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 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 ConeAngle(ToolInstance): help = "https://github.com/QChASM/SEQCROW/wiki/Cone-Angle-Tool" def __init__(self, session, name): super().__init__(session, name) from chimerax.ui import MainToolWindow self.tool_window = MainToolWindow(self) self.settings = _ConeAngleSettings(self.session, name) self.ligands = dict() self._build_ui() def _build_ui(self): layout = QFormLayout() self.cone_option = QComboBox() self.cone_option.addItems(["Tolman (Unsymmetrical)", "Exact"]) ndx = self.cone_option.findText(self.settings.cone_option, Qt.MatchExactly) self.cone_option.setCurrentIndex(ndx) layout.addRow("method:", self.cone_option) self.radii_option = QComboBox() self.radii_option.addItems(["Bondi", "UMN"]) ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly) self.radii_option.setCurrentIndex(ndx) layout.addRow("radii:", self.radii_option) self.display_cone = QCheckBox() self.display_cone.setChecked(self.settings.display_cone) layout.addRow("show cone:", self.display_cone) self.display_radii = QCheckBox() self.display_radii.setChecked(self.settings.display_radii) layout.addRow("show radii:", self.display_radii) set_ligand_button = QPushButton("set ligand to current selection") set_ligand_button.clicked.connect(self.set_ligand) layout.addRow(set_ligand_button) self.set_ligand_button = set_ligand_button calc_cone_button = QPushButton( "calculate cone angle for ligand on selected center") calc_cone_button.clicked.connect(self.calc_cone) layout.addRow(calc_cone_button) self.calc_cone_button = calc_cone_button remove_cone_button = QPushButton("remove cone visualizations") remove_cone_button.clicked.connect(self.del_cone) layout.addRow(remove_cone_button) self.remove_cone_button = remove_cone_button self.table = QTableWidget() self.table.setColumnCount(3) self.table.setHorizontalHeaderLabels([ 'model', 'center', 'cone angle (°)', ]) self.table.setSelectionBehavior(QTableWidget.SelectRows) self.table.setEditTriggers(QTableWidget.NoEditTriggers) self.table.resizeColumnToContents(0) self.table.resizeColumnToContents(1) self.table.resizeColumnToContents(2) self.table.horizontalHeader().setSectionResizeMode( 2, QHeaderView.Stretch) layout.addRow(self.table) menu = QMenuBar() export = menu.addMenu("&Export") clear = QAction("Clear data table", self.tool_window.ui_area) clear.triggered.connect(self.clear_table) export.addAction(clear) copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area) copy.triggered.connect(self.copy_csv) shortcut = QKeySequence(Qt.CTRL + Qt.Key_C) copy.setShortcut(shortcut) export.addAction(copy) save = QAction("&Save CSV...", self.tool_window.ui_area) save.triggered.connect(self.save_csv) #this shortcut interferes with main window's save shortcut #I've tried different shortcut contexts to no avail #thanks Qt... #shortcut = QKeySequence(Qt.CTRL + Qt.Key_S) #save.setShortcut(shortcut) #save.setShortcutContext(Qt.WidgetShortcut) export.addAction(save) delimiter = export.addMenu("Delimiter") comma = QAction("comma", self.tool_window.ui_area, checkable=True) comma.setChecked(self.settings.delimiter == "comma") comma.triggered.connect(lambda *args, delim="comma": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(comma) tab = QAction("tab", self.tool_window.ui_area, checkable=True) tab.setChecked(self.settings.delimiter == "tab") tab.triggered.connect(lambda *args, delim="tab": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(tab) space = QAction("space", self.tool_window.ui_area, checkable=True) space.setChecked(self.settings.delimiter == "space") space.triggered.connect(lambda *args, delim="space": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(space) semicolon = QAction("semicolon", self.tool_window.ui_area, checkable=True) semicolon.setChecked(self.settings.delimiter == "semicolon") semicolon.triggered.connect(lambda *args, delim="semicolon": self. settings.__setattr__("delimiter", delim)) delimiter.addAction(semicolon) add_header = QAction("&Include CSV header", self.tool_window.ui_area, checkable=True) add_header.setChecked(self.settings.include_header) add_header.triggered.connect(self.header_check) export.addAction(add_header) comma.triggered.connect( lambda *args, action=tab: action.setChecked(False)) comma.triggered.connect( lambda *args, action=space: action.setChecked(False)) comma.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) tab.triggered.connect( lambda *args, action=comma: action.setChecked(False)) tab.triggered.connect( lambda *args, action=space: action.setChecked(False)) tab.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) space.triggered.connect( lambda *args, action=comma: action.setChecked(False)) space.triggered.connect( lambda *args, action=tab: action.setChecked(False)) space.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=comma: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=tab: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=space: action.setChecked(False)) menu.setNativeMenuBar(False) self._menu = menu layout.setMenuBar(menu) menu.setVisible(True) self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def clear_table(self): are_you_sure = QMessageBox.question( None, "Clear table?", "Are you sure you want to clear the data table?", ) if are_you_sure != QMessageBox.Yes: return self.table.setRowCount(0) def header_check(self, state): """user has [un]checked the 'include header' option on the menu""" if state: self.settings.include_header = True else: self.settings.include_header = False def get_csv(self): if self.settings.delimiter == "comma": delim = "," elif self.settings.delimiter == "space": delim = " " elif self.settings.delimiter == "tab": delim = "\t" elif self.settings.delimiter == "semicolon": delim = ";" if self.settings.include_header: s = delim.join(["model", "center_atom", "cone_angle"]) s += "\n" else: s = "" for i in range(0, self.table.rowCount()): s += delim.join([ item.data(Qt.DisplayRole) for item in [self.table.item(i, j) for j in range(0, 3)] ]) s += "\n" return s def copy_csv(self): app = QApplication.instance() clipboard = app.clipboard() csv = self.get_csv() clipboard.setText(csv) self.session.logger.status("copied to clipboard") def save_csv(self): """save data on current tab to CSV file""" filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)") if filename: s = self.get_csv() with open(filename, 'w') as f: f.write(s.strip()) self.session.logger.status("saved to %s" % filename) def del_cone(self): for model in self.session.models.list(type=Generic3DModel): if model.name.startswith("Cone angle"): model.delete() def set_ligand(self, *args): self.ligands = {} for atom in selected_atoms(self.session): if atom.structure not in self.ligands: self.ligands[atom.structure] = [] self.ligands[atom.structure].append(atom) self.session.logger.status("set ligand to current selection") def calc_cone(self, *args): self.settings.cone_option = self.cone_option.currentText() self.settings.radii = self.radii_option.currentText() self.settings.display_radii = self.display_radii.checkState( ) == Qt.Checked self.settings.display_cone = self.display_cone.checkState( ) == Qt.Checked if self.cone_option.currentText() == "Tolman (Unsymmetrical)": method = "tolman" else: method = self.cone_option.currentText() radii = self.radii_option.currentText() return_cones = self.display_cone.checkState() == Qt.Checked display_radii = self.display_radii.checkState() == Qt.Checked # self.table.setRowCount(0) for center_atom in selected_atoms(self.session): rescol = ResidueCollection(center_atom.structure) at_center = rescol.find_exact(AtomSpec(center_atom.atomspec))[0] if center_atom.structure in self.ligands: comp = Component( rescol.find([ AtomSpec(atom.atomspec) for atom in self.ligands[center_atom.structure] ]), to_center=rescol.find_exact(AtomSpec( center_atom.atomspec)), key_atoms=rescol.find(BondedTo(at_center)), ) else: comp = Component( rescol.find(NotAny(at_center)), to_center=rescol.find_exact(AtomSpec( center_atom.atomspec)), key_atoms=rescol.find(BondedTo(at_center)), ) cone_angle = comp.cone_angle( center=rescol.find(AtomSpec(center_atom.atomspec)), method=method, radii=radii, return_cones=return_cones, ) if return_cones: cone_angle, cones = cone_angle s = ".transparency 0.5\n" for cone in cones: apex, base, radius = cone s += ".cone %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %.3f open\n" % ( *apex, *base, radius) stream = BytesIO(bytes(s, "utf-8")) bild_obj, status = read_bild(self.session, stream, "Cone angle %s" % center_atom) self.session.models.add(bild_obj, parent=center_atom.structure) if display_radii: s = ".note radii\n" s += ".transparency 75\n" color = None for atom in comp.atoms: chix_atom = atom.chix_atom if radii.lower() == "umn": r = VDW_RADII[chix_atom.element.name] elif radii.lower() == "bondi": r = BONDI_RADII[chix_atom.element.name] if color is None or chix_atom.color != color: color = chix_atom.color rgb = [x / 255. for x in chix_atom.color] rgb.pop(-1) s += ".color %f %f %f\n" % tuple(rgb) s += ".sphere %f %f %f %f\n" % (*chix_atom.coord, r) stream = BytesIO(bytes(s, "utf-8")) bild_obj, status = read_bild(self.session, stream, "Cone angle radii") self.session.models.add(bild_obj, parent=center_atom.structure) row = self.table.rowCount() self.table.insertRow(row) name = QTableWidgetItem() name.setData(Qt.DisplayRole, center_atom.structure.name) self.table.setItem(row, 0, name) center = QTableWidgetItem() center.setData(Qt.DisplayRole, center_atom.atomspec) self.table.setItem(row, 1, center) ca = QTableWidgetItem() ca.setData(Qt.DisplayRole, "%.2f" % cone_angle) self.table.setItem(row, 2, ca) self.table.resizeColumnToContents(0) self.table.resizeColumnToContents(1) self.table.resizeColumnToContents(2)
