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|
# populate_python_menus.py
# Copyright 2007, 2008 by Bernhard Lohkamp
# Copyright 2006, 2007, 2008 by The University of York
# Copyright 2015 by Medical Research Council
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
# import pygtk, gtk, pango
import coot
import gi
gi.require_version('Gtk', '4.0')
from gi.repository import Gtk
import coot_gui_api
import time
import numbers
import coot_utils
import coot_gui
import fitting
import shelx_extensions
import gui_prosmart
# rename this file populate_python_menus.py
if coot_gui_api.main_menubar():
def coot_menubar_menu_simple(s):
menu = Gtk.Menu()
menuitem = Gtk.MenuItem(s)
menuitem.set_submenu(menu)
main_menubar = coot_gui_api.main_menubar()
main_menubar.append(menuitem)
menuitem.show()
return menu
def coot_menubar_menu(menu_label_string):
def get_menu_bar_label_dict():
label_dict = {}
for menu_child in coot_gui_api.main_menubar().get_children():
label_dict[menu_child.get_children()[0].get_text()] = menu_child
return label_dict
try:
menu_label_dict = get_menu_bar_label_dict()
return menu_label_dict[menu_label_string].get_submenu()
except KeyError as e:
return coot_menubar_menu_simple(menu_label_string)
def get_existing_submenu(menu, submenu_label):
label_dict = {}
for menu_child in menu.get_children():
for c in menu_child.get_children():
try:
t = c.get_text()
print("########### populate_python_menus get_existing_submenu get_text on c:", t)
if t == submenu_label:
return menu_child
except KeyError as e:
pass
return None
# this should be added to the "Refine" module. It is not used here
# (it doesn't belong in "Calculate")
def add_refinement_options(submenu_refine):
coot_gui.add_simple_coot_menu_menuitem(
submenu_refine,
"Set Refinement Options...",
lambda func: coot_gui.refinement_options_gui())
submenu = Gtk.Menu()
menuitem2 = Gtk.MenuItem("Peptide Restraints...")
menuitem2.set_submenu(submenu)
submenu_refine.append(menuitem2)
menuitem2.show()
def add_restr_func1():
print('Planar Peptide Restraints added')
coot.add_planar_peptide_restraints()
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Add Planar Peptide Restraints",
lambda func: add_restr_func1())
def add_restr_func2():
print('Planar Peptide Restraints removed')
coot.remove_planar_peptide_restraints()
coot_gui.add_simple_coot_menu_menuitem(
submenu, "Remove Planar Peptide Restraints",
lambda func: add_restr_func2())
calculate_menu = coot_menubar_menu("Calculate")
draw_menu = coot_menubar_menu("Draw")
edit_menu = coot_menubar_menu("Edit")
submenu_all_molecule = Gtk.Menu()
submenu_maps = Gtk.Menu()
submenu_modelling = Gtk.Menu()
submenu_ncs = Gtk.Menu()
submenu_views = Gtk.Menu()
submenu_representation = Gtk.Menu()
submenu_pisa = Gtk.Menu()
submenu_modules = Gtk.Menu()
submenu_settings = Gtk.Menu()
# get rid of "all molecule" function for now - maybe for ever
# calculate_all_molecule_menu_item = get_existing_submenu(calculate_menu, "All Molecule...")
# calculate_all_molecule_menu_item.set_submenu(submenu_all_molecule)
calculate_maps_menu_item = get_existing_submenu(calculate_menu, "Map Tools...")
calculate_maps_menu_item.set_submenu(submenu_maps)
calculate_model_menu_item = get_existing_submenu(calculate_menu, "Modelling...")
calculate_model_menu_item.set_submenu(submenu_modelling)
calculate_ncs_menu_item = get_existing_submenu(calculate_menu, "NCS Tools...")
calculate_ncs_menu_item.set_submenu(submenu_ncs)
calculate_pisa_menu_item = get_existing_submenu(calculate_menu, "PISA...")
calculate_pisa_menu_item.set_submenu(submenu_pisa)
calculate_modules_menu_item = get_existing_submenu(calculate_menu, "Modules...")
calculate_modules_menu_item.set_submenu(submenu_modules)
draw_representation_menu_item = get_existing_submenu(draw_menu, "Representation Tools...")
draw_representation_menu_item.set_submenu(submenu_representation)
edit_settings_menu_item = get_existing_submenu(edit_menu, "Settings...")
