pymod_main.py 文件源码

def dope_from_main_menu(self):
        """
        Called when users decide calculate DOPE of a structure loaded in PyMod.
        """
        # Checks if the DOPE profiles can be computed.
        selection = self.get_selected_sequences()
        if not self.modeller.can_be_launched():
            self.show_error_message("MODELLER Error", "MODELLER is missing. In order to compute DOPE scores of a structure, MODELLER has to be installed.")
            return False
        if len(selection) == 0:
            self.show_error_message("Selection Error", "Please select at least one structure to assess.")
            return False
        if not self.all_sequences_have_structure():
            self.show_error_message("Selection Error", "Please select only elements that have a 3D structure currently loaded in PyMOL.")
            return False
        if len(set([seq.mother_index for seq in selection])) != 1:
            self.show_error_message("Selection Error", "You can assess multiple structures DOPE only if they are aligned in the same cluster.")
            return False

        # Ask users if they would like to color the sequences according to their DOPE values.
        title = "Color Option"
        message = "Would you like to color the selected sequences by their DOPE values, once they have been calculated?"
        color_by_dope_choice = tkMessageBox.askyesno(message=message, title=title, parent=pymod.main_window)

        # Initializes MODELLER.
        if self.modeller.run_internally():
            env = modeller.environ()
            env.io.atom_files_directory = []
            env.io.atom_files_directory.append(".")
            env.io.hetatm = True
            env.io.water = True
            env.libs.topology.read(file='$(LIB)/top_heav.lib')
            env.libs.parameters.read(file='$(LIB)/par.lib')
        else:
            env = None

        # Actually computes the DOPE scores of the polypeptide chains in the user selection.
        for element in selection:
            self.compute_dope(element,env=env)

        # Assigns to each residue of the selected chains a correspoding color according to its DOPE.
        self.assign_dope_items(selection)

        # Color the elements.
        if color_by_dope_choice:
            for element in selection:
                element.color_element_by_dope()
        self.gridder()

        # Shows the DOPE profiles plot.
        dope_graph_mode = None
        if len(selection) == 1:
            dope_graph_mode = "single"
        elif len(selection) >= 2:
            dope_graph_mode = "multiple"

        # Prepares the data to show in the plot.
        dope_plot_data = self.prepare_dope_plot_data(selection, mode = dope_graph_mode)

        # Shows the plot.
        self.show_dope_plot(dope_plot_data)