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 InformationWindow(QDialog): imageChanged = Signal(int, str) def __init__(self, id_, items, parent=None): super().__init__(parent) itemLabel = QLabel(self.tr("Item: ")) descriptionLabel = QLabel(self.tr("Description: ")) imageFileLabel = QLabel(self.tr("Image file: ")) self.createButtons() self.itemText = QLabel() self.descriptionEditor = QTextEdit() self.imageFileEditor = QComboBox() self.imageFileEditor.setModel(items.relationModel(1)) self.imageFileEditor.setModelColumn( items.relationModel(1).fieldIndex("file")) self.mapper = QDataWidgetMapper(self) self.mapper.setModel(items) self.mapper.setSubmitPolicy(QDataWidgetMapper.ManualSubmit) self.mapper.setItemDelegate(QSqlRelationalDelegate(self.mapper)) self.mapper.addMapping(self.imageFileEditor, 1) self.mapper.addMapping(self.itemText, 2, b"text") self.mapper.addMapping(self.descriptionEditor, 3) self.mapper.setCurrentIndex(id_) self.descriptionEditor.textChanged.connect(self.enableButtons) self.imageFileEditor.currentIndexChanged.connect(self.enableButtons) formLayout = QFormLayout() formLayout.addRow(itemLabel, self.itemText) formLayout.addRow(imageFileLabel, self.imageFileEditor) formLayout.addRow(descriptionLabel, self.descriptionEditor) layout = QVBoxLayout() layout.addLayout(formLayout) layout.addWidget(self.buttonBox) self.setLayout(layout) self.itemId = id_ self.displayedImage = self.imageFileEditor.currentText() self.setWindowFlags(Qt.Window) self.enableButtons(False) self.setWindowTitle(self.itemText.text()) def id(self): return self.itemId @Slot() def revert(self): self.mapper.revert() self.enableButtons(False) @Slot() def submit(self): newImage = self.imageFileEditor.currentText() if self.displayedImage != newImage: self.displayedImage = newImage self.imageChanged.emit(self.itemId, newImage) self.mapper.submit() self.mapper.setCurrentIndex(self.itemId) self.enableButtons(False) def createButtons(self): self.closeButton = QPushButton(self.tr("&Close")) self.revertButton = QPushButton(self.tr("&Revert")) self.submitButton = QPushButton(self.tr("&Submit")) self.closeButton.setDefault(True) self.closeButton.clicked.connect(self.close) self.revertButton.clicked.connect(self.revert) self.submitButton.clicked.connect(self.submit) self.buttonBox = QDialogButtonBox(self) self.buttonBox.addButton(self.submitButton, QDialogButtonBox.AcceptRole) self.buttonBox.addButton(self.revertButton, QDialogButtonBox.ResetRole) self.buttonBox.addButton(self.closeButton, QDialogButtonBox.RejectRole) @Slot() @Slot(bool) def enableButtons(self, enable=True): self.revertButton.setEnabled(enable) self.submitButton.setEnabled(enable)
class BondEditor(ToolInstance): help = "https://github.com/QChASM/SEQCROW/wiki/Bond-Editor-Tool" SESSION_ENDURING = False SESSION_SAVE = False def __init__(self, session, name): super().__init__(session, name) self.tool_window = MainToolWindow(self) self.settings = _BondEditorSettings(session, name) self._build_ui() def _build_ui(self): layout = QGridLayout() tabs = QTabWidget() layout.addWidget(tabs) ts_bond_tab = QWidget() ts_options = QFormLayout(ts_bond_tab) self.tsbond_color = ColorButton(has_alpha_channel=False, max_size=(16, 16)) self.tsbond_color.set_color(self.settings.tsbond_color) ts_options.addRow("color:", self.tsbond_color) self.tsbond_transparency = QSpinBox() self.tsbond_transparency.setRange(1, 99) self.tsbond_transparency.setValue(self.settings.tsbond_transparency) self.tsbond_transparency.setSuffix("%") ts_options.addRow("transparency:", self.tsbond_transparency) self.tsbond_radius = QDoubleSpinBox() self.tsbond_radius.setRange(0.01, 1) self.tsbond_radius.setDecimals(3) self.tsbond_radius.setSingleStep(0.005) self.tsbond_radius.setSuffix(" \u212B") self.tsbond_radius.setValue(self.settings.tsbond_radius) ts_options.addRow("radius:", self.tsbond_radius) draw_tsbonds = QPushButton("draw TS bonds on selected atoms/bonds") draw_tsbonds.clicked.connect(self.run_tsbond) ts_options.addRow(draw_tsbonds) self.draw_tsbonds = draw_tsbonds erase_tsbonds = QPushButton("erase selected TS bonds") erase_tsbonds.clicked.connect(self.run_erase_tsbond) ts_options.addRow(erase_tsbonds) self.erase_tsbonds = erase_tsbonds bond_tab = QWidget() bond_options = QFormLayout(bond_tab) self.bond_halfbond = QCheckBox() self.bond_halfbond.setChecked(self.settings.bond_halfbond) self.bond_halfbond.setToolTip( "each half of the bond will be colored according to the atom's color" ) bond_options.addRow("half-bond:", self.bond_halfbond) self.bond_color = ColorButton(has_alpha_channel=True, max_size=(16, 16)) self.bond_color.set_color(self.settings.bond_color) self.bond_color.setEnabled( self.bond_halfbond.checkState() != Qt.Checked) self.bond_halfbond.stateChanged.connect( lambda state, widget=self.bond_color: self.bond_color.setEnabled( state != Qt.Checked)) bond_options.addRow("color:", self.bond_color) self.bond_radius = QDoubleSpinBox() self.bond_radius.setRange(0.01, 1) self.bond_radius.setDecimals(3) self.bond_radius.setSingleStep(0.005) self.bond_radius.setSuffix(" \u212B") self.bond_radius.setValue(self.settings.bond_radius) bond_options.addRow("radius:", self.bond_radius) draw_tsbonds = QPushButton("draw bond between selected atoms") draw_tsbonds.clicked.connect(self.run_bond) bond_options.addRow(draw_tsbonds) self.draw_tsbonds = draw_tsbonds erase_bonds = QPushButton("erase selected bonds") erase_bonds.clicked.connect( lambda *, ses=self.session: run(ses, "delete bonds sel")) bond_options.addRow(erase_bonds) self.erase_bonds = erase_bonds hbond_tab = QWidget() hbond_options = QFormLayout(hbond_tab) self.hbond_color = ColorButton(has_alpha_channel=True, max_size=(16, 16)) self.hbond_color.set_color(self.settings.hbond_color) hbond_options.addRow("color:", self.hbond_color) self.hbond_radius = QDoubleSpinBox() self.hbond_radius.setDecimals(3) self.hbond_radius.setSuffix(" \u212B") self.hbond_radius.setValue(self.settings.hbond_radius) hbond_options.addRow("radius:", self.hbond_radius) self.hbond_dashes = QSpinBox() self.hbond_dashes.setRange(0, 28) self.hbond_dashes.setSingleStep(2) self.hbond_radius.setSingleStep(0.005) self.hbond_dashes.setValue(self.settings.hbond_dashes) hbond_options.addRow("dashes:", self.hbond_dashes) draw_hbonds = QPushButton("draw H-bonds") draw_hbonds.clicked.connect(self.run_hbond) hbond_options.addRow(draw_hbonds) self.draw_hbonds = draw_hbonds erase_hbonds = QPushButton("erase all H-bonds") erase_hbonds.clicked.connect( lambda *, ses=self.session: run(ses, "~hbonds")) hbond_options.addRow(erase_hbonds) self.erase_hbonds = erase_hbonds tm_bond_tab = QWidget() tm_bond_options = QFormLayout(tm_bond_tab) self.tm_bond_color = ColorButton(has_alpha_channel=True, max_size=(16, 16)) self.tm_bond_color.set_color(self.settings.tm_bond_color) tm_bond_options.addRow("color:", self.tm_bond_color) self.tm_bond_radius = QDoubleSpinBox() self.tm_bond_radius.setDecimals(3) self.tm_bond_radius.setSuffix(" \u212B") self.tm_bond_radius.setValue(self.settings.tm_bond_radius) tm_bond_options.addRow("radius:", self.tm_bond_radius) self.tm_bond_dashes = QSpinBox() self.tm_bond_dashes.setRange(0, 28) self.tm_bond_dashes.setSingleStep(2) self.tm_bond_radius.setSingleStep(0.005) self.tm_bond_dashes.setValue(self.settings.tm_bond_dashes) tm_bond_options.addRow("dashes:", self.tm_bond_dashes) draw_tm_bonds = QPushButton("draw metal coordination bonds") draw_tm_bonds.clicked.connect(self.run_tm_bond) tm_bond_options.addRow(draw_tm_bonds) self.draw_tm_bonds = draw_tm_bonds erase_tm_bonds = QPushButton("erase all metal coordination bonds") erase_tm_bonds.clicked.connect(self.del_tm_bond) tm_bond_options.addRow(erase_tm_bonds) self.erase_tm_bonds = erase_tm_bonds bond_length_tab = QWidget() bond_length_layout = QFormLayout(bond_length_tab) self.bond_distance = QDoubleSpinBox() self.bond_distance.setRange(0.5, 10.0) self.bond_distance.setSingleStep(0.05) self.bond_distance.setValue(1.51) self.bond_distance.setSuffix(" \u212B") bond_length_layout.addRow("bond length:", self.bond_distance) self.move_fragment = QComboBox() self.move_fragment.addItems(["both", "smaller", "larger"]) bond_length_layout.addRow("move side:", self.move_fragment) bond_lookup = QGroupBox("bond length lookup:") bond_lookup_layout = QGridLayout(bond_lookup) bond_lookup_layout.addWidget( QLabel("elements:"), 0, 0, ) self.ele1 = ElementButton("C", single_state=True) self.ele1.clicked.connect( lambda *args, button=self.ele1: self.open_ptable(button)) bond_lookup_layout.addWidget(self.ele1, 0, 1, Qt.AlignRight | Qt.AlignTop) bond_lookup_layout.addWidget(QLabel("-"), 0, 2, Qt.AlignHCenter | Qt.AlignVCenter) self.ele2 = ElementButton("C", single_state=True) self.ele2.clicked.connect( lambda *args, button=self.ele2: self.open_ptable(button)) bond_lookup_layout.addWidget(self.ele2, 0, 3, Qt.AlignLeft | Qt.AlignTop) bond_lookup_layout.addWidget(QLabel("bond order:"), 1, 0) self.bond_order = BondOrderSpinBox() self.bond_order.setRange(1., 3.) self.bond_order.setValue(1) self.bond_order.setSingleStep(0.5) self.bond_order.setDecimals(1) self.bond_order.valueChanged.connect(self.check_bond_lengths) bond_lookup_layout.addWidget(self.bond_order, 1, 1, 1, 3) bond_lookup_layout.setColumnStretch(0, 0) bond_lookup_layout.setColumnStretch(1, 0) bond_lookup_layout.setColumnStretch(2, 0) bond_lookup_layout.setColumnStretch(3, 1) bond_length_layout.addRow(bond_lookup) self.status = QStatusBar() self.status.setSizeGripEnabled(False) bond_lookup_layout.addWidget(self.status, 2, 0, 1, 4) self.do_bond_change = QPushButton("change selected bond lengths") self.do_bond_change.clicked.connect(self.change_bond_length) bond_length_layout.addRow(self.do_bond_change) tabs.addTab(bond_tab, "covalent bonds") tabs.addTab(ts_bond_tab, "TS bonds") tabs.addTab(hbond_tab, "H-bonds") tabs.addTab(tm_bond_tab, "coordination bonds") tabs.addTab(bond_length_tab, "bond length") self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def run_tsbond(self, *args): args = ["tsbond", "sel"] color = self.tsbond_color.get_color() args.extend(["color", "rgb(%i, %i, %i)" % tuple(color[:-1])]) self.settings.tsbond_color = tuple([c / 255. for c in color]) radius = self.tsbond_radius.value() args.extend(["radius", "%.3f" % radius]) self.settings.tsbond_radius = radius transparency = self.tsbond_transparency.value() args.extend(["transparency", "%i" % transparency]) self.settings.tsbond_transparency = transparency run(self.session, " ".join(args)) def run_erase_tsbond(self, *args): run(self.session, "~tsbond sel") def run_bond(self, *args): # TODO: switch to `bond sel` in 1.2 sel = selected_atoms(self.session) halfbond = self.bond_halfbond.checkState() == Qt.Checked self.settings.bond_halfbond = halfbond if not halfbond: color = self.bond_color.get_color() color = tuple(x / 255. for x in color) self.settings.bond_color = color radius = self.bond_radius.value() self.settings.bond_radius = radius for b in selected_bonds(self.session): b.halfbond = halfbond if not halfbond: b.color = np.array([int(x * 255) for x in color]) b.radius = radius for i, a1 in enumerate(sel): for a2 in sel[:i]: if a1.structure is a2.structure and a2 not in a1.neighbors: new_bond = a1.structure.new_bond(a1, a2) new_bond.halfbond = halfbond if not halfbond: new_bond.color = np.array( [int(x * 255) for x in color]) new_bond.radius = radius def run_hbond(self, *args): args = ["hbonds", "reveal", "true"] color = self.hbond_color.get_color() args.extend(["color", "rgb(%i, %i, %i)" % tuple(color[:-1])]) self.settings.hbond_color = tuple([c / 255. for c in color]) radius = self.hbond_radius.value() args.extend(["radius", "%.3f" % radius]) self.settings.hbond_radius = radius dashes = self.hbond_dashes.value() args.extend(["dashes", "%i" % dashes]) self.settings.hbond_dashes = dashes run(self.session, " ".join(args)) def run_tm_bond(self, *args): color = self.tm_bond_color.get_color() self.settings.tm_bond_color = tuple([c / 255. for c in color]) radius = self.tm_bond_radius.value() self.settings.tm_bond_radius = radius dashes = self.tm_bond_dashes.value() self.settings.tm_bond_dashes = dashes models = self.session.models.list(type=AtomicStructure) for model in models: rescol = ResidueCollection(model, bonds_matter=False) try: tm_list = rescol.find([ AnyTransitionMetal(), "Na", "K", "Rb", "Cs", "Fr", "Mg", "Ca", "Sr", "Ba", "Ra" ]) for tm in tm_list: for atom in rescol.atoms: if atom is tm: continue if atom.is_connected(tm): pbg = model.pseudobond_group( model.PBG_METAL_COORDINATION, create_type="normal") pbg.new_pseudobond(tm.chix_atom, atom.chix_atom) pbg.dashes = dashes pbg.color = color pbg.radius = radius except LookupError: pass def del_tm_bond(self, *args): models = self.session.models.list(type=AtomicStructure) for model in models: pbg = model.pseudobond_group(model.PBG_METAL_COORDINATION, create_type=None) if pbg is not None: pbg.delete() def open_ptable(self, button): self.tool_window.create_child_window("select element", window_class=PTable2, button=button, callback=self.check_bond_lengths) def check_bond_lengths(self, *args): ele1 = self.ele1.text() ele2 = self.ele2.text() key = ORDER_BOND_ORDER.key(ele1, ele2) order = "%.1f" % self.bond_order.value() if key in ORDER_BOND_ORDER.bonds and order in ORDER_BOND_ORDER.bonds[ key]: self.bond_distance.setValue(ORDER_BOND_ORDER.bonds[key][order]) self.status.showMessage("") else: self.status.showMessage("no bond data for %s-%s %sx bonds" % (ele1, ele2, order)) def change_bond_length(self, *args): dist = self.bond_distance.value() atom_pairs = [] sel = selected_atoms(self.session) if len(sel) == 2 and sel[0].structure is sel[1].structure: atom_pairs.append(sel) for bond in selected_bonds(self.session): if not all(atom in sel for atom in bond.atoms): atom_pairs.append(bond.atoms) for bond in selected_pseudobonds(self.session): if not all(atom in sel for atom in bond.atoms): atom_pairs.append(bond.atoms) for pair in atom_pairs: atom1, atom2 = pair frag1 = get_fragment(atom1, stop=atom2, max_len=atom1.structure.num_atoms) frag2 = get_fragment(atom2, stop=atom1, max_len=atom1.structure.num_atoms) v = atom2.coord - atom1.coord cur_dist = np.linalg.norm(v) change = dist - cur_dist if self.move_fragment.currentText() == "both": change = 0.5 * change frag1.coords -= change * v / cur_dist frag2.coords += change * v / cur_dist elif self.move_fragment.currentText() == "smaller": if len(frag1) < len(frag2) or (len(frag1) == len(frag2) and sum(frag1.elements.masses) < sum(frag2.elements.masses)): frag1.coords -= change * v / cur_dist else: frag2.coords += change * v / cur_dist elif self.move_fragment.currentText() == "larger": if len(frag1) > len(frag2) or (len(frag1) == len(frag2) and sum(frag1.elements.masses) > sum(frag2.elements.masses)): frag1.coords -= change * v / cur_dist else: frag2.coords += change * v / cur_dist
class LigandSterimol(ToolInstance): help = "https://github.com/QChASM/SEQCROW/wiki/Ligand-Sterimol-Tool" SESSION_ENDURING = False SESSION_SAVE = False def __init__(self, session, name): super().__init__(session, name) from chimerax.ui import MainToolWindow self.tool_window = MainToolWindow(self) self.settings = _SterimolSettings(self.session, name) self._build_ui() def _build_ui(self): layout = QFormLayout() self.radii_option = QComboBox() self.radii_option.addItems(["Bondi", "UMN"]) ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly) self.radii_option.setCurrentIndex(ndx) layout.addRow("radii:", self.radii_option) self.L_option = QComboBox() self.L_option.addItems([ "to centroid of coordinating atoms", "bisect angle between coordinating atoms" ]) ndx = self.L_option.findText(self.settings.L_option, Qt.MatchExactly) self.L_option.setCurrentIndex(ndx) layout.addRow("L axis:", self.L_option) self.sterimol2vec = QGroupBox("Sterimol2Vec") sterimol2vec_layout = QFormLayout(self.sterimol2vec) self.at_L = QDoubleSpinBox() self.at_L.setRange(-10, 30) self.at_L.setDecimals(2) self.at_L.setSingleStep(0.25) self.at_L.setValue(self.settings.at_L) sterimol2vec_layout.addRow("L value:", self.at_L) layout.addRow(self.sterimol2vec) self.sterimol2vec.setCheckable(True) self.sterimol2vec.toggled.connect(lambda x: self.at_L.setEnabled(x)) self.sterimol2vec.setChecked(self.settings.sterimol2vec) self.display_vectors = QCheckBox() self.display_vectors.setChecked(self.settings.display_vectors) layout.addRow("show vectors:", self.display_vectors) self.display_radii = QCheckBox() self.display_radii.setChecked(self.settings.display_radii) layout.addRow("show radii:", self.display_radii) calc_sterimol_button = QPushButton( "calculate parameters for selected ligands") calc_sterimol_button.clicked.connect(self.calc_sterimol) layout.addRow(calc_sterimol_button) self.calc_sterimol_button = calc_sterimol_button remove_sterimol_button = QPushButton("remove Sterimol visualizations") remove_sterimol_button.clicked.connect(self.del_sterimol) layout.addRow(remove_sterimol_button) self.remove_sterimol_button = remove_sterimol_button self.table = QTableWidget() self.table.setColumnCount(8) self.table.setHorizontalHeaderLabels([ 'model', 'coord. atoms', 'B\u2081', 'B\u2082', 'B\u2083', 'B\u2084', 'B\u2085', 'L', ]) self.table.setSelectionBehavior(QTableWidget.SelectRows) self.table.setEditTriggers(QTableWidget.NoEditTriggers) self.table.resizeColumnToContents(0) self.table.resizeColumnToContents(1) self.table.resizeColumnToContents(2) self.table.resizeColumnToContents(3) self.table.resizeColumnToContents(4) self.table.resizeColumnToContents(5) self.table.resizeColumnToContents(6) self.table.resizeColumnToContents(7) self.table.horizontalHeader().setSectionResizeMode( 2, QHeaderView.Stretch) self.table.horizontalHeader().setSectionResizeMode( 3, QHeaderView.Stretch) self.table.horizontalHeader().setSectionResizeMode( 4, QHeaderView.Stretch) self.table.horizontalHeader().setSectionResizeMode( 5, QHeaderView.Stretch) self.table.horizontalHeader().setSectionResizeMode( 6, QHeaderView.Stretch) self.table.horizontalHeader().setSectionResizeMode( 7, QHeaderView.Stretch) layout.addRow(self.table) menu = QMenuBar() export = menu.addMenu("&Export") clear = QAction("Clear data table", self.tool_window.ui_area) clear.triggered.connect(self.clear_table) export.addAction(clear) copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area) copy.triggered.connect(self.copy_csv) shortcut = QKeySequence(Qt.CTRL + Qt.Key_C) copy.setShortcut(shortcut) export.addAction(copy) save = QAction("&Save CSV...", self.tool_window.ui_area) save.triggered.connect(self.save_csv) #this shortcut interferes with main window's save shortcut #I've tried different shortcut contexts to no avail #thanks Qt... #shortcut = QKeySequence(Qt.CTRL + Qt.Key_S) #save.setShortcut(shortcut) #save.setShortcutContext(Qt.WidgetShortcut) export.addAction(save) delimiter = export.addMenu("Delimiter") comma = QAction("comma", self.tool_window.ui_area, checkable=True) comma.setChecked(self.settings.delimiter == "comma") comma.triggered.connect(lambda *args, delim="comma": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(comma) tab = QAction("tab", self.tool_window.ui_area, checkable=True) tab.setChecked(self.settings.delimiter == "tab") tab.triggered.connect(lambda *args, delim="tab": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(tab) space = QAction("space", self.tool_window.ui_area, checkable=True) space.setChecked(self.settings.delimiter == "space") space.triggered.connect(lambda *args, delim="space": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(space) semicolon = QAction("semicolon", self.tool_window.ui_area, checkable=True) semicolon.setChecked(self.settings.delimiter == "semicolon") semicolon.triggered.connect(lambda *args, delim="semicolon": self. settings.__setattr__("delimiter", delim)) delimiter.addAction(semicolon) add_header = QAction("&Include CSV header", self.tool_window.ui_area, checkable=True) add_header.setChecked(self.settings.include_header) add_header.triggered.connect(self.header_check) export.addAction(add_header) comma.triggered.connect( lambda *args, action=tab: action.setChecked(False)) comma.triggered.connect( lambda *args, action=space: action.setChecked(False)) comma.