edit_settings_menu_item.set_submenu(submenu_settings)
draw_views_menu_item = Gtk.MenuItem("Views")
draw_views_menu_item.set_submenu(submenu_views)
draw_menu.append(draw_views_menu_item)
draw_views_menu_item.show()
# ---------------------------------------------------------------------
# Modules
# ---------------------------------------------------------------------
def add_module_user_defined_restraints():
menu = coot_gui.coot_menubar_menu("Restraints")
import user_define_restraints
def add_calculate_modules_menu(submenu_modules):
coot_gui.add_simple_coot_menu_menuitem(
submenu_modules, "CCP4...",
lambda func: coot_gui.add_module_ccp4())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modules, "SHELX...",
lambda func: shelx_extensions.add_module_shelx())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modules, "User-defined Restraints...",
lambda func: add_module_user_defined_restraints())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modules, "ProSMART",
lambda func: gui_prosmart.add_module_prosmart())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modules, "Carbohydrate",
lambda func: gui_add_linked_cho.add_module_carbohydrate_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modules, "Cryo-EM",
lambda func: coot_gui.add_module_cryo_em())
# ---------------------------------------------------------------------
# Settings
# ---------------------------------------------------------------------
def add_edit_settings_menu(submenu_settings):
submenu = Gtk.Menu()
menuitem2 = Gtk.MenuItem("Rotate Translate Zone Mode...")
menuitem2.set_submenu(submenu)
submenu_settings.append(menuitem2)
menuitem2.show()
coot_gui.add_simple_coot_menu_menuitem(
submenu, "Rotate About Fragment Centre",
lambda func: coot.set_rotate_translate_zone_rotates_about_zone_centre(1))
coot_gui.add_simple_coot_menu_menuitem(
submenu, "Rotate About Second Clicked Atom",
lambda func: coot.set_rotate_translate_zone_rotates_about_zone_centre(0))
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings,
"Set Density Fit Graph Weight...",
lambda func: coot_gui.generic_single_entry("set weight (smaller means apparently better fit)",
str("%.2f" %residue_density_fit_scale_factor()), "Set it",
lambda text: set_den_gra_func(text)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings,
"Set Spin Speed",
lambda func: coot_gui.generic_single_entry("Set Spin Speed (smaller is slower)",
str(coot.idle_function_rotate_angle()), "Set it",
lambda text: coot.set_idle_function_rotate_angle(float(text))))
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings, "Nudge Centre...",
lambda func: coot_gui.nudge_screen_centre_gui())
def all_mol_symm_func():
for imol in coot_utils.molecule_number_list():
if coot_utils.valid_model_molecule_qm(imol):
coot.set_symmetry_whole_chain(imol, 1)
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings, "All Molecules use \"Near Chains\" Symmetry",
lambda func: [valid_model_molecule_qm(imol) and
coot.set_symmetry_whole_chain(imol, 1) for imol in coot_utils.molecule_number_list()])
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings, "Save Graphics Size and Positions",
lambda func: coot.graphics_window_size_and_position_to_preferences())
def save_dialog_func():
coot.post_model_fit_refine_dialog()
coot.post_go_to_atom_window()
def delete_event(*args):
window.destroy()
return False
def go_func(*args):
save_dialog_positions_to_preferences_file()
window.destroy()
window = Gtk.Window(gtk.WINDOW_TOPLEVEL)
label_text = " When happy, press \"Save\" to save \n" + " dialog positions"
label = Gtk.Label(label_text)
h_sep = Gtk.HSeparator()
cancel_button = Gtk.Button(" Cancel ")
go_button = Gtk.Button(" Save ")
vbox = Gtk.VBox(False, 4)
hbox = Gtk.HBox(False, 4)
hbox.pack_start(go_button, False, False, 6)
hbox.pack_start(cancel_button, False, False, 6)
vbox.pack_start(label, False, False, 6)
vbox.pack_start(h_sep, False, False, 6)
vbox.pack_start(hbox, False, False, 6)
window.add(vbox)
go_button.connect("clicked", go_func)
cancel_button.connect("clicked", lambda w: window.destroy())
window.show_all()
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings, "Save Dialog Positions...",
lambda func: save_dialog_func())
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings, "Key Bindings...", lambda func: coot_gui.key_bindings_gui())
def install_and_show_key_bindings():
coot_utils.file_to_preferences("template_key_bindings.py") # copy and evaluate
coot_gui.key_bindings_gui()
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings, "Python: Install Template Keybindings",
lambda func: install_and_show_key_bindings())
def quick_save_func(txt):
try:
n = int(txt)
gobject.timeout_add(1000*n, quick_save)
except:
print("BL INFO:: could not add timer for auto save!")
