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 fill_table(self): """adds test names to the table""" mgr = self.session.test_manager for name in mgr.tests.keys(): row = self.table.rowCount() self.table.insertRow(row) test_name = QTableWidgetItem() test_name.setData(Qt.DisplayRole, name) self.table.setItem(row, 0, test_name)
def add_ligand(tool): rows = tool.ligand_table.rowCount() if rows != 0: rows -= 1 ligand_name = QTableWidgetItem() name = "<click to choose>" is_c2 = Qt.Unchecked enabled = True if rows > 0: name = tool.ligand_table.item(rows - 1, 0).text() is_c2 = tool.ligand_table.cellWidget(rows - 1, 1).layout().itemAt(0).widget().checkState() enabled = tool.ligand_table.cellWidget(rows - 1, 1).layout().itemAt(0).widget().isEnabled() ligand_name.setData(Qt.DisplayRole, name) tool.ligand_table.setItem(rows, 0, ligand_name) widget_that_lets_me_horizontally_align_a_checkbox = QWidget() widget_layout = QHBoxLayout(widget_that_lets_me_horizontally_align_a_checkbox) c2 = QCheckBox() c2.setEnabled(enabled) c2.setCheckState(is_c2) widget_layout.addWidget(c2, 0, Qt.AlignHCenter) widget_layout.setContentsMargins(0, 0, 0, 0) tool.ligand_table.setCellWidget( rows, 1, widget_that_lets_me_horizontally_align_a_checkbox ) 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("Q").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) tool.ligand_table.setCellWidget( rows, 2, widget_that_lets_me_horizontally_align_an_icon ) rows += 1 tool.ligand_table.insertRow(rows) widget_that_lets_me_horizontally_align_an_icon = QWidget() widget_layout = QHBoxLayout(widget_that_lets_me_horizontally_align_an_icon) ligand_add = QLabel("add ligand") widget_layout.addWidget(ligand_add, 0, Qt.AlignHCenter) widget_layout.setContentsMargins(0, 0, 0, 0) tool.ligand_table.setCellWidget(rows, 1, widget_that_lets_me_horizontally_align_an_icon)
def update(self, *_): t = self.region_table t.setRowCount(0) m = self.isolde.selected_model if m is None: return from Qt.QtWidgets import QTableWidgetItem pa = self.problem_aggregator outliers_only = self.outliers_only_checkbox.isChecked() restraint_types = [ cb.text() for cb in self.restraint_checkboxes if cb.isChecked() ] validation_types = [ cb.text() for cb in self.validation_checkboxes if cb.isChecked() ] clusters, noise = pa.problem_zones( m, restraint_types=restraint_types, validation_types=validation_types, validation_outliers_only=outliers_only, cutoff=self.cutoff_spinbox.value(), min_points=self.cluster_spinbox.value()) t.clear() t.setColumnCount(1 + len(restraint_types) + len(validation_types)) t.setRowCount(len(clusters)) labels = [ t.replace(' ', '\n') for t in ['Total'] + restraint_types + validation_types ] t.setHorizontalHeaderLabels(labels) for i, cluster in enumerate(clusters): atoms = pa.cluster_atoms(cluster) issue_count = QTableWidgetItem(str(len(cluster))) issue_count.setData(self._data_role, atoms) t.setItem(i, 0, issue_count) for j, it in enumerate(restraint_types + validation_types): vtype = pa.registered_type(it) vcount = len([v for v in cluster if isinstance(v, vtype)]) t.setItem(i, j + 1, QTableWidgetItem(str(vcount)))
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
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 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)
