def _addmenu(data, menu):
'''Fill a menu from "data"'''
menu.setTearOffEnabled(True)
menu.setWindowTitle(menu.title()) # needed for Windows
for item in data:
if item[0] == 'separator':
menu.addSeparator()
elif item[0] == 'menu':
_addmenu(item[2], menu.addMenu(item[1].replace('&', '&&')))
elif item[0] == 'command':
command = item[2]
if command is None:
print('warning: skipping', item)
else:
if isinstance(command, str):
command = lambda c=command: cmd.do(c)
menu.addAction(item[1], command)
elif item[0] == 'check':
if len(item) > 4:
menu.addAction(
SettingAction(self, cmd, item[2], item[1], item[3],
item[4]))
else:
menu.addAction(
SettingAction(self, cmd, item[2], item[1]))
elif item[0] == 'radio':
label, name, value = item[1:4]
try:
group, type_, values = actiongroups[item[2]]
except KeyError:
group = QtWidgets.QActionGroup(self)
type_, values = cmd.get_setting_tuple(name)
actiongroups[item[2]] = group, type_, values
action = QtWidgets.QAction(label, self)
action.triggered.connect(lambda _=0, args=(name, value):
cmd.set(*args, log=1, quiet=0))
self.setting_callbacks[cmd.setting._get_index(
name)].append(
lambda v, V=value, a=action: a.setChecked(v == V))
group.addAction(action)
menu.addAction(action)
action.setCheckable(True)
if values[0] == value:
action.setChecked(True)
elif item[0] == 'open_recent_menu':
self.open_recent_menu = menu.addMenu('Open Recent...')
else:
print('error:', item)
def __init__(self, parent=None, filename='', title='Text Editor'):
super(TextEditor, self).__init__()
self.highlight = None
self.root = self
self.root.setWindowTitle(title)
menubar = self.root.menuBar()
filemenu = menubar.addMenu("File")
filemenu.addAction("Open", self.doOpen, QtGui.QKeySequence("Ctrl+O"))
filemenu.addAction("Save", self.doSave, QtGui.QKeySequence("Ctrl+S"))
filemenu.addAction("Save as ...", self.doSaveAs,
QtGui.QKeySequence("Ctrl+Shift+S"))
syntaxmenu = menubar.addMenu("Syntax")
syntaxgroup = QtWidgets.QActionGroup(self)
self.syntaxactions = {}
for label in ['Python', 'PML', 'Plain Text']:
key = label.split()[0].lower()
action = syntaxmenu.addAction(label,
lambda t=key: self.setSyntax(t))
syntaxgroup.addAction(action)
action.setCheckable(True)
self.syntaxactions[key] = action
self.text = QtWidgets.QPlainTextEdit()
self.text.setFont(getMonospaceFont())
self.root.setCentralWidget(self.text)
connectFontContextMenu(self.text)
self._open(filename)
self.root.show()
self.root.raise_()
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())