coot_gui.add_simple_coot_menu_menuitem(
submenu_settings, "Enable Quick-Save checkpointing...",
lambda func: coot_gui.generic_single_entry("Checkpoint interval (seconds)",
"30",
" Start Auto-saving ",
lambda txt:
quick_save_func(txt)))
def fit_protein_func1(imol):
if coot.imol_refinement_map() == -1:
coot.add_status_bar_text("oops. Must set a map to fit")
else:
global continue_multi_refine
continue_multi_refine = True
fitting.interruptible_fit_protein(imol, fitting.fit_protein_fit_function)
def fit_protein_func2(imol):
if coot.imol_refinement_map() == -1:
coot.add_status_bar_text("oops. Must set a map to fit")
else:
global continue_multi_refine
continue_multi_refine = True
fitting.interruptible_fit_protein(imol, fitting.fit_protein_stepped_refine_function)
def fit_protein_func3(imol):
if coot.imol_refinement_map() == -1:
coot.add_status_bar_text("oops. Must set a map to fit")
else:
global continue_multi_refine
continue_multi_refine = True
fitting.interruptible_fit_protein(imol, fitting.fit_protein_rama_fit_function)
# --- add_edit_settings_menu() ends here
def mask_map_func():
f = ""
molecule_list = coot_utils.molecule_number_list()
if not molecule_list == []:
for i in molecule_list:
if coot.is_valid_map_molecule(molecule_list[i]):
print("%s is a valid map molecule" % molecule_list[i])
f = str(molecule_list[i])
break
else:
print("BL WARNING:: dunno what to do!? No map found")
f = False
return f
def mask_map_func1(active_state):
print("changed active_state to ", active_state)
def mask_map_func2(imol, texts_list, invert_mask_qm):
# map imol
text_1 = texts_list[0]
# atom selection
text_2 = texts_list[1]
# radius
text_3 = texts_list[2]
continue_qm = False
try:
n = int(text_1)
continue_qm = True
except:
print(
"BL WARNING:: input %s for Map molecule number is not an integer.\nBailing out" % n)
if (continue_qm):
if (invert_mask_qm):
invert = 1
else:
invert = 0
print("debug:: invert-mask? is", invert)
if (text_3 != "default"):
try:
new_radius = float(text_3)
coot.set_map_mask_atom_radius(new_radius)
except:
print(
"BL WARNING:: could not set map mask radius to %s. It's not a number" % text_3)
coot.mask_map_by_atom_selection(n, imol, text_2, invert)
def mask_map_radius_func():
rad = coot.map_mask_atom_radius()
if (rad > 0):
return str(rad)
else:
return "default"
def add_calculate_maps_menu(submenu_maps):
#---------------------------------------------------------------------
# Map Tools...
#---------------------------------------------------------------------
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Mask Map by Atom Selection...",
lambda func: coot_gui.molecule_chooser_gui("Define the molecule that has atoms to mask the map",
lambda imol: coot_gui.generic_multiple_entries_with_check_button(
[[" Map molecule number: ", mask_map_func],
[" Atom selection: ", "//A/1"],
["Radius around atoms: ", mask_map_radius_func]],
[" Invert Masking? ", lambda active_state: mask_map_func1(active_state)],
" Mask Map ", lambda text_list, invert: mask_map_func2(imol, text_list, invert))))
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Copy Map...",
lambda func: coot_gui.map_molecule_chooser_gui("Map to Copy...",
lambda imol: coot.copy_molecule(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Make a Smoother Copy...",
lambda func: coot_gui.map_molecule_chooser_gui("Map Molecule to Smoothenize...",
lambda imol: coot.smooth_map(imol, 1.25)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Make a Very Smooth Copy...",
lambda func: coot_gui.map_molecule_chooser_gui("Map Molecule to Smoothenize...",
lambda imol: coot.smooth_map(imol, 2.0)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Make a Difference Map...",
lambda func: coot_gui.make_difference_map_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Transform map by LSQ model fit...",
lambda func: coot_gui.transform_map_using_lsq_matrix_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Average Maps...",
lambda func: coot_gui.average_map_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Map Density Histogram...",
lambda func: coot_gui.map_molecule_chooser_gui("Choose the map",
lambda imol: coot.map_histogram(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Brighten Maps",
lambda func: coot_utils.brighten_maps())
def set_diff_map_func(imol):
print("setting map number %s to be a difference map" %imol)
coot.set_map_is_difference_map(imol)
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Set map is a difference map...",
