEntry.setValidator(QtGui.QDoubleValidator())
self.rgbfovLabel = QLabel(self)
self.rgbfovLabel.move(10, 200)
self.rgbfovLabel.setText("RGB FOV deg.")
self.rgbfovEntry = QLineEdit(self)
self.rgbfovEntry.move(180, 200)
self.rgbfovEntry.resize(140, 30)
self.rgbfovEntry.setValidator(QtGui.QDoubleValidator())
self.lrdistanceLabel = QLabel(self)
self.lrdistanceLabel.move(10, 240)
self.lrdistanceLabel.resize(200, 30)
self.lrdistanceLabel.setText("Left - Right distance cm.")
self.lrdistanceEntry = QLineEdit(self)
self.lrdistanceEntry.move(180, 240)
self.lrdistanceEntry.resize(140, 30)
self.lrdistanceEntry.setValidator(QtGui.QDoubleValidator())
self.lrgbdistanceLabel = QLabel(self)
self.lrgbdistanceLabel.move(10, 280)
self.lrgbdistanceLabel.resize(200, 30)
self.lrgbdistanceLabel.setText("Left - RGB distance cm.")
self.lrgbdistanceEntry = QLineEdit(self)
self.lrgbdistanceEntry.move(180, 280)
self.lrgbdistanceEntry.resize(140, 30)
self.lrgbdistanceEntry.setValidator(QtGui.QDoubleValidator())
self.saveButton = QPushButton("Save", self)
self.saveButton.resize(100, 30)
self.saveButton.clicked.connect(self.save)
self.cancelButton = QPushButton("Cancel", self)
self.cancelButton.resize(100, 30)
self.cancelButton.clicked.connect(self.cancel)
self.toggle_depth(False)
def toggle_depth(self, checked):
if checked:
self.leftfovLabel.setVisible(True)
self.leftfovEntry.setVisible(True)
self.rightfovLabel.setVisible(True)
self.rightfovEntry.setVisible(True)
self.rgbfovLabel.setVisible(True)
self.rgbfovEntry.setVisible(True)
self.lrdistanceLabel.setVisible(True)
self.lrdistanceEntry.setVisible(True)
self.lrgbdistanceLabel.setVisible(True)
self.lrgbdistanceEntry.setVisible(True)
self.saveButton.move(200, 330)
self.cancelButton.move(30, 330)
self.resize(330, 380)
else:
self.leftfovLabel.setVisible(False)
self.leftfovEntry.setVisible(False)
self.rightfovLabel.setVisible(False)
self.rightfovEntry.setVisible(False)
self.rgbfovLabel.setVisible(False)
self.rgbfovEntry.setVisible(False)
self.lrdistanceLabel.setVisible(False)
self.lrdistanceEntry.setVisible(False)
self.lrgbdistanceLabel.setVisible(False)
self.lrgbdistanceEntry.setVisible(False)
self.saveButton.move(200, 120)
self.cancelButton.move(30, 120)
self.resize(330, 170)
def save(self, *args, **kwargs):
try:
data = {
"name": self.nameEntry.text(),
"color_count": int(self.colorEntry.text()),
"mono_count": int(self.monoEntry.text()),
}
if self.depthPresent.isChecked():
data.update({
"depth":
True,
"left_fov_deg":
float(self.leftfovEntry.text()),
"right_fov_deg":
float(self.rightfovEntry.text()),
"rgb_fov_deg":
float(self.rgbfovEntry.text()),
"left_to_right_distance_cm":
float(self.lrdistanceEntry.text()),
"left_to_rgb_distance_cm":
float(self.lrgbdistanceEntry.text()),
})
append_to_json(
data,
Path(__file__).parent.parent / Path('custom_devices.json'))
self.close()
INITIALIZE()
self.instance.getRegisteredTools(['NodeBoxTool'])[0].refresh()
except Exception as e:
QMessageBox.warning(self, "Warning", str(e))
def cancel(self):
self.close()
class EditableTearOffTabBar(TearOffTabBar, object):
"""
Extended implementation of an editable tab bar with:
- Rename functionality
- Tear off functionality
"""
tab_label_renamed = Signal(str, str)
request_remove = Signal(int)
tab_changed = Signal(int)
def __init__(self, parent=None):
super(EditableTearOffTabBar, self).__init__(parent=parent)
self._editor = QLineEdit(self)
self._editor.setWindowFlags(Qt.Popup)
self._editor.setFocusProxy(self)
self._editor.setFocusPolicy(Qt.StrongFocus)
self._editor.editingFinished.connect(self.handle_editing_finished)
self._editor.installEventFilter(self)
self._editor.setValidator(QRegExpValidator(nameRegExp))
self._edit_index = -1
def edit_tab(self, index):
"""
This set the tab in edit mode
This method is called when double click on the tab
:param index: int, Index of the tab to be renamed
"""
# Show the editable line and position it on top of the selected tab
rect = self.tabRect(index)
self._editor.setFixedSize(rect.size())
self._editor.move(self.parent().mapToGlobal(rect.topLeft()))
self._editor.setText(self.tabText(index))
if not self._editor.isVisible():
self._editor.show()
self._edit_index = index
def handle_editing_finished(self):
"""
This finish the edit of the tab name
"""
# This method only works of we are editing any tab
if self._edit_index >= 0:
# Hide the text and update tab text
self._editor.hide()
old_text = self.tabText(self.__editIndex)
new_text = self._editor.text()
if old_text != new_text:
names = [self.tabText(i) for i in range(self.count())]
new_text = naming.get_numeric_name(new_text, names)
self.setTabText(self._edit_index, new_text)
self.tab_label_renamed.emit(old_text, new_text)
self._edit_index = -1
def eventFilter(self, widget, event):
"""
If we click (with mouse or keyboard) on registered widgets we hide the editor
"""
if event.type(
) == QEvent.MouseButtonPress and not self._editor.geometry().contains(
event.globalPos()) or event.type(
) == QEvent.KeyPress and event.key() == Qt.Key_Escape:
self._editor.hide()
return False
return QTabBar.eventFilter(self, widget, event)