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) tab.triggered.connect( lambda *args, action=comma: action.setChecked(False)) tab.triggered.connect( lambda *args, action=space: action.setChecked(False)) tab.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) space.triggered.connect( lambda *args, action=comma: action.setChecked(False)) space.triggered.connect( lambda *args, action=tab: action.setChecked(False)) space.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=comma: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=tab: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=space: action.setChecked(False)) menu.setNativeMenuBar(False) self._menu = menu layout.setMenuBar(menu) menu.setVisible(True) self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def clear_table(self): are_you_sure = QMessageBox.question( None, "Clear table?", "Are you sure you want to clear the data table?", ) if are_you_sure != QMessageBox.Yes: return self.table.setRowCount(0) def calc_sterimol(self, *args): self.settings.radii = self.radii_option.currentText() self.settings.display_radii = self.display_radii.checkState( ) == Qt.Checked self.settings.display_vectors = self.display_vectors.checkState( ) == Qt.Checked self.settings.at_L = self.at_L.value() self.settings.sterimol2vec = self.sterimol2vec.isChecked() self.settings.L_option = self.L_option.currentText() targets, neighbors, datas = sterimol_cmd( self.session, selected_atoms(self.session), radii=self.radii_option.currentText(), showVectors=self.display_vectors.checkState() == Qt.Checked, showRadii=self.display_radii.checkState() == Qt.Checked, return_values=True, at_L=self.at_L.value() if self.sterimol2vec.isChecked() else None, bisect_L=self.L_option.currentText() == "bisect angle between coordinating atoms", ) if len(targets) == 0: return if self.settings.delimiter == "comma": delim = "," elif self.settings.delimiter == "space": delim = " " elif self.settings.delimiter == "tab": delim = "\t" elif self.settings.delimiter == "semicolon": delim = ";" # self.table.setRowCount(0) for t, b, data in zip(targets, neighbors, datas): row = self.table.rowCount() self.table.insertRow(row) targ = QTableWidgetItem() targ.setData(Qt.DisplayRole, t) self.table.setItem(row, 0, targ) neigh = QTableWidgetItem() neigh.setData(Qt.DisplayRole, delim.join(b)) self.table.setItem(row, 1, neigh) l = np.linalg.norm(data["L"][1] - data["L"][0]) b1 = np.linalg.norm(data["B1"][1] - data["B1"][0]) b2 = np.linalg.norm(data["B2"][1] - data["B2"][0]) b3 = np.linalg.norm(data["B3"][1] - data["B3"][0]) b4 = np.linalg.norm(data["B4"][1] - data["B4"][0]) b5 = np.linalg.norm(data["B5"][1] - data["B5"][0]) li = QTableWidgetItem() li.setData(Qt.DisplayRole, "%.2f" % l) self.table.setItem(row, 7, li) b1i = QTableWidgetItem() b1i.setData(Qt.DisplayRole, "%.2f" % b1) self.table.setItem(row, 2, b1i) b2i = QTableWidgetItem() b2i.setData(Qt.DisplayRole, "%.2f" % b2) self.table.setItem(row, 3, b2i) b3i = QTableWidgetItem() b3i.setData(Qt.DisplayRole, "%.2f" % b3) self.table.setItem(row, 4, b3i) b4i = QTableWidgetItem() b4i.setData(Qt.DisplayRole, "%.2f" % b4) self.table.setItem(row, 5, b4i) b5i = QTableWidgetItem() b5i.setData(Qt.DisplayRole, "%.2f" % b5) self.table.setItem(row, 6, b5i) for i in range(0, 7): if i == 1: continue self.table.resizeColumnToContents(i) def header_check(self, state): """user has [un]checked the 'include header' option on the menu""" if state: self.settings.include_header = True else: self.settings.include_header = False def get_csv(self): if self.settings.delimiter == "comma": delim = "," elif self.settings.delimiter == "space": delim = " " elif self.settings.delimiter == "tab": delim = "\t" elif self.settings.delimiter == "semicolon": delim = ";" if self.settings.include_header: s = delim.join([ "substituent_atom", "bonded_atom", "B1", "B2", "B3", "B4", "B5", "L" ]) s += "\n" else: s = "" for i in range(0, self.table.rowCount()): s += delim.join([ item.data(Qt.DisplayRole) for item in [self.table.item(i, j) for j in range(0, 8)] ]) s += "\n" return s def copy_csv(self): app = QApplication.instance() clipboard = app.clipboard() csv = self.get_csv() clipboard.setText(csv) self.session.logger.status("copied to clipboard") def save_csv(self): """save data on current tab to CSV file""" filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)") if filename: s = self.get_csv() with open(filename, 'w') as f: f.write(s.strip()) self.session.logger.status("saved to %s" % filename) def del_sterimol(self): for model in self.session.models.list(type=Generic3DModel): if model.name.startswith("Sterimol"): model.delete() def display_help(self): """Show the help for this tool in the help viewer.""" from chimerax.core.commands import run run(self.session, 'open %s' % self.help if self.help is not None else "")
class _ElementPicker(ToolInstance): def __init__(self, *args): super().__init__(*args) self.tool_window = MainToolWindow(self) self._build_ui() def _build_ui(self): layout = QFormLayout() initial_elements = [] if ChangeElementMouseMode.element: initial_elements = [ChangeElementMouseMode.element] else: initial_elements = ["C"] self.periodic_table = PeriodicTable(select_multiple=False, initial_elements=initial_elements) self.periodic_table.elementSelectionChanged.connect( self.element_changed) layout.addRow(self.periodic_table) 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) self.vsepr.currentTextChanged.connect(self.element_changed) layout.addRow("shape:", self.vsepr) self.keep_open = QCheckBox() layout.addRow("keep table open:", self.keep_open) if ChangeElementMouseMode.vsepr: ndx = self.vsepr.findText(ChangeElementMouseMode.vsepr, Qt.MatchExactly) if ndx != -1: self.vsepr.setCurrentIndex(ndx) do_it = QPushButton("set element and shape") do_it.clicked.connect(self.set_selected) layout.addRow(do_it) self.keep_open.stateChanged.connect( lambda state: do_it.setVisible(state != Qt.Checked)) self.keep_open.stateChanged.connect(self.element_changed) self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def element_changed(self): if self.keep_open.checkState() != Qt.Checked: return element = self.periodic_table.selectedElements() if element: ChangeElementMouseMode.element = element[0] ChangeElementMouseMode.vsepr = self.vsepr.currentText() self.session.logger.status( "change element mouse mode set to use %s %s" % (ChangeElementMouseMode.vsepr, ChangeElementMouseMode.element)) def set_selected(self, *args): element = self.periodic_table.selectedElements() if element: ChangeElementMouseMode.element = element[0] ChangeElementMouseMode.vsepr = self.vsepr.currentText() self.session.logger.status( "change element mouse mode set to use %s %s" % (ChangeElementMouseMode.vsepr, ChangeElementMouseMode.element)) if self.keep_open.checkState() != Qt.Checked: self.delete()
class AARONInputBuilder(ToolInstance): SESSION_ENDURING = False SESSION_SAVE = False def __init__(self, session, name): super().__init__(session, name) self.theory_settings = _InputGeneratorSettings(session, "Build QM Input", version="3") self.tool_window = MainToolWindow(self) self._build_ui() def _build_ui(self): layout = QGridLayout() tab_widget = QTabWidget() layout.addWidget(tab_widget) structure_widget = QWidget() structure_layout = QGridLayout(structure_widget) tab_widget.addTab(structure_widget, "structure") self.structure_source = QComboBox() self.structure_source.addItems( ["AARON template", "file", "coordination complexes", "SMILES"]) structure_layout.addWidget(QLabel("structure source:"), 0, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) structure_layout.addWidget( self.structure_source, 0, 1, 1, 1, ) open_button = QPushButton("open") open_button.clicked.connect(self.open_template) structure_layout.addWidget( open_button, 0, 2, 1, 1, ) # SMILES options self.smiles_options = QGroupBox("SMILES options") smiles_layout = QFormLayout(self.smiles_options) structure_layout.addWidget(self.smiles_options, 1, 0, 1, 3, Qt.AlignTop | Qt.AlignHCenter) self.smiles_line = QLineEdit() smiles_layout.addRow("SMILES string:", self.smiles_line) self.smiles_options.setVisible( self.structure_source.currentText() == "SMILES") self.structure_source.currentTextChanged.connect( lambda text: self.smiles_options.setVisible(text == "SMILES")) # coordination complexes options self.coord_comp_options = QGroupBox("Coordination Complex Options") coord_layout = QFormLayout(self.coord_comp_options) structure_layout.addWidget(self.coord_comp_options, 1, 0, 1, 3, Qt.AlignTop | Qt.AlignHCenter) create_coord_items(self, coord_layout, allow_minimization=False, default_ele="Pd") self.coord_comp_options.setVisible( self.structure_source.currentText() == "coordination complexes") self.structure_source.currentTextChanged.connect( lambda text: self.coord_comp_options.setVisible( text == "coordination complexes")) # aaron template options self.aaron_options = QGroupBox("AARON template structures") aaron_layout = QFormLayout(self.aaron_options) structure_layout.addWidget(self.aaron_options, 1, 0, 1, 3, Qt.AlignTop | Qt.AlignHCenter) self.aaron_options.setVisible( self.structure_source.currentText() == "AARON template") self.structure_source.currentTextChanged.connect( lambda text: self.aaron_options.setVisible(text == "AARON template" )) # file options self.file_options = QGroupBox("single file options") file_layout = QFormLayout(self.file_options) structure_layout.addWidget(self.file_options, 1, 0, 1, 3, Qt.AlignTop | Qt.AlignHCenter) file_widget = QWidget() file_browse_layout = QGridLayout(file_widget) self.template_file = QLineEdit() file_browse_layout.addWidget(self.template_file, 0, 0, 1, 1, Qt.AlignCenter) browse_button = QPushButton("browse...") # browse_button.clicked.connect(self.browse_file_template) file_browse_layout.addWidget(browse_button, 0, 1, 1, 1, Qt.AlignCenter) file_browse_layout.setColumnStretch(0, 1) file_browse_layout.setColumnStretch(1, 0) margins = file_browse_layout.contentsMargins() file_browse_layout.setContentsMargins(margins.left(), 0, margins.right(), 0) file_layout.addRow("file:", file_widget) self.file_options.setVisible( self.structure_source.currentText() == "file") self.structure_source.currentTextChanged.connect( lambda text: self.file_options.setVisible(text == "file")) self.optimize_template = QCheckBox() self.optimize_template.setCheckState(Qt.Checked) structure_layout.addWidget( QLabel("optimize template:"), 2, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter, ) structure_layout.addWidget( self.optimize_template, 2, 1, 1, 2, Qt.AlignLeft | Qt.AlignVCenter, ) structure_layout.setColumnStretch(0, 0) structure_layout.setColumnStretch(1, 1) structure_layout.setColumnStretch(2, 0) # structure changes changes_widget = QWidget() changes_layout = QGridLayout(changes_widget) tab_widget.addTab(changes_widget, "changes") # HPC settings hpc_widget = QWidget() hpc_layout = QGridLayout(hpc_widget) tab_widget.addTab(hpc_widget, "HPC") # theory settings theory_widget = QWidget() theory_layout = QGridLayout(theory_widget) tab_widget.addTab(theory_widget, "theory") # results results_widget = QWidget() results_layout = QGridLayout(results_widget) tab_widget.addTab(results_widget, "results") self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def open_template(self): pass
