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 _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 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 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 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