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 fill_table(self, ndx): self.table.setRowCount(0) self.freq_table.setRowCount(0) self.fundamental_table.setRowCount(0) # self.overtone_table.setRowCount(0) self.combo_table.setRowCount(0) if ndx < 0: self.fundamental_table.setVisible(False) self.combo_table.setVisible(False) return fr = self.file_selector.currentData() item = QTableWidgetItem() item.setData(Qt.DisplayRole, "name") val = QTableWidgetItem() val.setData(Qt.DisplayRole, fr.name) self.table.insertRow(0) self.table.setItem(0, 0, item) self.table.setItem(0, 1, val) for info in fr.other.keys(): if info == "archive" and not self.settings.archive: continue if any( isinstance(fr.other[info], obj) for obj in [str, float, int]): row = self.table.rowCount() self.table.insertRow(row) item = QTableWidgetItem() info_name = info.replace("_", " ") val = fr.other[info] if info == "mass": info_name += " (%s)" % self.settings.mass if self.settings.mass == "Da": val /= UNIT.AMU_TO_KG elif info == "temperature": info_name += " (K)" elif (any(info == s for s in nrg_infos) or info.lower().endswith("energy") or info.startswith("E(")): if self.settings.energy == "Hartree": info_name += " (E<sub>h</sub>)" else: info_name += " (%s)" % self.settings.energy info_name = info_name.replace("orrelation", "orr.") info_name = info_name.replace("Same-spin", "SS") info_name = info_name.replace("Opposite-spin", "OS") if self.settings.energy == "kcal/mol": val *= UNIT.HART_TO_KCAL elif self.settings.energy == "kJ/mol": val *= 4.184 * UNIT.HART_TO_KCAL val = "%.6f" % val elif info.startswith("optical rotation"): info_name += " (°)" elif any(info == x for x in pg_infos): info_name = info.replace("_", " ") if re.search("\d", val): val = re.sub(r"(\d+)", r"<sub>\1</sub>", val) # gaussian uses * for infinity val = val.replace("*", "<sub>∞</sub>") # psi4 uses _inf_ val = val.replace("_inf_", "<sub>∞</sub>") if any(val.endswith(char) for char in "vhdsiVHDSI"): val = val[:-1] + "<sub>" + val[-1].lower() + "</sub>" if "<sub>" in info_name: self.table.setCellWidget(row, 0, QLabel(info_name)) else: item = QTableWidgetItem() item.setData(Qt.DisplayRole, info_name) self.table.setItem(row, 0, item) value = QTableWidgetItem() val = str(val) if "<sub>" in val: self.table.setCellWidget(row, 1, QLabel(val)) else: value.setData(Qt.DisplayRole, val) self.table.setItem(row, 1, value) elif isinstance(fr.other[info], Theory): theory = fr.other[info] if theory.method is not None: row = self.table.rowCount() self.table.insertRow(row) item = QTableWidgetItem() item.setData(Qt.DisplayRole, "method") self.table.setItem(row, 0, item) value = QTableWidgetItem() value.setData(Qt.DisplayRole, theory.method.name) self.table.setItem(row, 1, value) if theory.basis is not None: if theory.basis.basis: for basis in theory.basis.basis: row = self.table.rowCount() self.table.insertRow(row) item = QTableWidgetItem() if not basis.elements: item.setData(Qt.DisplayRole, "basis set") else: item.setData( Qt.DisplayRole, "basis for %s" % ", ".join(basis.elements)) self.table.setItem(row, 0, item) value = QTableWidgetItem() value.setData(Qt.DisplayRole, basis.name) self.table.setItem(row, 1, value) if theory.basis.ecp: for ecp in theory.basis.ecp: row = self.table.rowCount() self.table.insertRow(row) item = QTableWidgetItem() if ecp.elements is None: item.setData(Qt.DisplayRole, "ECP") else: item.setData(Qt.DisplayRole, "ECP %s" % " ".join(ecp.elements)) self.table.setItem(row, 0, item) value = QTableWidgetItem() value.setData(Qt.DisplayRole, ecp.name) self.table.setItem(row, 1, value) elif (hasattr(fr.other[info], "__iter__") and all(isinstance(x, float) for x in fr.other[info]) and len(fr.other[info]) > 1): row = self.table.rowCount() self.table.insertRow(row) item = QTableWidgetItem() info_name = info.replace("_", " ") vals = fr.other[info] if "rotational_temperature" in info: info_name = info_name.replace( "temperature", "constants (%s)" % self.settings.rot_const) if self.settings.rot_const == "GHz": vals = [ x * PHYSICAL.KB / (PHYSICAL.PLANCK * (10**9)) for x in vals ] item.setData(Qt.DisplayRole, info_name) self.table.setItem(row, 