def build_regular_colors_submenu(self, target_menu, color_mode, elements_to_color=None): if color_mode == "single": elements_to_color = self.parent_group.pymod_element # Regular color scheme of the element. add_qt_menu_command( target_menu, "Default Color", lambda: self.parent_group.main_window.color_selection( color_mode, elements_to_color, "regular")) # Build PyMOL color palette menu. self.build_color_palette_submenu(color_mode, elements_to_color, target_menu, "PyMOL Colors", pmdt.pymol_regular_colors_list) ''' # Build PyMOL light color pallette. self.build_color_palette_submenu(color_mode, elements_to_color, target_menu, "PyMOL Light Colors", pmdt.pymol_light_colors_list) ''' # Build PyMod color palette. self.build_color_palette_submenu(color_mode, elements_to_color, target_menu, "PyMod Colors", pmdt.pymod_regular_colors_list) target_menu.addSeparator() # Custom color selection. add_qt_menu_command(target_menu, "Pick Color", lambda a=None, m=color_mode, e=elements_to_color: self.open_color_dialog_from_context(m, e))
def build_header_popup_menu(self): """ Builds the popup menu that appears when users left-clicks with on the sequence header in the main window left pan. """ self.context_menu = Header_context_menu(self) # Places the single sequence submenus in a separate submenu in order to distinguish it # from the selection submenu. if len(self.parent_group.pymod.get_selected_sequences()) > 1: self.single_sequence_context_submenu = QtWidgets.QMenu( self.parent_group.pymod_element.my_header, self.context_menu) self.context_menu.addMenu(self.single_sequence_context_submenu) self.single_element_target_submenu = self.single_sequence_context_submenu # Places the single sequence submenus in the main context menu. else: add_qt_menu_command(self.context_menu, self.parent_group.pymod_element.my_header, None) self.single_element_target_submenu = self.context_menu self.context_menu.addSeparator() # Builds a popup menu for sequence elements. if not self.parent_group.pymod_element.is_cluster(): self.build_single_sequence_header_popup_menu() # For cluster elements (alignments or blast-search elements). else: self.build_cluster_popup_menu(self.single_element_target_submenu, mode="cluster", extra_spacer=True) self.update_left_popup_menu()
def build_cluster_options_menu(self): """ Submenu with options to manage a sequence within its cluster. """ self.cluster_context_submenu = QtWidgets.QMenu( 'Cluster Options', self.single_element_target_submenu) self.single_element_target_submenu.addMenu( self.cluster_context_submenu) add_qt_menu_command(self.cluster_context_submenu, "Extract Sequence from Cluster", self.extract_from_cluster)
def builds_features_menu(self): self.features_context_submenu = QtWidgets.QMenu( 'Features', self.single_element_target_submenu) add_qt_menu_command( self.features_context_submenu, "Show Features", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "custom")) add_qt_menu_command( self.features_context_submenu, "Delete Features", lambda: self.parent_group.pymod.delete_features_from_context_menu( self.parent_group.pymod_element)) self.single_element_target_submenu.addMenu( self.features_context_submenu)
def build_color_palette_submenu(self, color_mode, elements_to_color, target_submenu, title, list_of_colors): new_palette_submenu = QtWidgets.QMenu(title, target_submenu) target_submenu.addMenu(new_palette_submenu) for color in list_of_colors: add_qt_menu_command( parent=new_palette_submenu, label=color, command=lambda a=None, c=color: self.parent_group.main_window. color_selection(color_mode, elements_to_color, "regular", c), fg_color=self.parent_group.main_window. get_regular_sequence_color(color), bg_color="#ABABAB")
def contextMenuEvent(self, event): """ Shows the context menu when right clickings on the sequence of an element. """ if self.parent_group.pymod_element.is_cluster(): return None alignment_id = self.get_mousecurrent_position_on_string(event) if alignment_id in ("start", "end"): return None alignment_id = alignment_id - 1 self.context_menu = Header_context_menu(self) add_qt_menu_command(self.context_menu, self.parent_group.pymod_element.my_header, None) self.context_menu.addSeparator() if self.parent_group.pymod_element.has_structure(): add_qt_menu_command( self.context_menu, "Select Residue in PyMOL", command=lambda a=None, aid=alignment_id: self. select_residue_in_pymol_from_sequence_text(aid)) add_qt_menu_command( self.context_menu, "Center Residue in PyMOL", command=lambda a=None, aid=alignment_id: self. center_residue_in_pymol_from_sequence_text(aid)) self.context_menu.addSeparator() add_qt_menu_command(self.context_menu, "Add Residue Feature", command=lambda a=None, aid=alignment_id: self. add_feature_from_sequence_text(aid)) action = self.context_menu.exec_(self.mapToGlobal(event.pos()))