# do we need this wrapper?
lambda func: coot_gui.map_molecule_chooser_gui("Which map should be considered a difference map?",
lambda imol: set_diff_map_func(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Another (contour) level...",
lambda func: coot.another_level())
coot_gui.add_simple_coot_menu_menuitem(
submenu_maps,
"Multi-chicken...",
lambda func: coot_gui.map_molecule_chooser_gui("Choose a molecule for multiple contouring",
lambda imol: (coot.set_map_displayed(imol, 0), coot_utils.multi_chicken(imol))))
def add_calculate_modelling_menu(submenu_maps):
#---------------------------------------------------------------------
# Molecule functions/Modelling
#
#---------------------------------------------------------------------
def add_hydrogens_with_coot_reduce():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.coot_reduce(aa_imol)
def add_hydrogens_refmac_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot_utils.add_hydrogens_using_refmac(aa_imol)
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Add Hydrogens",
lambda func: add_hydrogens_with_coot_reduce())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Add Hydrogens using Refmac",
lambda func: add_hydrogens_refmac_func())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Add Other Solvent Molecules...",
lambda func: coot_gui.solvent_ligands_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Arrange Waters Around Protein...",
lambda func: coot_gui.molecule_chooser_gui(
"Arrange waters in molecule: ",
lambda imol: coot.move_waters_to_around_protein(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Assign (force) HETATMs for this Residue",
lambda func: coot_utils.using_active_atom(coot.hetify_residue,
"aa_imol", "aa_chain_id", "aa_res_no", "aa_ins_code"))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Assign HETATM to molecule...",
lambda func: coot_gui.molecule_chooser_gui("Assign HETATMs as per PDB definition",
lambda imol: coot.assign_hetatms(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Atoms with Zero Occupancies...",
lambda func: coot_gui.molecule_chooser_gui(
"Which molecule to check for Atoms with zero occupancies?",
lambda imol: coot_gui.zero_occ_atoms_gui(imol)))
# --- D --------
def delete_sidechains_for_active_chain():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.delete_sidechains_for_chain(aa_imol, aa_chain_id)
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Delete Side-chain Atoms for Active Chain",
lambda x: delete_sidechains_for_active_chain())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Duplicate range (pick atoms)",
lambda func: coot_gui.duplicate_range_by_atom_pick())
# --- F --------
def get_smiles_pdbe_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
comp_id = coot.residue_name(aa_imol, aa_chain_id, aa_res_no, aa_ins_code)
coot_utils.get_SMILES_for_comp_id_from_pdbe(comp_id)
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Fetch PDBe description for this ligand",
lambda func: coot_utils.get_smiles_pdbe_func())
def get_pdbe_ligand_func(comp_id):
status = coot_utils.get_SMILES_for_comp_id_from_pdbe(comp_id)
coot.get_monomer(comp_id)
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Fetch PDBe Ligand Description",
lambda func: coot_gui.generic_single_entry("Fetch PDBe Ligand Desciption for comp_id:",
"", " Fetch ", lambda comp_id: get_pdbe_ligand_func(comp_id)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Fix Nomenclature Errors...",
lambda func: coot_gui.molecule_chooser_gui("Fix Nomenclature Error in molecule:",
lambda imol: coot.fix_nomenclature_errors(imol)))
# --- I --------
def chiral_centre_inverter_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.invert_chiral_centre(aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name)
coot_gui.add_simple_coot_menu_menuitem(submenu_modelling,
"Invert This Chiral Centre",
lambda func:
chiral_centre_inverter_func())
# --- M ---
def make_link_ext_func(*args):
m_spec_1 = args[0]
m_spec_2 = args[1]
imol_1 = coot_utils.atom_spec_to_imol(m_spec_1)
imol_2 = coot_utils.atom_spec_to_imol(m_spec_2)
spec_1 = m_spec_1[2:]
spec_2 = m_spec_2[2:]
if not (imol_1 == imol_2):
print("Mismatch molecules")
else:
coot.make_link_py(imol_1, spec_1, spec_2, "dummy", 0.1)
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Make Link (click 2 atoms)...",
lambda func:
coot.user_defined_click_py(2, make_link_ext_func))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Merge Water Chains...",
lambda func: coot_gui.molecule_chooser_gui("Merge Water Chains in molecule:",
lambda imol: coot_utils.merge_solvent_chains(imol)))
def mon_dict_func(text):
idealized = 0