0, item) value = QTableWidgetItem() value.setData(Qt.DisplayRole, ", ".join(["%.4f" % x for x in vals])) self.table.setItem(row, 1, value) if "frequency" in fr.other: self.tabs.setTabEnabled(1, True) freq_data = fr.other['frequency'].data for i, mode in enumerate(freq_data): row = self.freq_table.rowCount() self.freq_table.insertRow(row) freq = FreqTableWidgetItem() freq.setData( Qt.DisplayRole, "%.2f%s" % (abs(mode.frequency), "i" if mode.frequency < 0 else "")) freq.setData(Qt.UserRole, i) self.freq_table.setItem(row, 0, freq) if mode.symmetry: text = mode.symmetry if re.search("\d", text): text = re.sub(r"(\d+)", r"<sub>\1</sub>", text) if text.startswith("SG"): text = "Σ" + text[2:] elif text.startswith("PI"): text = "Π" + text[2:] elif text.startswith("DLT"): text = "Δ" + text[3:] if any(text.endswith(char) for char in "vhdugVHDUG"): text = text[:-1] + "<sub>" + text[-1].lower( ) + "</sub>" label = QLabel(text) label.setAlignment(Qt.AlignCenter) self.freq_table.setCellWidget(row, 1, label) intensity = QTableWidgetItem() if mode.intensity is not None: intensity.setData(Qt.DisplayRole, round(mode.intensity, 2)) self.freq_table.setItem(row, 2, intensity) forcek = QTableWidgetItem() if mode.forcek is not None: forcek.setData(Qt.DisplayRole, round(mode.forcek, 2)) self.freq_table.setItem(row, 3, forcek) if fr.other["frequency"].anharm_data: self.fundamental_table.setVisible(True) self.combo_table.setVisible(True) freq = fr.other["frequency"] self.tabs.setTabEnabled(2, True) anharm_data = sorted( freq.anharm_data, key=lambda x: x.harmonic_frequency, ) for i, mode in enumerate(anharm_data): row = self.fundamental_table.rowCount() self.fundamental_table.insertRow(row) fund = FreqTableWidgetItem() fund.setData( Qt.DisplayRole, "%.2f%s" % (abs(mode.frequency), "i" if mode.frequency < 0 else "")) fund.setData(Qt.UserRole, i) self.fundamental_table.setItem(row, 0, fund) delta_anh = QTableWidgetItem() delta_anh.setData(Qt.DisplayRole, round(mode.delta_anh, 2)) self.fundamental_table.setItem(row, 1, delta_anh) intensity = QTableWidgetItem() if mode.intensity is not None: intensity.setData(Qt.DisplayRole, round(mode.intensity, 2)) self.fundamental_table.setItem(row, 2, intensity) for overtone in mode.overtones: row = self.combo_table.rowCount() self.combo_table.insertRow(row) fund = FreqTableWidgetItem() fund.setData( Qt.DisplayRole, "%.2f%s" % (abs(mode.frequency), "i" if mode.frequency < 0 else "")) fund.setData(Qt.UserRole, i) self.combo_table.setItem(row, 0, fund) fund = FreqTableWidgetItem() fund.setData(Qt.UserRole, i) self.combo_table.setItem(row, 1, fund) ot = FreqTableWidgetItem() ot.setData( Qt.DisplayRole, "%.2f%s" % (abs(overtone.frequency), "i" if overtone.frequency < 0 else "")) ot.setData(Qt.UserRole, i) self.combo_table.setItem(row, 2, ot) intensity = QTableWidgetItem() if overtone.intensity is not None: intensity.setData(Qt.DisplayRole, round(overtone.intensity, 2)) self.combo_table.setItem(row, 3, intensity) for key in mode.combinations: for combination in mode.combinations[key]: row = self.combo_table.rowCount() self.combo_table.insertRow(row) fund = FreqTableWidgetItem() fund.setData( Qt.DisplayRole, "%.2f%s" % (abs(mode.frequency), "i" if mode.frequency < 0 else "")) fund.setData(Qt.UserRole, i) self.combo_table.setItem(row, 0, fund) other_freq = freq.anharm_data[key].frequency fund = FreqTableWidgetItem() fund.setData( Qt.DisplayRole, "%.2f%s" % (abs(other_freq), "i" if other_freq < 0 else "")) fund.setData(Qt.UserRole, i + len(freq.anharm_data) * key) self.combo_table.setItem(row, 1, fund) combo = FreqTableWidgetItem() combo.setData( Qt.DisplayRole, "%.2f%s" % (abs(combination.frequency), "i" if