def build_models_submenu(self): """ Build an "Modeling Session n" voice in the "Models" submenu once some models have been built. """ # Delete the old models submenu. self.models_menu.clear() if self.pymod.modeling_session_list != []: for modeling_session in self.pymod.modeling_session_list: # Adds a modeling session submenu to the PyMod main menu. label_text = "Modeling Session %s" % ( modeling_session.session_id) modeling_session_submenu = QtWidgets.QMenu(label_text, self) self.models_menu.addMenu(modeling_session_submenu) add_qt_menu_command(modeling_session_submenu, "Export to File", lambda a=None, ms=modeling_session: self. pymod.save_modeling_session(ms)) add_qt_menu_command(modeling_session_submenu, "DOPE Profile", lambda a=None, ms=modeling_session: self. pymod.show_session_profile(ms)) add_qt_menu_command(modeling_session_submenu, "Assessment Table", lambda a=None, ms=modeling_session: self. pymod.show_assessment_table(ms)) else: add_qt_menu_command(self.models_menu, "There aren't any models")
def build_domains_menu(self): self.domains_context_submenu = QtWidgets.QMenu( 'Domains', self.single_element_target_submenu) add_qt_menu_command( self.domains_context_submenu, "Split into Domains", lambda a=None, pe=self.parent_group.pymod_element: self. parent_group.pymod.launch_domain_splitting(pe)) if self.parent_group.pymod_element.derived_domains_list: add_qt_menu_command( self.domains_context_submenu, "Fuse Domains Alignments", lambda a=None, pe=self.parent_group.pymod_element: self. parent_group.pymod.launch_domain_fuse(pe)) self.single_element_target_submenu.addMenu( self.domains_context_submenu)
def build_selection_cluster_menu(self): self.selection_cluster_context_submenu = QtWidgets.QMenu( 'Cluster Options', self.selection_context_submenu) self.selection_context_submenu.addMenu( self.selection_cluster_context_submenu) add_qt_menu_command(self.selection_cluster_context_submenu, "Extract Sequences from their Clusters", self.extract_selection_from_cluster) selected_sequences = self.parent_group.pymod.get_selected_sequences() mothers_set = set([s.mother for s in selected_sequences]) if len(mothers_set) == 1: if len(selected_sequences) < len( self.parent_group.pymod_element.mother.get_children()): add_qt_menu_command( self.selection_cluster_context_submenu, "Extract Sequences to New Cluster", self.extract_selection_to_new_cluster_from_left_menu)
def build_selection_sequence_menu(self): self.selection_sequence_context_submenu = QtWidgets.QMenu( 'Sequences', self.selection_context_submenu) self.selection_context_submenu.addMenu( self.selection_sequence_context_submenu) add_qt_menu_command(self.selection_sequence_context_submenu, "Save Selection to File", self.save_selection_from_left_pane) add_qt_menu_command(self.selection_sequence_context_submenu, "Copy Selection to Clipboard", self.copy_selection) self.selection_sequence_context_submenu.addSeparator() add_qt_menu_command(self.selection_sequence_context_submenu, "Duplicate Selection", self.duplicate_selection) add_qt_menu_command(self.selection_sequence_context_submenu, "Delete Selection", self.delete_many_sequences)
def build_cluster_edit_menu(self, target_menu): self.cluster_edit_context_submenu = QtWidgets.QMenu( 'Edit Cluster', target_menu) target_menu.addMenu(self.cluster_edit_context_submenu) add_qt_menu_command(self.cluster_edit_context_submenu, "Save Alignment To File", self.save_alignment_from_left_pan) self.cluster_edit_context_submenu.addSeparator() add_qt_menu_command(self.cluster_edit_context_submenu, "Delete Gap Only Columns", self.delete_gap_only_columns_from_left_pane) add_qt_menu_command(self.cluster_edit_context_submenu, "Transfer Alignment", self.transfer_alignment_from_left_pane) self.cluster_edit_context_submenu.addSeparator() add_qt_menu_command(self.cluster_edit_context_submenu, "Delete Cluster", self.delete_alignment_from_left_pane)
def build_alignment_submenu(self): """ Build an "Alignment N" voice in the "Alignments" submenu when alignment N is performed. """ # Delete the old alignment submenu. self.alignments_menu.clear() # Then rebuilds it with the new alignments. alignment_list = self.pymod.get_cluster_elements() if alignment_list != []: for alignment_element in alignment_list: # Adds the alignment submenu for each cluster loaded in PyMod to the PyMod main menu. label_text = alignment_element.my_header single_alignment_submenu = QtWidgets.QMenu(label_text, self) self.alignments_menu.addMenu(single_alignment_submenu) # Save to a file dialog. add_qt_menu_command( single_alignment_submenu, "Save to File", # The first argument in Qt