class PrecisionRotate(ToolInstance): help = "https://github.com/QChASM/SEQCROW/wiki/Rotate-Tool" SESSION_ENDURING = False SESSION_SAVE = False def __init__(self, session, name): super().__init__(session, name) self.tool_window = MainToolWindow(self) self.settings = _PrecisionRotateSettings(session, name) self.bonds = {} self.bond_centers = {} self.groups = {} self.perpendiculars = {} self.perp_centers = {} self.manual_center = {} self._build_ui() self._show_rot_vec = self.session.triggers.add_handler( SELECTION_CHANGED, self.show_rot_vec) global_triggers = get_triggers() self._changes = global_triggers.add_handler("changes done", self.show_rot_vec) self.show_rot_vec() def _build_ui(self): layout = QGridLayout() layout.addWidget(QLabel("center of rotation:"), 0, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) self.cor_button = QComboBox() self.cor_button.addItems( ["automatic", "select atoms", "view's center of rotation"]) layout.addWidget(self.cor_button, 0, 1, 1, 1, Qt.AlignTop) self.set_cor_selection = QPushButton("set selection") self.cor_button.currentTextChanged.connect( lambda t, widget=self.set_cor_selection: widget.setEnabled( t == "select atoms")) self.set_cor_selection.clicked.connect(self.manual_cor) layout.addWidget(self.set_cor_selection, 0, 2, 1, 1, Qt.AlignTop) self.set_cor_selection.setEnabled(False) layout.addWidget(QLabel("rotation vector:"), 1, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) self.vector_option = QComboBox() self.vector_option.addItems([ "axis", "view axis", "bond", "perpendicular to plane", "centroid of atoms", "custom" ]) layout.addWidget(self.vector_option, 1, 1, 1, 1, Qt.AlignVCenter) vector = QWidget() vector.setToolTip("vector will be normalized before rotating") vector_layout = QHBoxLayout(vector) vector_layout.setContentsMargins(0, 0, 0, 0) self.vector_x = QDoubleSpinBox() self.vector_y = QDoubleSpinBox() self.vector_z = QDoubleSpinBox() self.vector_z.setValue(1.0) for c, t in zip([self.vector_x, self.vector_y, self.vector_z], [" x", " y", " z"]): c.setSingleStep(0.01) c.setRange(-100, 100) # c.setSuffix(t) c.valueChanged.connect(self.show_rot_vec) vector_layout.addWidget(c) layout.addWidget(vector, 1, 2, 1, 1, Qt.AlignTop) vector.setVisible(self.vector_option.currentText() == "custom") self.vector_option.currentTextChanged.connect( lambda text, widget=vector: widget.setVisible(text == "custom")) self.view_axis = QComboBox() self.view_axis.addItems(["z", "y", "x"]) layout.addWidget(self.view_axis, 1, 2, 1, 1, Qt.AlignTop) self.view_axis.setVisible( self.vector_option.currentText() == "view axis") self.vector_option.currentTextChanged.connect( lambda text, widget=self.view_axis: widget.setVisible(text == "view axis")) self.axis = QComboBox() self.axis.addItems(["z", "y", "x"]) layout.addWidget(self.axis, 1, 2, 1, 1, Qt.AlignTop) self.axis.setVisible(self.vector_option.currentText() == "axis") self.vector_option.currentTextChanged.connect( lambda text, widget=self.axis: widget.setVisible(text == "axis")) self.bond_button = QPushButton("set selected bond") self.bond_button.clicked.connect(self.set_bonds) layout.addWidget(self.bond_button, 1, 2, 1, 1, Qt.AlignTop) self.bond_button.setVisible(self.vector_option.currentText() == "bond") self.vector_option.currentTextChanged.connect( lambda text, widget=self.bond_button: widget.setVisible(text == "bond")) self.perp_button = QPushButton("set selected atoms") self.perp_button.clicked.connect(self.set_perpendicular) layout.addWidget(self.perp_button, 1, 2, 1, 1, Qt.AlignTop) self.perp_button.setVisible( self.vector_option.currentText() == "perpendicular to plane") self.vector_option.currentTextChanged.connect( lambda text, widget=self.perp_button: widget.setVisible( text == "perpendicular to plane")) self.group_button = QPushButton("set selected atoms") self.group_button.clicked.connect(self.set_group) layout.addWidget(self.group_button, 1, 2, 1, 1, Qt.AlignTop) self.group_button.setVisible( self.vector_option.currentText() == "centroid of atoms") self.vector_option.currentTextChanged.connect( lambda text, widget=self.group_button: widget.setVisible( text == "centroid of atoms")) layout.addWidget(QLabel("angle:"), 2, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) self.angle = QDoubleSpinBox() self.angle.setRange(-360, 360) self.angle.setSingleStep(5) self.angle.setSuffix("°") layout.addWidget(self.angle, 2, 1, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) layout.addWidget(QLabel("preview rotation axis:"), 3, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) self.display_rot_vec = QCheckBox() self.display_rot_vec.setCheckState(Qt.Checked) self.display_rot_vec.stateChanged.connect(self.show_rot_vec) layout.addWidget(self.display_rot_vec, 3, 1, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) rotate_button = QPushButton("rotate selected atoms") rotate_button.clicked.connect(self.do_rotate) layout.addWidget(rotate_button, 4, 0, 1, 3, Qt.AlignTop) self.rotate_button = rotate_button self.status_bar = QStatusBar() self.status_bar.setSizeGripEnabled(False) layout.addWidget(self.status_bar, 5, 0, 1, 3, Qt.AlignTop) self.vector_option.currentTextChanged.connect(self.show_auto_status) self.cor_button.currentIndexChanged.connect( lambda *args: self.show_auto_status("select atoms")) self.cor_button.currentIndexChanged.connect(self.show_rot_vec) self.set_cor_selection.clicked.connect(self.show_rot_vec) self.vector_option.currentIndexChanged.connect(self.show_rot_vec) self.axis.currentIndexChanged.connect(self.show_rot_vec) self.view_axis.currentIndexChanged.connect(self.show_rot_vec) self.bond_button.clicked.connect(self.show_rot_vec) self.perp_button.clicked.connect(self.show_rot_vec) self.group_button.clicked.connect(self.show_rot_vec) layout.setRowStretch(0, 0) layout.setRowStretch(1, 0) layout.setRowStretch(2, 0) layout.setRowStretch(3, 0) layout.setRowStretch(4, 0) layout.setRowStretch(5, 1) layout.setColumnStretch(0, 0) layout.setColumnStretch(1, 1) layout.setColumnStretch(2, 1) self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def manual_cor(self, *args): selection = selected_atoms(self.session) models = {} for atom in selection: if atom.structure not in models: models[atom.structure] = [atom] else: models[atom.structure].append(atom) self.manual_center = {} for model in models: atoms = models[model] coords = np.array([atom.coord for atom in atoms]) self.manual_center[model] = np.mean(coords, axis=0) def show_auto_status(self, text): if self.cor_button.currentText() == "automatic": if text == "bond": self.status_bar.showMessage( "center set to one of the bonded atoms") elif text == "perpendicular to plane": self.status_bar.showMessage("center set to centroid of atoms") else: self.status_bar.showMessage( "center set to centroid of rotating atoms") elif self.cor_button.currentText() == "select atoms": self.status_bar.showMessage( "center set to centroid of specified atoms") else: self.status_bar.showMessage( "center set to view's center of rotation") def set_bonds(self, *args): bonds = selected_bonds(self.session) if len(bonds) == 0: self.session.logger.error("no bonds selected") return models = [bond.structure for bond in bonds] if any(models.count(m) > 1 for m in models): self.session.logger.error( "multiple bonds selected on the same structure") return self.bonds = { model: (bond.atoms[0].coord - bond.atoms[1].coord) for model, bond in zip(models, bonds) } self.bond_centers = { model: bond.atoms[1].coord for model, bond in zip(models, bonds) } def set_perpendicular(self, *args): atoms = selected_atoms(self.session) if len(atoms) == 0: self.session.logger.error("no atoms selected") return self.perpendiculars = {} self.perp_centers = {} models = set(atom.structure for atom in atoms) for model in models: atom_coords = [] for atom in atoms: if atom.structure is model: atom_coords.append(atom.coord) if len(atom_coords) < 3: self.session.logger.error("fewer than 3 atoms selected on %s" % model.atomspec) continue xyz = np.array(atom_coords) xyz -= np.mean(atom_coords, axis=0) R = np.dot(xyz.T, xyz) u, s, vh = np.linalg.svd(R, compute_uv=True) vector = u[:, -1] self.perpendiculars[model] = vector self.perp_centers[model] = np.mean(atom_coords, axis=0) def set_group(self, *args): atoms = selected_atoms(self.session) if len(atoms) == 0: self.session.logger.error("no atoms selected") return self.groups = {} models = set(atom.structure for atom in atoms) for model in models: atom_coords = [] for atom in atoms: if atom.structure is model: atom_coords.append(atom.coord) self.groups[model] = np.mean(atom_coords, axis=0) def do_rotate(self, *args): selection = selected_atoms(self.session) models = {} for atom in selection: if atom.structure not in models: models[atom.structure] = [atom] else: models[atom.structure].append(atom) if len(models.keys()) == 0: return if self.vector_option.currentText() == "axis": if self.axis.currentText() == "z": vector = np.array([0., 0., 1.]) elif self.axis.currentText() == "y": vector = np.array([0., 1., 0.]) elif self.axis.currentText() == "x": vector = np.array([1., 0., 0.]) elif self.vector_option.currentText() == "view axis": if self.view_axis.currentText() == "z": vector = self.session.view.camera.get_position().axes()[2] elif self.view_axis.currentText() == "y": vector = self.session.view.camera.get_position().axes()[1] elif self.view_axis.currentText() == "x": vector = self.session.view.camera.get_position().axes()[0] elif self.vector_option.currentText() == "bond": vector = self.bonds elif self.vector_option.currentText() == "perpendicular to plane": vector = self.perpendiculars elif self.vector_option.currentText() == "centroid of atoms": vector = self.groups elif self.vector_option.currentText() == "custom": x = self.vector_x.value() y = self.vector_y.value() z = self.vector_z.value() vector = np.array([x, y, z]) angle = np.deg2rad(self.angle.value()) center = {} for model in models: atoms = models[model] coords = np.array([atom.coord for atom in atoms]) center[model] = np.mean(coords, axis=0) if self.cor_button.currentText() == "automatic": if self.vector_option.currentText() == "perpendicular to plane": center = self.perp_centers elif self.vector_option.currentText() == "bond": center = self.bond_centers elif self.cor_button.currentText() == "select atoms": center = self.manual_center else: center = self.session.main_view.center_of_rotation for model in models: if isinstance(vector, dict): if model not in vector.keys(): continue else: v = vector[model] else: v = vector if isinstance(center, dict): if model not in center.keys(): continue else: c = center[model] else: c = center if self.vector_option.currentText( ) == "centroid of atoms" and self.cor_button.currentText( ) != "automatic": v = v - c v = v / np.linalg.norm(v) q = np.hstack(([np.cos(angle / 2)], v * np.sin(angle / 2))) q /= np.linalg.norm(q) qs = q[0] qv = q[1:] xyz = np.array([a.coord for a in models[model]]) xyz -= c xprod = np.cross(qv, xyz) qs_xprod = 2 * qs * xprod qv_xprod = 2 * np.cross(qv, xprod) xyz += qs_xprod + qv_xprod + c for t, coord in zip(models[model], xyz): t.coord = coord def show_rot_vec(self, *args): for model in self.session.models.list(type=Generic3DModel): if model.name == "rotation vector": model.delete() if self.display_rot_vec.checkState() == Qt.Unchecked: return selection = selected_atoms(self.session) if len(selection) == 0: return models = {} for atom in selection: if atom.structure not in models: models[atom.structure] = [atom] else: models[atom.structure].append(atom) if len(models.keys()) == 0: return if self.vector_option.currentText() == "axis": if self.axis.currentText() == "z": vector = np.array([0., 0., 1.]) elif self.axis.currentText() == "y": vector = np.array([0., 1., 0.]) elif self.axis.currentText() == "x": vector = np.array([1., 0., 0.]) elif self.vector_option.currentText() == "view axis": if self.view_axis.currentText() == "z": vector = self.session.view.camera.get_position().axes()[2] elif self.view_axis.currentText() == "y": vector = self.session.view.camera.get_position().axes()[1] elif self.view_axis.currentText() == "x": vector = self.session.view.camera.get_position().axes()[0] elif self.vector_option.currentText() == "bond": vector = self.bonds elif self.vector_option.currentText() == "perpendicular to plane": vector = self.perpendiculars elif self.vector_option.currentText() == "centroid of atoms": vector = self.groups elif self.vector_option.currentText() == "custom": x = self.vector_x.value() y = self.vector_y.value() z = self.vector_z.value() vector = np.array([x, y, z]) center = {} for model in models: atoms = models[model] coords = np.array([atom.coord for atom in atoms]) center[model] = np.mean(coords, axis=0) if self.cor_button.currentText() == "automatic": if self.vector_option.currentText() == "perpendicular to plane": center = self.perp_centers elif self.vector_option.currentText() == "bond": center = self.bond_centers elif self.cor_button.currentText() == "select atoms": center = self.manual_center else: center = self.session.main_view.center_of_rotation for model in models: if isinstance(vector, dict): if model not in vector.keys(): continue else: v = vector[model] else: v = vector if isinstance(center, dict): if model not in center.keys(): continue else: c = center[model] else: c = center if self.vector_option.currentText( ) == "centroid of atoms" and self.cor_button.currentText( ) != "automatic": v = v - c if np.linalg.norm(v) == 0: continue residues = [] for atom in models[model]: if atom.residue not in residues: residues.append(atom.residue) v_c = c + v s = ".color red\n" s += ".arrow %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f 0.2 0.4 0.7\n" % ( *c, *v_c) stream = BytesIO(bytes(s, 'utf-8')) bild_obj, status = read_bild(self.session, stream, "rotation vector") self.session.models.add(bild_obj, parent=model) def delete(self): self.session.triggers.remove_handler(self._show_rot_vec) global_triggers = get_triggers() global_triggers.remove_handler(self._changes) for model in self.session.models.list(type=Generic3DModel): if model.name == "rotation vector": model.delete() return super().delete() def close(self): self.session.triggers.remove_handler(self._show_rot_vec) global_triggers = get_triggers() global_triggers.remove_handler(self._changes) for model in self.session.models.list(type=Generic3DModel): if model.name == "rotation vector": model.delete() return super().close()
class PercentVolumeBuried(ToolInstance): help = "https://github.com/QChASM/SEQCROW/wiki/Buried-Volume-Tool" SESSION_ENDURING = False SESSION_SAVE = False def __init__(self, session, name): super().__init__(session, name) self.tool_window = MainToolWindow(self) self.settings = _VburSettings(self.session, name) self.ligand_atoms = [] self._build_ui() def _build_ui(self): layout = QGridLayout() tabs = QTabWidget() calc_widget = QWidget() calc_layout = QFormLayout(calc_widget) settings_widget = QWidget() settings_layout = QFormLayout(settings_widget) steric_map_widget = QWidget() steric_layout = QFormLayout(steric_map_widget) cutout_widget = QWidget() vol_cutout_layout = QFormLayout(cutout_widget) layout.addWidget(tabs) tabs.addTab(calc_widget, "calculation") tabs.addTab(settings_widget, "settings") tabs.addTab(steric_map_widget, "steric map") tabs.addTab(cutout_widget, "volume cutout") self.radii_option = QComboBox() self.radii_option.addItems(["Bondi", "UMN"]) ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly) self.radii_option.setCurrentIndex(ndx) settings_layout.addRow("radii:", self.radii_option) self.scale = QDoubleSpinBox() self.scale.setValue(self.settings.vdw_scale) self.scale.setSingleStep(0.01) self.scale.setRange(1., 1.5) settings_layout.addRow("VDW scale:", self.scale) set_ligand_atoms = QPushButton("set ligands to current selection") set_ligand_atoms.clicked.connect(self.set_ligand_atoms) set_ligand_atoms.setToolTip( "specify atoms to use in calculation\n" + "by default, all atoms will be used unless a single center is specified\n" + "in the case of a single center, all atoms except the center is used" ) calc_layout.addRow(set_ligand_atoms) self.set_ligand_atoms = set_ligand_atoms self.radius = QDoubleSpinBox() self.radius.setValue(self.settings.center_radius) self.radius.setSuffix(" \u212B") self.radius.setDecimals(1) self.radius.setSingleStep(0.1) self.radius.setRange(1., 15.) settings_layout.addRow("radius around center:", self.radius) self.method = QComboBox() self.method.addItems(["Lebedev", "Monte-Carlo"]) self.method.setToolTip("Lebedev: deterministic method\n" + "Monte-Carlo: non-deterministic method") ndx = self.method.findText(self.settings.method, Qt.MatchExactly) self.method.setCurrentIndex(ndx) settings_layout.addRow("integration method:", self.method) leb_widget = QWidget() leb_layout = QFormLayout(leb_widget) leb_layout.setContentsMargins(0, 0, 0, 0) self.radial_points = QComboBox() self.radial_points.addItems(["20", "32", "64", "75", "99", "127"]) self.radial_points.setToolTip( "more radial points will give more accurate results, but integration will take longer" ) ndx = self.radial_points.findText(self.settings.radial_points, Qt.MatchExactly) self.radial_points.setCurrentIndex(ndx) leb_layout.addRow("radial points:", self.radial_points) self.angular_points = QComboBox() self.angular_points.addItems([ "110", "194", "302", "590", "974", "1454", "2030", "2702", "5810" ]) self.angular_points.setToolTip( "more angular points will give more accurate results, but integration will take longer" ) ndx = self.angular_points.findText(self.settings.angular_points, Qt.MatchExactly) self.angular_points.setCurrentIndex(ndx) leb_layout.addRow("angular points:", self.angular_points) settings_layout.addRow(leb_widget) mc_widget = QWidget() mc_layout = QFormLayout(mc_widget) mc_layout.setContentsMargins(0, 0, 0, 0) self.min_iter = QSpinBox() self.min_iter.setValue(self.settings.minimum_iterations) self.min_iter.setRange(0, 10000) self.min_iter.setToolTip( "each iteration is 3000 points\n" + "iterations continue until convergence criteria are met") mc_layout.addRow("minimum interations:", self.min_iter) settings_layout.addRow(mc_widget) if self.settings.method == "Lebedev": mc_widget.setVisible(False) elif self.settings.method == "Monte-Carlo": leb_widget.setVisible(False) self.report_component = QComboBox() self.report_component.addItems(["total", "quadrants", "octants"]) ndx = self.report_component.findText(self.settings.report_component, Qt.MatchExactly) self.report_component.setCurrentIndex(ndx) settings_layout.addRow("report