from __future__ import absolute_import, division, print_function from six.moves import cPickle as pickle from six.moves import range try : import gobject except ImportError : gobject = None import sys class coot_extension_gui(object): def __init__(self, title): import gtk self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) scrolled_win = gtk.ScrolledWindow() self.outside_vbox = gtk.VBox(False, 2) self.inside_vbox = gtk.VBox(False, 0) self.window.set_title(title) self.inside_vbox.set_border_width(0) self.window.add(self.outside_vbox) self.outside_vbox.pack_start(scrolled_win, True, True, 0) scrolled_win.add_with_viewport(self.inside_vbox) scrolled_win.set_policy(gtk.POLICY_AUTOMATIC, gtk.POLICY_AUTOMATIC) def finish_window(self): import gtk self.outside_vbox.set_border_width(2) ok_button = gtk.Button(" Close ") self.outside_vbox.pack_end(ok_button, False, False, 0) ok_button.connect("clicked", lambda b: self.destroy_window()) self.window.connect("delete_event", lambda a, b: self.destroy_window()) self.window.show_all() def destroy_window(self, *args): self.window.destroy() self.window = None def confirm_data(self, data): for data_key in self.data_keys : outlier_list = data.get(data_key) if outlier_list is not None and len(outlier_list) > 0 : return True return False def create_property_lists(self, data): import gtk for data_key in self.data_keys : outlier_list = data[data_key] if outlier_list is None or len(outlier_list) == 0 : continue else : frame = gtk.Frame(self.data_titles[data_key]) vbox = gtk.VBox(False, 2) frame.set_border_width(6) frame.add(vbox) self.add_top_widgets(data_key, vbox) self.inside_vbox.pack_start(frame, False, False, 5) list_obj = residue_properties_list( columns=self.data_names[data_key], column_types=self.data_types[data_key], rows=outlier_list, box=vbox) # Molprobity result viewer class coot_molprobity_todo_list_gui(coot_extension_gui): data_keys = [ "rama", "rota", "cbeta", "probe" ] data_titles = { "rama" : "Ramachandran outliers", "rota" : "Rotamer outliers", "cbeta" : "C-beta outliers", "probe" : "Severe clashes" } data_names = { "rama" : ["Chain", "Residue", "Name", "Score"], "rota" : ["Chain", "Residue", "Name", "Score"], "cbeta" : ["Chain", "Residue", "Name", "Conf.", "Deviation"], "probe" : ["Atom 1", "Atom 2", "Overlap"] } if (gobject is not None): data_types = { "rama" : [gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_FLOAT, gobject.TYPE_PYOBJECT], "rota" : [gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_FLOAT, gobject.TYPE_PYOBJECT], "cbeta" : [gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_FLOAT, gobject.TYPE_PYOBJECT], "probe" : [gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_FLOAT, gobject.TYPE_PYOBJECT] } else : data_types = dict([ (s, []) for s in ["rama","rota","cbeta","probe"] ]) def __init__(self, data_file=None, data=None): assert ([data, data_file].count(None) == 1) if (data is None): data = load_pkl(data_file) if not self.confirm_data(data): return coot_extension_gui.__init__(self, "MolProbity to-do list") self.dots_btn = None self.dots2_btn = None self._overlaps_only = True self.window.set_default_size(420, 600) self.create_property_lists(data) self.finish_window() def add_top_widgets(self, data_key, box): import gtk if data_key == "probe" : hbox = gtk.HBox(False, 2) self.dots_btn = gtk.CheckButton("Show Probe dots") hbox.pack_start(self.dots_btn, False, False, 5) self.dots_btn.connect("toggled", self.toggle_probe_dots) self.dots2_btn = gtk.CheckButton("Overlaps only") hbox.pack_start(self.dots2_btn, False, False, 5) self.dots2_btn.connect("toggled", self.toggle_all_probe_dots) self.dots2_btn.set_active(True) self.toggle_probe_dots() box.pack_start(hbox, False, False, 0) def toggle_probe_dots(self, *args): if self.dots_btn is not None : show_dots = self.dots_btn.get_active() overlaps_only = self.dots2_btn.get_active() if show_dots : self.dots2_btn.set_sensitive(True) else : self.dots2_btn.set_sensitive(False) show_probe_dots(show_dots, overlaps_only) def toggle_all_probe_dots(self, *args): if self.dots2_btn is not None : self._overlaps_only = self.dots2_btn.get_active() self.toggle_probe_dots() class rsc_todo_list_gui(coot_extension_gui): data_keys = ["by_res", "by_atom"] data_titles = ["Real-space correlation by residue", "Real-space correlation by atom"] data_names = {} data_types = {} class residue_properties_list(object): def __init__(self, columns, column_types, rows, box, default_size=(380,200)): assert len(columns) == (len(column_types) - 1) if (len(rows) > 0) and (len(rows[0]) != len(column_types)): raise RuntimeError("Wrong number of rows:\n%s" % str(rows[0])) import gtk self.liststore = gtk.ListStore(*column_types) self.listmodel = gtk.TreeModelSort(self.liststore) self.listctrl = gtk.TreeView(self.listmodel) self.listctrl.column = [None]*len(columns) self.listctrl.cell = [None]*len(columns) for i, column_label in enumerate(columns): cell = gtk.CellRendererText() column = gtk.TreeViewColumn(column_label) self.listctrl.append_column(column) column.set_sort_column_id(i) column.pack_start(cell, True) column.set_attributes(cell, text=i) self.listctrl.get_selection().set_mode(gtk.SELECTION_SINGLE) for row in rows : self.listmodel.get_model().append(row) self.listctrl.connect("cursor-changed", self.OnChange) sw = gtk.ScrolledWindow() w, h = default_size if len(rows) > 10 : sw.set_size_request(w, h) else : sw.set_size_request(w, 30 + (20 * len(rows))) sw.set_policy(gtk.POLICY_AUTOMATIC, gtk.POLICY_AUTOMATIC) box.pack_start(sw, False, False, 5) inside_vbox = gtk.VBox(False, 0) sw.add(self.listctrl) def OnChange(self, treeview): import coot # import dependency selection = self.listctrl.get_selection() (model, tree_iter) = selection.get_selected() if tree_iter is not None : row = model[tree_iter] xyz = row[-1] if isinstance(xyz, tuple) and len(xyz) == 3 : set_rotation_centre(*xyz) set_zoom(30) graphics_draw() def show_probe_dots(show_dots, overlaps_only): import coot # import dependency n_objects = number_of_generic_objects() sys.stdout.flush() if show_dots : for object_number in range(n_objects): obj_name = generic_object_name(object_number) if overlaps_only and not obj_name in ["small overlap", "bad overlap"] : sys.stdout.flush() set_display_generic_object(object_number, 0) else : set_display_generic_object(object_number, 1) else : sys.stdout.flush() for object_number in range(n_objects): set_display_generic_object(object_number, 0) def load_pkl(file_name): pkl = open(file_name, "rb") data = pickle.load(pkl) pkl.close() return data