is a 'False' value, therefore we need to add a dummy 'a' variable # in order to pass the 'alignment_element' object. lambda a=None, e=alignment_element: self.pymod. save_alignment_to_file_from_ali_menu(e)) single_alignment_submenu.addSeparator() # Matrices submenu. single_alignment_matrices_submenu = QtWidgets.QMenu( 'Matrices', self) single_alignment_submenu.addMenu( single_alignment_matrices_submenu) add_qt_menu_command(single_alignment_matrices_submenu, "Sequence Identity Matrix", lambda a=None, e=alignment_element: self. pymod.display_identity_matrix(e)) add_qt_menu_command( single_alignment_matrices_submenu, "RMSD Matrix", lambda a=None, e=alignment_element: self.pymod. display_rmsd_matrix_from_alignments_menu(e)) # Trees. if alignment_element.initial_number_of_sequences > 2: single_alignment_trees_submenu = QtWidgets.QMenu( 'Trees', self) single_alignment_submenu.addMenu( single_alignment_trees_submenu) if alignment_element.algorithm in pymod_vars.can_show_guide_tree: add_qt_menu_command( single_alignment_trees_submenu, "Show Guide Tree", lambda a=None, e=alignment_element: self.pymod. show_guide_tree_from_alignments_menu(e)) if alignment_element.algorithm in pymod_vars.can_show_dendrogram and alignment_element.tree_file_path is not None: add_qt_menu_command( single_alignment_trees_submenu, "Show SALIGN Dendrogram", lambda a=None, e=alignment_element: self.pymod. show_dendrogram_from_alignments_menu(e)) if len(alignment_element.get_children()) >= 2: add_qt_menu_command( single_alignment_trees_submenu, "Build Tree from Alignment", lambda a=None, e=alignment_element: self.pymod. build_tree_from_alignments_menu(e)) # Evolutionary conservation. single_alignment_evolutionary_submenu = QtWidgets.QMenu( 'Evolutionary Conservation', self) single_alignment_submenu.addMenu( single_alignment_evolutionary_submenu) single_seq_evolutionary_submenu = QtWidgets.QMenu( 'Sequence Conservation', self) single_alignment_evolutionary_submenu.addMenu( single_seq_evolutionary_submenu) add_qt_menu_command( single_seq_evolutionary_submenu, "Entropy", lambda a=None, e=alignment_element: self.pymod. launch_entropy_scorer_from_main_menu(e)) add_qt_menu_command(single_seq_evolutionary_submenu, "CAMPO", lambda a=None, e=alignment_element: self. pymod.launch_campo_from_main_menu(e)) add_qt_menu_command(single_seq_evolutionary_submenu, "Pair Conservation", lambda a=None, e=alignment_element: self. pymod.launch_pc_from_main_menu(e)) single_str_evolutionary_submenu = QtWidgets.QMenu( 'Structural Conservation', self) single_alignment_evolutionary_submenu.addMenu( single_str_evolutionary_submenu) add_qt_menu_command(single_str_evolutionary_submenu, "SCR_FIND", lambda a=None, e=alignment_element: self. pymod.launch_scr_find_from_main_menu(e)) # Render alignment. single_alignment_render_submenu = QtWidgets.QMenu( 'Render Alignment', self) single_alignment_submenu.addMenu( single_alignment_render_submenu) add_qt_menu_command(single_alignment_render_submenu, "Generate Logo through WebLogo 3", lambda a=None, e=alignment_element: self. pymod.launch_weblogo_from_main_menu(e)) add_qt_menu_command(single_alignment_render_submenu, "Launch ESPript in Web Browser", lambda a=None, e=alignment_element: self. pymod.launch_espript_from_main_menu(e)) else: add_qt_menu_command(self.alignments_menu, "There aren't any alignments")
def make_main_menu(self): """ This method is called when initializing the main window in order to build its main menu. """ self.menubar = self.menuBar() self.menubar.setNativeMenuBar(False) #--------------- # "File" menu. - #--------------- self.file_menu = self.menubar.addMenu('File') # Sequences submenu. self.sequences_submenu = QtWidgets.QMenu('Sequences and Structures', self) self.file_menu.addMenu(self.sequences_submenu) add_qt_menu_command(self.sequences_submenu, 'Open from File', self.pymod.open_file_from_the_main_menu) add_qt_menu_command(self.sequences_submenu, 'Add Raw Sequence', self.pymod.show_raw_seq_input_window) add_qt_menu_command(self.sequences_submenu, 'Import PyMOL Objects', self.pymod.import_pymol_selections_from_main_menu) # self.file_menu.addSeparator() # Submenu to open alignments. self.alignment_files_submenu = QtWidgets.QMenu('Alignments', self) self.file_menu.addMenu(self.alignment_files_submenu) add_qt_menu_command(self.alignment_files_submenu, 'Open from File', self.pymod.open_alignment_from_main_menu) # Submenu to open results files from external programs. self.external_results_submenu = QtWidgets.QMenu( 'External Programs Results', self) self.file_menu.addMenu(self.external_results_submenu) self.hhsuite_results_submenu = QtWidgets.QMenu('HH-suite', self) self.external_results_submenu.addMenu(self.hhsuite_results_submenu) add_qt_menu_command(self.hhsuite_results_submenu, 