volume:", self.report_component) self.use_scene = QCheckBox() self.use_scene.setChecked(self.settings.use_scene) self.use_scene.setToolTip( "quadrants/octants will use the orientation the molecule is displayed in" ) settings_layout.addRow("use display orientation:", self.use_scene) self.method.currentTextChanged.connect( lambda text, widget=leb_widget: widget.setVisible(text == "Lebedev" )) self.method.currentTextChanged.connect( lambda text, widget=mc_widget: widget.setVisible(text == "Monte-Carlo")) self.use_centroid = QCheckBox() self.use_centroid.setChecked(self.settings.use_centroid) self.use_centroid.setToolTip( "place the center between selected atoms\n" + "might be useful for polydentate ligands") calc_layout.addRow("use centroid of centers:", self.use_centroid) self.steric_map = QCheckBox() self.steric_map.setChecked(self.settings.steric_map) self.steric_map.setToolTip( "produce a 2D projection of steric bulk\ncauses buried volume to be reported for individual quadrants" ) steric_layout.addRow("create steric map:", self.steric_map) self.num_pts = QSpinBox() self.num_pts.setRange(25, 250) self.num_pts.setValue(self.settings.num_pts) self.num_pts.setToolTip("number of points along x and y axes") steric_layout.addRow("number of points:", self.num_pts) self.include_vbur = QCheckBox() self.include_vbur.setChecked(self.settings.include_vbur) steric_layout.addRow("label quadrants with %V<sub>bur</sub>", self.include_vbur) self.map_shape = QComboBox() self.map_shape.addItems(["circle", "square"]) ndx = self.map_shape.findText(self.settings.map_shape, Qt.MatchExactly) self.map_shape.setCurrentIndex(ndx) steric_layout.addRow("map shape:", self.map_shape) self.auto_minmax = QCheckBox() self.auto_minmax.setChecked(self.settings.auto_minmax) steric_layout.addRow("automatic min. and max.:", self.auto_minmax) self.map_min = QDoubleSpinBox() self.map_min.setRange(-15., 0.) self.map_min.setSuffix(" \u212B") self.map_min.setSingleStep(0.1) self.map_min.setValue(self.settings.map_min) steric_layout.addRow("minimum value:", self.map_min) self.map_max = QDoubleSpinBox() self.map_max.setRange(0., 15.) self.map_max.setSuffix(" \u212B") self.map_max.setSingleStep(0.1) self.map_max.setValue(self.settings.map_max) steric_layout.addRow("maximum value:", self.map_max) self.num_pts.setEnabled(self.settings.steric_map) self.steric_map.stateChanged.connect( lambda state, widget=self.num_pts: widget.setEnabled(state == Qt. Checked)) self.include_vbur.setEnabled(self.settings.steric_map) self.steric_map.stateChanged.connect( lambda state, widget=self.include_vbur: widget.setEnabled( state == Qt.Checked)) self.map_shape.setEnabled(self.settings.steric_map) self.steric_map.stateChanged.connect( lambda state, widget=self.map_shape: widget.setEnabled(state == Qt. Checked)) self.auto_minmax.setEnabled(self.settings.steric_map) self.steric_map.stateChanged.connect( lambda state, widget=self.auto_minmax: widget.setEnabled( state == Qt.Checked)) self.map_min.setEnabled(not self.settings.auto_minmax and self.settings.steric_map) self.steric_map.stateChanged.connect( lambda state, widget=self.map_min, widget2=self.auto_minmax: widget .setEnabled(state == Qt.Checked and not widget2.isChecked())) self.auto_minmax.stateChanged.connect( lambda state, widget=self.map_min, widget2=self.steric_map: widget. setEnabled(not state == Qt.Checked and widget2.isChecked())) self.map_max.setEnabled(not self.settings.auto_minmax and self.settings.steric_map) self.steric_map.stateChanged.connect( lambda state, widget=self.map_max, widget2=self.auto_minmax: widget .setEnabled(state == Qt.Checked and not widget2.isChecked())) self.auto_minmax.stateChanged.connect( lambda state, widget=self.map_max, widget2=self.steric_map: widget. setEnabled(not state == Qt.Checked and widget2.isChecked())) self.display_cutout = QComboBox() self.display_cutout.addItems(["no", "free", "buried"]) ndx = self.display_cutout.findText(self.settings.display_cutout, Qt.MatchExactly) self.display_cutout.setCurrentIndex(ndx) self.display_cutout.setToolTip("show free or buried volume") vol_cutout_layout.addRow("display volume:", self.display_cutout) self.point_spacing = QDoubleSpinBox() self.point_spacing.setDecimals(3) self.point_spacing.setRange(0.01, 0.5) self.point_spacing.setSingleStep(0.005) self.point_spacing.setSuffix(" \u212B") self.point_spacing.setValue(self.settings.point_spacing) self.point_spacing.setToolTip( "distance between points on cutout\n" + "smaller spacing will narrow gaps, but increase time to create the cutout" ) vol_cutout_layout.addRow("point spacing:", self.point_spacing) self.intersection_scale = QDoubleSpinBox() self.intersection_scale.setDecimals(2) self.intersection_scale.setRange(1., 10.) self.intersection_scale.setSingleStep(0.5) self.intersection_scale.setSuffix("x") self.intersection_scale.setToolTip( "relative density of points where VDW radii intersect\n" + "higher density will narrow gaps, but increase time to create cutout" ) self.intersection_scale.setValue(self.settings.intersection_scale) vol_cutout_layout.addRow("intersection density:", self.intersection_scale) self.cutout_labels = QComboBox() self.cutout_labels.addItems(["none", "quadrants", "octants"]) ndx = self.cutout_labels.findText(self.settings.cutout_labels, Qt.MatchExactly) self.cutout_labels.setCurrentIndex(ndx) vol_cutout_layout.addRow("label sections:", self.cutout_labels) self.point_spacing.setEnabled(self.settings.display_cutout != "no") self.intersection_scale.setEnabled( self.settings.display_cutout != "no") self.cutout_labels.setEnabled(self.settings.display_cutout != "no") self.display_cutout.currentTextChanged.connect( lambda text, widget=self.point_spacing: widget.setEnabled(text != "no")) self.display_cutout.currentTextChanged.connect( lambda text, widget=self.intersection_scale: widget.setEnabled( text != "no")) self.display_cutout.currentTextChanged.connect( lambda text, widget=self.cutout_labels: widget.setEnabled(text != "no")) calc_vbur_button = QPushButton( "calculate % buried volume for selected centers") calc_vbur_button.clicked.connect(self.calc_vbur) calc_layout.addRow(calc_vbur_button) self.calc_vbur_button = calc_vbur_button remove_vbur_button = QPushButton( "remove % buried volume visualizations") remove_vbur_button.clicked.connect(self.del_vbur) vol_cutout_layout.addRow(remove_vbur_button) self.table = QTableWidget() self.table.setColumnCount(3) self.table.setHorizontalHeaderLabels(['model', 'center', '%Vbur']) self.table.setSelectionBehavior(QTableWidget.SelectRows) self.table.setEditTriggers(QTableWidget.NoEditTriggers) self.table.resizeColumnToContents(0) self.table.resizeColumnToContents(1) self.table.resizeColumnToContents(2) self.table.horizontalHeader().setSectionResizeMode( 0, QHeaderView.Interactive) self.table.horizontalHeader().setSectionResizeMode( 1, QHeaderView.Interactive) self.table.horizontalHeader().setSectionResizeMode( 2, QHeaderView.Stretch) calc_layout.addRow(self.table) menu = QMenuBar() export = menu.addMenu("&Export") clear = QAction("Clear data table", self.tool_window.ui_area) clear.triggered.connect(self.clear_table) export.addAction(clear) copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area) copy.triggered.connect(self.copy_csv) shortcut = QKeySequence(Qt.CTRL + Qt.Key_C) copy.setShortcut(shortcut) export.addAction(copy) self.copy = copy save = QAction("&Save CSV...", self.tool_window.ui_area) save.triggered.connect(self.save_csv) #this shortcut interferes with main window's save shortcut #I've tried different shortcut contexts to no avail #thanks Qt... #shortcut = QKeySequence(Qt.CTRL + Qt.Key_S) #save.setShortcut(shortcut) #save.setShortcutContext(Qt.WidgetShortcut) export.addAction(save) delimiter = export.addMenu("Delimiter") comma = QAction("comma", self.tool_window.ui_area, checkable=True) comma.setChecked(self.settings.delimiter == "comma") comma.triggered.connect(lambda *args, delim="comma": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(comma) tab = QAction("tab", self.tool_window.ui_area, checkable=True) tab.setChecked(self.settings.delimiter == "tab") tab.triggered.connect(lambda *args, delim="tab": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(tab) space = QAction("space", self.tool_window.ui_area, checkable=True) space.setChecked(self.settings.delimiter == "space") space.triggered.connect(lambda *args, delim="space": self.settings. __setattr__("delimiter", delim)) delimiter.addAction(space) semicolon = QAction("semicolon", self.tool_window.ui_area, checkable=True) semicolon.setChecked(self.settings.delimiter == "semicolon") semicolon.triggered.connect(lambda *args, delim="semicolon": self. settings.__setattr__("delimiter", delim)) delimiter.addAction(semicolon) add_header = QAction("&Include CSV header", self.tool_window.ui_area, checkable=True) add_header.setChecked(self.settings.include_header) add_header.triggered.connect(self.header_check) export.addAction(add_header) comma.triggered.connect( lambda *args, action=tab: action.setChecked(False)) comma.triggered.connect( lambda *args, action=space: action.setChecked(False)) comma.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) tab.triggered.connect( lambda *args, action=comma: action.setChecked(False)) tab.triggered.connect( lambda *args, action=space: action.setChecked(False)) tab.