combination.frequency < 0 else "")) combo.setData(Qt.UserRole, i) self.combo_table.setItem(row, 2, combo) intensity = QTableWidgetItem() if combination.intensity is not None: intensity.setData( Qt.DisplayRole, round(combination.intensity, 2)) self.combo_table.setItem(row, 3, intensity) else: self.fundamental_table.setVisible(False) self.combo_table.setVisible(False) self.tabs.setTabEnabled(2, False) else: self.fundamental_table.setVisible(False) self.combo_table.setVisible(False) self.tabs.setTabEnabled(1, False) self.tabs.setTabEnabled(2, False) self.table.resizeColumnToContents(0) self.table.resizeColumnToContents(1) self.freq_table.resizeColumnToContents(0) self.freq_table.resizeColumnToContents(1) self.freq_table.resizeColumnToContents(2) self.apply_filter()
def 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 _update_unparameterised_residues_list(self, *_, ff=None, ambiguous=None, unmatched=None, residues=None): table = self._residue_table tlist = self._template_list if not table.isVisible(): return table.setRowCount(0) tlist.clear() if ambiguous is None and unmatched is None: if self.isolde.selected_model is None: return residues = self.isolde.selected_model.residues h = residues.atoms[residues.atoms.element_names == 'H'] addh = False from ..dialog import choice_warning if not len(h): addh = choice_warning( 'This model does not appear to have hydrogens. Would you like to add them first?' ) elif self.suspiciously_low_h(residues): addh = choice_warning( 'This model has significantly fewer hydrogens than expected for a natural molecule. Would you like to run AddH first?' ) elif self.waters_without_h(residues): addh = choice_warning( 'Some or all waters are missing hydrogens. Would you like to add them first?' ) if addh: from chimerax.core.commands import run run(self.session, 'addh') from chimerax.atomic import Residues residues = Residues( sorted(residues, key=lambda r: (r.chain_id, r.number, r.insertion_code))) if ff is None: ffmgr = self.isolde.forcefield_mgr ff = ffmgr[self.isolde.sim_params.forcefield] ligand_db = ffmgr.ligand_db(self.isolde.sim_params.forcefield) from ..openmm.openmm_interface import find_residue_templates, create_openmm_topology template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) top, residue_templates = create_openmm_topology( residues.atoms, template_dict) _, ambiguous, unmatched = ff.assignTemplates( top, ignoreExternalBonds=True, explicit_templates=residue_templates) from Qt.QtWidgets import QTableWidgetItem table.setRowCount(len(unmatched) + len(ambiguous)) count = 0 for r in unmatched: by_name, by_comp = ff.find_possible_templates(r) cx_res = residues[r.index] data = ( cx_res.chain_id, cx_res.name + ' ' + str(cx_res.number), ) for j, d in enumerate(data): item = QTableWidgetItem(d) item.setData(USER_ROLE, (cx_res, by_name, by_comp)) table.setItem(count, j, item) count += 1 for r, template_info in ambiguous.items(): cx_res = residues[r.index] data = (cx_res.chain_id, cx_res.name + ' ' + str(cx_res.number), ', '.join([ti[0].name for ti in template_info])) for j, d in enumerate(data): item = QTableWidgetItem(d) item.setData(USER_ROLE, (cx_res, [], [[ti[0].name, 0] for ti in template_info])) table.setItem(count, j, item) count += 1 table.resizeColumnsToContents()
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.L_style = self.L_style.currentText() model_names, targets, 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, LCorrection=self.settings.L_style, ) if len(model_names) == 0: return # self.table.setRowCount(0) for t, b, data in zip(model_names, targets, 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, 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)