'Template Search (.hhr)', self.pymod.open_hhsuite_hhr_from_main_menu) add_qt_menu_command(self.hhsuite_results_submenu, 'Multiple Sequence Alignment (.a3m)', self.pymod.open_hhsuite_a3m_from_main_menu) self.file_menu.addSeparator() # Workspace submenu. self.sessions_submenu = QtWidgets.QMenu('Sessions', self) self.file_menu.addMenu(self.sessions_submenu) add_qt_menu_command(self.sessions_submenu, 'New', self.pymod.start_new_session_from_main_menu) add_qt_menu_command(self.sessions_submenu, 'Save', self.pymod.save_session_from_main_menu) add_qt_menu_command(self.sessions_submenu, 'Open', self.pymod.open_session_from_main_menu) self.file_menu.addSeparator() # Exit command. add_qt_menu_command(self.file_menu, 'Exit', self.pymod.exit_from_main_menu) #---------------- # "Tools" menu. - #---------------- self.tools_menu = self.menubar.addMenu('Tools') # Database search for homologous sequences. self.database_search_submenu = QtWidgets.QMenu('Database Search', self) self.tools_menu.addMenu(self.database_search_submenu) self.blast_tools_submenu = QtWidgets.QMenu('BLAST', self) self.database_search_submenu.addMenu(self.blast_tools_submenu) add_qt_menu_command( self.blast_tools_submenu, 'Local BLAST', lambda: self.pymod.launch_blast_algorithm("blastp")) add_qt_menu_command(self.blast_tools_submenu, 'Remote BLAST', lambda: self.pymod.launch_blast_algorithm("blast")) add_qt_menu_command( self.database_search_submenu, 'PSI-BLAST', lambda: self.pymod.launch_blast_algorithm("psi-blast")) self.database_search_submenu.addSeparator() add_qt_menu_command( self.database_search_submenu, 'phmmer', lambda: self.pymod.launch_hmmer_algorithm("phmmer")) add_qt_menu_command( self.database_search_submenu, 'jackhmmer', lambda: self.pymod.launch_hmmer_algorithm("jackhmmer")) add_qt_menu_command( self.database_search_submenu, 'hmmsearch', lambda: self.pymod.launch_hmmer_algorithm("hmmsearch")) # Alignment tools self.alignments_tools_submenu = QtWidgets.QMenu( 'Alignment Tools', self) self.tools_menu.addMenu(self.alignments_tools_submenu) # Sequence alignment tools. self.sequence_alignments_submenu = QtWidgets.QMenu( 'Sequence Alignment', self) self.alignments_tools_submenu.addMenu(self.sequence_alignments_submenu) add_qt_menu_command( self.sequence_alignments_submenu, 'ClustalW', lambda: self.pymod.launch_alignment_from_the_main_menu( "clustalw", "regular")) add_qt_menu_command( self.sequence_alignments_submenu, 'Clustal Omega', lambda: self.pymod.launch_alignment_from_the_main_menu( "clustalo", "regular")) add_qt_menu_command( self.sequence_alignments_submenu, 'MUSCLE', lambda: self.pymod.launch_alignment_from_the_main_menu( "muscle", "regular")) add_qt_menu_command( self.sequence_alignments_submenu, 'SALIGN (Sequence Alignment)', lambda: self.pymod.launch_alignment_from_the_main_menu( "salign-seq", "regular")) # Profile alignment tools. self.sequence_profile_alignments_submenu = QtWidgets.QMenu( 'Profile Alignment', self) self.alignments_tools_submenu.addMenu( self.sequence_profile_alignments_submenu) add_qt_menu_command( self.sequence_profile_alignments_submenu, 'ClustalW', lambda: self.pymod.launch_alignment_from_the_main_menu( "clustalw", "profile")) add_qt_menu_command( self.sequence_profile_alignments_submenu, 'Clustal Omega', lambda: self.pymod.launch_alignment_from_the_main_menu( "clustalo", "profile")) add_qt_menu_command( self.sequence_profile_alignments_submenu, 'SALIGN (Sequence Alignment)', lambda: self.pymod.launch_alignment_from_the_main_menu( "salign-seq", "profile")) # Structural alignment tools. self.structural_alignment_submenu = QtWidgets.QMenu( 'Structural Alignment', self) self.alignments_tools_submenu.addMenu( self.structural_alignment_submenu) # add_qt_menu_command(self.structural_alignment_submenu, 'Superpose', self.pymod.superpose_from_main_menu) add_qt_menu_command( self.structural_alignment_submenu, 'CE Alignment', lambda: self.pymod.launch_alignment_from_the_main_menu( "ce", "regular")) add_qt_menu_command( self.structural_alignment_submenu, 'SALIGN (Structure Alignment)', lambda: self.pymod.launch_alignment_from_the_main_menu( "salign-str", "regular")) # Domain tools. self.domain_analysis_submenu = QtWidgets.QMenu('Domains Analysis', self) self.tools_menu.addMenu(self.domain_analysis_submenu) self.hmmscan_tools_submenu = QtWidgets.QMenu('hmmscan', self) self.domain_analysis_submenu.addMenu(self.hmmscan_tools_submenu) add_qt_menu_command(self.hmmscan_tools_submenu, 'Local hmmscan', lambda: self.pymod.launch_domain_analysis("local")) add_qt_menu_command( self.hmmscan_tools_submenu, 'Remote hmmscan', lambda: self.pymod.launch_domain_analysis("remote")) # Structural