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) space.triggered.connect( lambda *args, action=comma: action.setChecked(False)) space.triggered.connect( lambda *args, action=tab: action.setChecked(False)) space.triggered.connect( lambda *args, action=semicolon: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=comma: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=tab: action.setChecked(False)) semicolon.triggered.connect( lambda *args, action=space: action.setChecked(False)) menu.setNativeMenuBar(False) self._menu = menu layout.setMenuBar(menu) menu.setVisible(True) self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def clear_table(self): are_you_sure = QMessageBox.question( None, "Clear table?", "Are you sure you want to clear the data table?", ) if are_you_sure != QMessageBox.Yes: return self.table.setRowCount(0) def set_ligand_atoms(self): self.ligand_atoms = selected_atoms(self.session) self.session.logger.status("set ligand to current selection") def calc_vbur(self): args = dict() cur_sel = selected_atoms(self.session) if len(cur_sel) == 0: return models = [] for atom in cur_sel: if atom.structure not in models: models.append(atom.structure) center = [] for atom in cur_sel: center.append(atom) args["center"] = center radii = self.radii_option.currentText() self.settings.radii = radii args["radii"] = radii scale = self.scale.value() self.settings.vdw_scale = scale args["scale"] = scale radius = self.radius.value() self.settings.center_radius = radius args["radius"] = radius steric_map = self.steric_map.checkState() == Qt.Checked self.settings.steric_map = steric_map args["steric_map"] = steric_map use_scene = self.use_scene.checkState() == Qt.Checked self.settings.use_scene = use_scene args["useScene"] = use_scene num_pts = self.num_pts.value() self.settings.num_pts = num_pts args["num_pts"] = num_pts include_vbur = self.include_vbur.checkState() == Qt.Checked self.settings.include_vbur = include_vbur use_centroid = self.use_centroid.checkState() == Qt.Checked self.settings.use_centroid = use_centroid args["useCentroid"] = use_centroid shape = self.map_shape.currentText() self.settings.map_shape = shape args["shape"] = shape report_component = self.report_component.currentText() self.settings.report_component = report_component args["reportComponent"] = report_component method = self.method.currentText() self.settings.method = method if method == "Lebedev": args["method"] = "lebedev" rad_pts = self.radial_points.currentText() self.settings.radial_points = rad_pts args["radialPoints"] = rad_pts ang_pts = self.angular_points.currentText() self.settings.angular_points = ang_pts args["angularPoints"] = ang_pts elif method == "Monte-Carlo": args["method"] = "mc" min_iter = self.min_iter.value() self.settings.minimum_iterations = min_iter args["minimumIterations"] = min_iter display_cutout = self.display_cutout.currentText() self.settings.display_cutout = display_cutout if display_cutout != "no": args["displaySphere"] = display_cutout if display_cutout != "no": point_spacing = self.point_spacing.value() self.settings.point_spacing = point_spacing args["pointSpacing"] = point_spacing intersection_scale = self.intersection_scale.value() self.settings.intersection_scale = intersection_scale args["intersectionScale"] = intersection_scale cutout_labels = self.cutout_labels.currentText() self.settings.cutout_labels = cutout_labels args["labels"] = cutout_labels if len(self.ligand_atoms) > 0: args["onlyAtoms"] = [a for a in self.ligand_atoms if not a.deleted] if len(args["onlyAtoms"]) == 0: args["onlyAtoms"] = None auto_minmax = self.auto_minmax.checkState() == Qt.Checked self.settings.auto_minmax = auto_minmax if not auto_minmax: map_max = self.map_max.value() self.settings.map_max = map_max map_min = self.settings.map_min self.settings.map_min = map_min info = percent_vbur_cmd(self.session, models, return_values=True, **args) # self.table.setRowCount(0) if steric_map: for mdl, cent, vbur, map_info in info: row = self.table.rowCount() self.table.insertRow(row) m = QTableWidgetItem() m.setData(Qt.DisplayRole, mdl.name) self.table.setItem(row, 0, m) c = QTableWidgetItem() c.setData(Qt.DisplayRole, cent) self.table.setItem(row, 1, c) v = QTableWidgetItem() if report_component == "octants": v.setData(Qt.DisplayRole, ",".join(["%.1f" % x for x in vbur])) elif report_component == "quadrants": v.setData( Qt.DisplayRole, ",".join("%.1f" % x for x in [ vbur[0] + vbur[7], vbur[1] + vbur[6], vbur[2] + vbur[5], vbur[3] + vbur[4], ])) else: if hasattr(vbur, "__iter__"): v.setData(Qt.DisplayRole, "%.1f" % sum(vbur)) else: v.setData(Qt.DisplayRole, "%.1f" % vbur) v.setTextAlignment(Qt.AlignHCenter | Qt.AlignVCenter) self.table.setItem(row, 2, v) x, y, z, min_alt, max_alt = map_info plot = self.tool_window.create_child_window( "steric map of %s" % mdl.name, window_class=StericMap) if auto_minmax: plot.set_data(x, y, z, min_alt, max_alt, vbur, radius, include_vbur) else: plot.set_data(x, y, z, map_min, map_max, vbur, radius, include_vbur) else: for mdl, cent, vbur in info: row = self.table.rowCount() self.table.insertRow(row) m = QTableWidgetItem() m.setData(Qt.DisplayRole, mdl.name) self.table.setItem(row, 0, m) c = QTableWidgetItem() c.setData(Qt.DisplayRole, cent) self.table.setItem(row, 1, c) v = QTableWidgetItem() if report_component == "octants": v.setData(Qt.DisplayRole, ",".join(["%.1f" % x for x in vbur])) elif report_component == "quadrants": v.setData( Qt.DisplayRole, ",".join("%.1f" % x for x in [ vbur[0] + vbur[7], vbur[1] + vbur[6], vbur[2] + vbur[5], vbur[3] + vbur[4], ])) else: if hasattr(vbur, "__iter__"): v.setData(Qt.DisplayRole, "%.1f" % sum(vbur)) else: v.setData(Qt.DisplayRole, "%.1f" % vbur) v.setTextAlignment(Qt.AlignHCenter | Qt.AlignVCenter) self.table.setItem(row, 2, v) self.table.resizeColumnToContents(1) self.table.resizeColumnToContents(2) def header_check(self, state): """user has [un]checked the 'include header' option on the menu""" if state: self.settings.include_header = True else: self.settings.include_header = False def get_csv(self): if self.settings.delimiter == "comma": delim = "," elif self.settings.delimiter == "space": delim = " " elif self.settings.delimiter == "tab": delim = "\t" elif self.settings.delimiter == "semicolon": delim = ";" if self.settings.include_header: s = delim.join(["model", "center", "%Vbur"]) s += "\n" else: s = "" for i in range(0, self.table.rowCount()): s += delim.join([ item.data(Qt.DisplayRole) for item in [self.table.item(i, j) for j in range(0, 3)] ]) s += "\n" return s def copy_csv(self): app = QApplication.instance() clipboard = app.clipboard() csv = self.get_csv() clipboard.setText(csv) self.session.logger.status("copied to clipboard") def save_csv(self): """save data on current tab to CSV file""" filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)") if filename: s = self.get_csv() with open(filename, 'w') as f: f.write(s.strip()) self.session.logger.status("saved to %s" % filename) def del_vbur(self): for model in self.session.models.list(type=Surface): if model.name.startswith("%Vbur") or model.name.startswith( "%Vfree"): model.delete() def display_help(self): """Show the help for this tool in the help viewer.""" from chimerax.core.commands import run run(self.session, 'open %s' % self.help if self.help is not None else "")
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 Linter(ToolInstance): """ tool to run python linters on files the UI has a list of files, an option to choose the linter, and a button to run the linter results are printed to the log """ def __init__(self, session, name): super().__init__(session, name) self.tool_window = MainToolWindow(self) self.settings = _LinterSettings(self.session, name) self._build_ui() def _build_ui(self): layout = QFormLayout() self.table = QTableWidget() self.table.setColumnCount(2) self.table.setHorizontalHeaderLabels(["file", "remove"]) self.table.horizontalHeader().setStretchLastSection(False) self.table.horizontalHeader().setSectionResizeMode( 0, QHeaderView.Stretch) self.table.horizontalHeader().setSectionResizeMode( 1, QHeaderView.Fixed) self.table.cellClicked.connect(self.table_clicked) layout.addRow(self.table) self.linters = QComboBox() self.linters.addItems([ "pyflakes", "flake8", "mypy", "pydocstyle", "pylint", ]) ndx = self.linters.findText(self.settings.linter, Qt.MatchExactly) self.linters.setCurrentIndex(ndx) layout.addRow(self.linters) lint = QPushButton("run linter") lint.clicked.connect(self.run_linter) layout.addRow(lint) self.add_files(loads(self.settings.files)) self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def table_clicked(self, row, column): """ if the last row is clicked, open a file browser and add the files to the list otherwise, if the 2nd column is clicked (the trash can), remove that row """ if row == self.table.rowCount() - 1 or self.table.rowCount() == 1: filenames = QFileDialog.getOpenFileNames( filter="Python Files (*.py)") if filenames[0]: self.table.setRowCount(self.table.rowCount() - 1) self.add_files(filenames[0]) elif column == 1: self.table.removeRow(row) def add_files(self, filenames): """add filenames (list(str)) to the table""" for f in filenames: row = self.table.rowCount() self.table.insertRow(row) file_item = QTableWidgetItem() file_item.setData(Qt.DisplayRole, f) self.table.setItem(row, 0, file_item) widget_that_lets_me_horizontally_align_an_icon = QWidget() widget_layout = QHBoxLayout( widget_that_lets_me_horizontally_align_an_icon) section_remove = QLabel() dim = int(1.5 * section_remove.fontMetrics().boundingRect("Z").height()) section_remove.setPixmap( QIcon(section_remove.style().standardIcon( QStyle.SP_DialogDiscardButton)).pixmap(dim, dim)) widget_layout.addWidget(section_remove, 0, Qt.AlignHCenter) widget_layout.setContentsMargins(0, 0, 0, 0) self.table.setCellWidget( row, 1, widget_that_lets_me_horizontally_align_an_icon) self.add_last_row() def add_last_row(self): """add the "add files" button to the bottom of the table""" row = self.table.rowCount() self.table.insertRow(row) add_row = QTableWidgetItem() add_row.setData(Qt.DisplayRole, "add files") self.table.setItem(row, 0, add_row) def run_linter(self): """execute linter""" previous_files = [] linter = self.linters.currentText() for row in range(0, self.table.rowCount() - 1): fname = self.table.item(row, 0).text() previous_files.append(fname) run(self.session, "linter \"%s\" linter %s" % (fname, linter)) self.settings.files = dumps(previous_files) self.settings.linter = linter