analysis. self.structural_analysis_submenu = QtWidgets.QMenu( 'Structural Analysis', self) self.tools_menu.addMenu(self.structural_analysis_submenu) add_qt_menu_command(self.structural_analysis_submenu, 'Ramachandran Plot', self.pymod.ramachandran_plot_from_main_menu) add_qt_menu_command(self.structural_analysis_submenu, 'Contact Map', self.pymod.contact_map_from_main_menu) add_qt_menu_command(self.structural_analysis_submenu, 'Structural Divergence Plot', self.pymod.sda_from_main_menu) self.structural_analysis_submenu.addSeparator() add_qt_menu_command(self.structural_analysis_submenu, 'Assess with DOPE', self.pymod.dope_from_main_menu) self.structural_analysis_submenu.addSeparator() add_qt_menu_command(self.structural_analysis_submenu, 'PSIPRED', self.pymod.launch_psipred_from_main_menu) # Modeling. self.modeling_submenu = QtWidgets.QMenu('Modeling', self) self.tools_menu.addMenu(self.modeling_submenu) add_qt_menu_command(self.modeling_submenu, "MODELLER (Homology Modeling)", self.pymod.launch_modeller_hm_from_main_menu) add_qt_menu_command(self.modeling_submenu, "MODELLER (Loop Modeling)", self.pymod.launch_modeller_lr_from_main_menu) # Options. self.tools_menu.addSeparator() add_qt_menu_command(self.tools_menu, 'Options', self.pymod.show_pymod_options_window) #--------------------- # "Alignments" menu. - #--------------------- self.alignments_menu = self.menubar.addMenu('Alignments') self.build_alignment_submenu() #----------------- # "Models" menu. - #----------------- # When the plugin is started there are no models. self.models_menu = self.menubar.addMenu('Models') self.build_models_submenu() #-------------------- # "Selection" menu. - #-------------------- self.main_selection_menu = self.menubar.addMenu('Selection') add_qt_menu_command(self.main_selection_menu, 'Select All [Ctrl+a]', self.pymod.select_all_from_main_menu) add_qt_menu_command(self.main_selection_menu, 'Deselect All [Esc]', self.pymod.deselect_all_from_main_menu) # Structures selection submenu. self.selection_structures_menu = QtWidgets.QMenu('Structures', self) self.main_selection_menu.addMenu(self.selection_structures_menu) add_qt_menu_command(self.selection_structures_menu, 'Show All in PyMOL [Ctrl+s]', self.pymod.show_all_structures_from_main_menu) add_qt_menu_command(self.selection_structures_menu, 'Hide All in PyMOL [Ctrl+h]', self.pymod.hide_all_structures_from_main_menu) self.selection_structures_menu.addSeparator() add_qt_menu_command(self.selection_structures_menu, 'Select All', self.pymod.select_all_structures_from_main_menu) add_qt_menu_command(self.selection_structures_menu, 'Deselect All', self.pymod.deselect_all_structures_from_main_menu) # Clusters selection submenu. self.selection_clusters_menu = QtWidgets.QMenu('Clusters', self) self.main_selection_menu.addMenu(self.selection_clusters_menu) add_qt_menu_command(self.selection_clusters_menu, 'Expand All', self.pymod.expand_all_clusters_from_main_menu) add_qt_menu_command(self.selection_clusters_menu, 'Collapse All', self.pymod.collapse_all_clusters_from_main_menu) #------------------ # "Display" menu. - #------------------ self.display_menu = self.menubar.addMenu('Display') if self.pymod.DEVELOP: add_qt_menu_command(self.display_menu, 'Print Selected Sequences', command=self.print_selected) # Color menu. self.main_color_menu = QtWidgets.QMenu('Color all Sequences', self) self.display_menu.addMenu(self.main_color_menu) add_qt_menu_command( self.main_color_menu, 'By Default Color', command=lambda: self.color_selection("all", None, "regular")) self.main_residues_colors_menu = QtWidgets.QMenu( 'By Residue Properties', self) self.main_color_menu.addMenu(self.main_residues_colors_menu) add_qt_menu_command( self.main_residues_colors_menu, 'Residue Type', command=lambda: self.color_selection("all", None, "residue_type")) add_qt_menu_command( self.main_residues_colors_menu, 'Polarity', command=lambda: self.color_selection("all", None, "polarity")) add_qt_menu_command(self.main_color_menu, 'By Secondary Structure', command=lambda: self.color_selection( "all", None, "secondary-auto")) # Font selection. self.font_selection_menu = QtWidgets.QMenu('Font Selection', self) self.display_menu.addMenu(self.font_selection_menu) if self.pymod.DEVELOP: add_qt_menu_command(self.display_menu, 'Font Type and Size', self.pymod.change_font_from_main_menu) # Font size selection. self.font_size_selection_menu = QtWidgets.QMenu('Font Size', self) self.font_selection_menu.addMenu(self.font_size_selection_menu) font_size_action_group = QtWidgets.QActionGroup( self.font_size_selection_menu) font_size_action_group.setExclusive(True) for font_size in ("6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16"): action = font_size_action_group.addAction( QtWidgets.QAction(font_size, self.font_size_selection_menu, checkable=True)) self.font_size_selection_menu.addAction(action) if font_size == str(self.font_size): action.setChecked(True) action.triggered.connect(lambda a=None, t=None, s=font_size: self. pymod.change_font_from_action(t, s)) # Font type selection. self.font_type_selection_menu = QtWidgets.QMenu('Font Type', self) self.font_selection_menu.addMenu(self.font_type_selection_menu) font_type_action_group = QtWidgets.QActionGroup( self.font_type_selection_menu) font_type_action_group.setExclusive(True) for font_type in self.get_available_fonts(): action = font_type_action_group.addAction( QtWidgets.QAction(font_type, self.font_type_selection_menu, checkable=True)) self.font_type_selection_menu.addAction(action) if font_type == str(self.font): action.setChecked(True) action.triggered.connect(lambda a=None, t=font_type, s=None: self. pymod.change_font_from_action(t, s)) #--------------- # "Help" menu. - #--------------- self.help_menu = self.menubar.addMenu('Help') if self.pymod.DEVELOP: add_qt_menu_command(self.help_menu, 'Test', self.pymod.launch_default) add_qt_menu_command(self.help_menu, 'Online Documentation', self.pymod.open_online_documentation) add_qt_menu_command(self.help_menu, 'About', self.pymod.show_about_dialog) self.help_menu.addSeparator() add_qt_menu_command(self.help_menu, "Install PyMod Components", self.pymod.launch_components_installation) add_qt_menu_command(self.help_menu, "Check for Database Updates", self.pymod.launch_databases_update) if self.pymod.TEST: self.help_menu.addSeparator() self.examples_menu = QtWidgets.QMenu('Examples', self) self.help_menu.addMenu(self.examples_menu) add_qt_menu_command( self.examples_menu, "Load random sequence from UniProt", lambda a=None: self.pymod.load_uniprot_random()) add_qt_menu_command(self.examples_menu, "Load random PDB entry", lambda a=None: self.pymod.load_pdb_random())
def build_selection_structure_menu(self): self.selection_structure_context_submenu = QtWidgets.QMenu( 'Structures', self.selection_context_submenu) self.selection_context_submenu.addMenu( self.selection_structure_context_submenu) if self.parent_group.pymod.all_sequences_have_structure(): add_qt_menu_command( self.selection_structure_context_submenu, "Show chains in PyMOL", self.show_selected_chains_in_pymol_from_popup_menu) add_qt_menu_command( self.selection_structure_context_submenu, "Hide chains in PyMOL", self.hide_selected_chains_in_pymol_from_popup_menu) self.selection_structure_context_submenu.addSeparator() add_qt_menu_command( self.selection_structure_context_submenu, "Show Chains as Hedgehog", self.show_hedgehog_chains_in_pymol_from_popup_menu) add_qt_menu_command(self.selection_structure_context_submenu, "Show Heteroatoms", self.show_het_chains_in_pymol_from_popup_menu) add_qt_menu_command(self.selection_structure_context_submenu, "Hide Heteroatoms", self.hide_het_chains_in_pymol_from_popup_menu) elif self.parent_group.pymod.all_sequences_have_fetchable_pdbs(): add_qt_menu_command( self.selection_structure_context_submenu, "Fetch PDB Files", lambda: self.parent_group.pymod.fetch_pdb_files( "selection", None))
def build_multiple_color_menu(self, mode, cluster_target_menu=None): """ Used to build the color menu of both Selection and cluster elements popup menus. """ if mode == "selection": target_menu = self.context_menu color_selection_mode = "selection" color_selection_target = None sequences_list = self.parent_group.pymod.get_selected_sequences() # color_selection_target = sequences_list color_target_label = "Selection" elif mode == "cluster": target_menu = cluster_target_menu color_selection_mode = "multiple" if self.parent_group.pymod_element.is_cluster(): color_selection_target = self.parent_group.pymod_element.get_children( ) sequences_list = self.parent_group.pymod_element.get_children() else: color_selection_target = self.parent_group.pymod_element.mother.get_children( ) sequences_list = self.parent_group.pymod_element.mother.get_children( ) color_target_label = "Cluster" # Builds the selection color menu. multiple_color_menu = QtWidgets.QMenu('Color', target_menu) # A submenu to choose a single color used to color all the residues of a sequence. multiple_regular_colors_menu = QtWidgets.QMenu( "Color whole %s by" % (color_target_label), multiple_color_menu ) # Menu(multiple_color_menu, tearoff=0, bg='white', activebackground='black', activeforeground='white') self.build_regular_colors_submenu( multiple_regular_colors_menu, color_selection_mode, elements_to_color=color_selection_target) multiple_color_menu.addMenu(multiple_regular_colors_menu) # multiple_color_menu.addSeparator() # Colors each kind of residue in a sequence in a different way. multiple_residues_colors_menu = QtWidgets.QMenu( 'By Residue Properties', target_menu) add_qt_menu_command( multiple_residues_colors_menu, "Residue Type", command=lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "residue_type")) add_qt_menu_command( multiple_residues_colors_menu, "Polarity", command=lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "polarity")) multiple_color_menu.addMenu(multiple_residues_colors_menu) # Secondary structure colors. n_selected_seqs = len(sequences_list) n_structures = len([e for e in sequences_list if e.has_structure()]) n_seq_with_predicted_sec_str = len([ e for e in sequences_list if e.has_predicted_secondary_structure() ]) if n_structures + n_seq_with_predicted_sec_str == n_selected_seqs: # multiple_color_menu.addSeparator() multiple_sec_str_color_menu = QtWidgets.QMenu( 'By Secondary Structure', multiple_color_menu) multiple_color_menu.addMenu(multiple_sec_str_color_menu) # Available when all the selected sequences have a 3D structure. if n_structures == n_selected_seqs: add_qt_menu_command( multiple_sec_str_color_menu, "Observed", lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "secondary-observed")) # Available only if all the sequences have a predicted secondary structure. if n_seq_with_predicted_sec_str == n_selected_seqs: add_qt_menu_command( multiple_sec_str_color_menu, "Predicted by PSIPRED", lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "secondary-predicted")) # Available if there is at least one element with a 3D structure or a secondary # structure prediction. if not n_structures == n_selected_seqs: add_qt_menu_command( multiple_sec_str_color_menu, "Auto (Observed + Predicted)", lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "secondary-auto")) # Conservation colors. sel_has_campo_scores = all( [e.has_campo_scores() for e in sequences_list]) sel_has_entropy_scores = all( [e.has_entropy_scores() for e in sequences_list]) if sel_has_campo_scores or sel_has_entropy_scores: multiple_cons_colors_menu = QtWidgets.QMenu( 'By Conservation', multiple_color_menu) multiple_color_menu.addMenu(multiple_cons_colors_menu) if sel_has_campo_scores: add_qt_menu_command( multiple_cons_colors_menu, "CAMPO scores", lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "campo-scores")) if sel_has_entropy_scores: add_qt_menu_command( multiple_cons_colors_menu, "Entropy scores", lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "entropy-scores")) # Energy colors. if all([e.has_dope_scores() for e in sequences_list]): # multiple_color_menu.addSeparator() multiple_energy_colors_menu = QtWidgets.QMenu( 'By Energy', multiple_color_menu) multiple_color_menu.addMenu(multiple_energy_colors_menu) add_qt_menu_command( multiple_energy_colors_menu, "DOPE scores", lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "dope")) # Color by domain. if all([e.has_domains() for e in sequences_list]): add_qt_menu_command( multiple_color_menu, "By Domain", lambda: self.parent_group.main_window.color_selection( color_selection_mode, color_selection_target, "domains")) return multiple_color_menu
def build_sequence_menu(self): """ Submenu with options for manipulating a sequence loaded in PyMod. """ self.sequence_context_submenu = QtWidgets.QMenu( 'Sequence', self.single_element_target_submenu) self.single_element_target_submenu.addMenu( self.sequence_context_submenu) add_qt_menu_command(self.sequence_context_submenu, "Save Sequence to File", self.save_sequence_from_left_pane) add_qt_menu_command(self.sequence_context_submenu, "Copy Sequence to Clipboard", self.copy_sequence_to_clipboard) self.sequence_context_submenu.addSeparator() add_qt_menu_command(self.sequence_context_submenu, "Edit Sequence", self.edit_sequence_from_context) add_qt_menu_command(self.sequence_context_submenu, "Search Sub-sequence", self.search_string_from_context) self.sequence_context_submenu.addSeparator() add_qt_menu_command(self.sequence_context_submenu, "Duplicate Sequence", self.duplicate_sequence_from_the_left_pane) add_qt_menu_command(self.sequence_context_submenu, "Delete Sequence", self.delete_sequence_from_the_left_pane)
def build_color_menu(self): """ Color submenu containing all the option to color for a single sequence. """ self.color_context_submenu = QtWidgets.QMenu( 'Color', self.single_element_target_submenu) self.single_element_target_submenu.addMenu(self.color_context_submenu) # A submenu to choose a single color used to color all the residues of a sequence. self.regular_colors_context_submenu = QtWidgets.QMenu( 'Color whole Sequence by', self.color_context_submenu) self.color_context_submenu.addMenu(self.regular_colors_context_submenu) self.build_regular_colors_submenu(self.regular_colors_context_submenu, "single") # Colors each kind of residue in a sequence in a different way. self.residues_colors_context_submenu = QtWidgets.QMenu( 'By Residue Properties', self.color_context_submenu) self.color_context_submenu.addMenu( self.residues_colors_context_submenu) add_qt_menu_command( self.residues_colors_context_submenu, "Residue Type", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "residue_type")) add_qt_menu_command( self.residues_colors_context_submenu, "Polarity", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "polarity")) # Secondary structure colors. if self.parent_group.can_be_colored_by_secondary_structure(): # self.color_context_submenu.addSeparator() self.sec_str_color_submenu = QtWidgets.QMenu( 'By Secondary Structure', self.color_context_submenu) self.color_context_submenu.addMenu(self.sec_str_color_submenu) if self.parent_group.pymod_element.has_structure(): add_qt_menu_command( self.sec_str_color_submenu, "Observed", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "secondary-observed")) if self.parent_group.pymod_element.has_predicted_secondary_structure( ): add_qt_menu_command( self.sec_str_color_submenu, "Predicted by PSIPRED", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "secondary-predicted")) # Conservation colors. if self.parent_group.pymod_element.has_campo_scores( ) or self.parent_group.pymod_element.has_entropy_scores(): # self.color_context_submenu.addSeparator() self.conservation_colors_menu = QtWidgets.QMenu( 'By Conservation', self.color_context_submenu) self.color_context_submenu.addMenu(self.conservation_colors_menu) if self.parent_group.pymod_element.has_campo_scores(): add_qt_menu_command( self.conservation_colors_menu, "CAMPO scores", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "campo-scores")) if self.parent_group.pymod_element.has_entropy_scores(): add_qt_menu_command( self.conservation_colors_menu, "Entropy scores", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "entropy-scores")) # Energy colors. if self.parent_group.pymod_element.has_dope_scores(): # self.color_context_submenu.addSeparator() self.energy_colors_menu = QtWidgets.QMenu( 'By Energy', self.color_context_submenu) self.color_context_submenu.addMenu(self.energy_colors_menu) add_qt_menu_command( self.energy_colors_menu, "DOPE scores", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "dope")) # Color by domain. if self.parent_group.pymod_element.has_domains(): add_qt_menu_command( self.color_context_submenu, "By Domain", lambda: self.parent_group.main_window.color_selection( "single", self.parent_group.pymod_element, "domains"))
def build_structure_menu(self): """ Submenu for elements that have a structure loaded in PyMOL. """ self.structure_context_submenu = QtWidgets.QMenu( 'Structure', self.single_element_target_submenu) if self.parent_group.pymod_element.has_structure(): self.single_element_target_submenu.addMenu( self.structure_context_submenu) # add_qt_menu_command(self.structure_context_submenu, "PDB Chain Information", self.show_structure_info) add_qt_menu_command(self.structure_context_submenu, "Save PDB Chain to File", self.save_structure_from_left_pane) self.structure_context_submenu.addSeparator() add_qt_menu_command(self.structure_context_submenu, "Center Chain in PyMOL", self.center_chain_in_pymol_from_header_entry) # TODO: a switch would be nice. add_qt_menu_command(self.structure_context_submenu, "Show Chain in PyMOL", self.show_chain_in_pymol_from_header_entry) add_qt_menu_command(self.structure_context_submenu, "Hide Chain in PyMOL", self.hide_chain_in_pymol_from_header_entry) self.structure_context_submenu.addSeparator() add_qt_menu_command(self.structure_context_submenu, "Show Chain as Hedgehog", self.show_hedgehog_in_pymol_from_header_entry) add_qt_menu_command(self.structure_context_submenu, "Show Heteroatoms", self.show_het_in_pymol_from_header_entry) add_qt_menu_command(self.structure_context_submenu, "Hide Heteroatoms", self.hide_het_in_pymol_from_header_entry) self.single_element_target_submenu.addMenu( self.structure_context_submenu) else: if self.parent_group.pymod_element.pdb_is_fetchable(): add_qt_menu_command( self.structure_context_submenu, "Fetch PDB File", lambda: self.parent_group.pymod.fetch_pdb_files( "single", self.parent_group.pymod_element)) # self.structure_context_submenu.addSeparator() # add_qt_menu_command(self.structure_context_submenu, "Associate 3D Structure", lambda: self.parent_group.pymod.associate_structure_from_popup_menu(self.parent_group.pymod_element)) self.single_element_target_submenu.addMenu( self.structure_context_submenu)