new_model = coot.get_monomer_from_dictionary(text, idealized)
if not coot_utils.valid_model_molecule_qm(new_model):
coot.get_monomer(text)
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Monomer from Dictionary",
lambda func:
coot_gui.generic_single_entry("Pull coordinates from CIF dictionary for 3-letter-code:", "",
" Get Coords ",
lambda text: mon_dict_func(text)))
# -- N --
def new_mol_sphere_func1(imol, text):
try:
radius = float(text)
args = [imol] + coot_utils.rotation_centre() + [radius, 0]
coot.new_molecule_by_sphere_selection(*args)
except:
print("WARNING:: no valid radius", text)
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"New Molecule by Sphere...",
lambda func: coot_gui.generic_chooser_and_entry(
"Choose a molecule from which to select a sphere of atoms:",
"Radius:", "10.0",
lambda imol, text: new_mol_sphere_func1(imol, text)))
def new_mol_sym_func1(imol, text):
from types import ListType
pre_shift = origin_pre_shift(imol)
if (type(pre_shift) is not ListType):
print("bad pre-shift aborting")
else:
coot.new_molecule_by_symop(imol, text,
pre_shift[0],
pre_shift[1],
pre_shift[2])
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"New Molecule from Symmetry Op...",
lambda func: coot_gui.generic_chooser_and_entry(
"Molecule from which to generate a symmetry copy",
"SymOp", "X,Y,Z",
lambda imol, text: new_mol_sym_func1(imol, text)))
# --- P ---
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Phosphorylate this residue",
lambda func: coot_utils.phosphorylate_active_residue())
# ---- R ---------
# --- Ren ---
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Rename Residue...",
lambda func: coot_gui.rename_residue_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Renumber Waters...",
lambda func: coot_gui.molecule_chooser_gui(
"Renumber waters of which molecule?",
lambda imol: coot.renumber_waters(imol)))
# --- Reo ---
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Reorder Chains...",
lambda func: coot_gui.molecule_chooser_gui("Sort Chain IDs in molecule:",
lambda imol: coot.sort_chains(imol))) # an internal function
# --- Res ---
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Residue Type Selection...",
lambda func: coot_gui.generic_chooser_and_entry("Choose a molecule to select residues from: ","Residue Type:","",
lambda imol, text: (coot.new_molecule_by_residue_type_selection(imol, text),
coot.update_go_to_atom_window_on_new_mol())))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Residues with Alt Confs...",
lambda func: coot_gui.molecule_chooser_gui(
"Which molecule to check for Alt Confs?",
lambda imol: coot_gui.alt_confs_gui(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Residues with Cis Peptide Bonds...",
lambda func: coot_gui.molecule_chooser_gui("Choose a molecule for checking for Cis Peptides",
lambda imol: coot_gui.cis_peptides_gui(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Residues with Missing Atoms...",
lambda func: coot_gui.molecule_chooser_gui(
"Which molecule to check for Missing Atoms?",
lambda imol: coot_gui.missing_atoms_gui(imol)))
# --- Rig ---
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Rigid Body Fit Residue Ranges...",
lambda func:
coot_gui.residue_range_gui(lambda imol, ls: coot.rigid_body_refine_by_residue_ranges_py(imol, ls),
"Rigid Body Refine",
" Fit "))
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Rigid Body Fit Molecule...",
lambda func: coot_gui.molecule_chooser_gui("Rigid Body Fit Molecule",
lambda imol: coot.rigid_body_refine_by_atom_selection(imol, "//")))
# ---- S --------
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Superpose ligands",
lambda func: coot_gui.superpose_ligand_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"Symm Shift Reference Chain Here",
lambda func: coot.move_reference_chain_to_symm_chain_position())
# ---- W ---------
def whats_this():
central_residue = coot.active_residue_py()
res_name = coot.residue_name(*central_residue[0:4])
mol_no = central_residue[0]
n = coot.comp_id_to_name_py(res_name)
s = "(mol. no: " + str(mol_no) + ") " + \
res_name + ": " + \
n if isinstance(n, str) else " <no-name-found>"
coot.add_status_bar_text(s)
coot_gui.add_simple_coot_menu_menuitem(
submenu_modelling,
"What's this?",
lambda func: whats_this())
def add_calculate_ncs_menu(submenu_ncs):
#---------------------------------------------------------------------
# NCS functions
#
#---------------------------------------------------------------------
def copy_ncs_range_func(imol, chain_id, text1, text2):
try:
r1 = int(text1)
r2 = int(text2)
if (chain_id == ncs.ncs_master_chain_id(imol)):
coot.copy_residue_range_from_ncs_master_to_others(imol, chain_id, r1, r2)
else:
# different given master to current master
# ask what to do.
txt = "Current master chain is %s, but you asked to copy from %s.\n" \
%(ncs_master_chain_id(imol), chain_id)
txt += "Apply this master change?\n\n"
txt += "N.B. if no, then nothing is copied."
r = coot_gui.yes_no_dialog(txt, "Change Master")
if r:
coot.ncs_control_change_ncs_master_to_chain_id(imol, chain_id)
coot.copy_residue_range_from_ncs_master_to_others(imol, chain_id, r1, r2)
## could change master back?!
else:
coot.info_dialog("Master chain was not changed and copy not applied.")
except:
print("WARNING:: no valid number input")
coot_gui.add_simple_coot_menu_menuitem(
submenu_ncs,
"Copy NCS Residue Range...",
lambda func: coot_gui.generic_chooser_and_entry("Apply NCS Range from Master",
"Master Chain ID",
coot_utils.get_first_ncs_master_chain(), # returns "" on fail
lambda imol, chain_id: coot_gui.generic_double_entry("Start of Residue Number Range",
"End of Residue Number Range",
"", "", False, False,
"Apply NCS Residue Range",
lambda text1, text2: copy_ncs_range_func(imol, chain_id, text1, text2))))
def copy_ncs_chain_func(imol, chain_id):
ncs_chains = ncs_chain_ids(imol)
if (ncs_chains):
# maybe this could be a function to avoid repetition.
if (chain_id == ncs.ncs_master_chain_id(imol)):
# hunkey dorey
coot.copy_from_ncs_master_to_others(imol, chain_id)
else:
# different given master to current master
# ask what to do.
txt = "Current master chain is %s, but you asked to copy from %s.\n" \
%(ncs_master_chain_id(imol), chain_id)
txt += "Apply this master change?\n\n"
txt += "N.B. if no, then nothing is copied."
r = coot_gui.yes_no_dialog(txt, "Change Master")
if r:
coot.ncs_control_change_ncs_master_to_chain_id(imol, chain_id)
coot.copy_from_ncs_master_to_others(imol, chain_id)
## could change master back?!
else:
coot.info_dialog("Master chain was not changed and copy not applied.")
else:
s = "You need to define NCS operators for molecule " + str(imol)
coot.info_dialog(s)
coot_gui.add_simple_coot_menu_menuitem(
submenu_ncs,
"Copy NCS Chain...",
lambda func: coot_gui.generic_chooser_and_entry("Apply NCS edits from NCS Master Chain to Other Chains",
"Master Chain ID",
coot_utils.get_first_ncs_master_chain(), # can return "".
lambda imol, chain_id: copy_ncs_chain_func(imol, chain_id)))
def ncs_ghost_res_range_func(imol):
def handle_go_function(resno_1_text, resno_2_text):
cont = False
try:
resno_1 = int(resno_1_text)
resno_2 = int(resno_2_text)
cont = True
except:
print("WARNING:: input residue numbers have to be integers")
if cont:
ghost_ncs_chain_ids = ncs_chain_ids(imol)
if (type(ghost_ncs_chain_ids) is ListType):
# because we can have hetero-NCS,
# but we ignore NCS other that
# that of the first type.
ghost_chain_list = ghost_ncs_chain_ids[0]
ncs.manual_ncs_ghosts(imol, resno_1, resno_2, ghost_chain_list)
from types import ListType
label_1 = "Start ResNumber"
label_2 = "End ResNumber"
entry_1_default_text = "10"
entry_2_default_text = "20"
go_button_label = "Regenerate Ghosts"
coot_gui.generic_double_entry(label_1, label_2, entry_1_default_text,
entry_2_default_text, False, False,
go_button_label, handle_go_function)
coot_gui.add_simple_coot_menu_menuitem(
submenu_ncs,
"NCS Ghosts by Residue Range...",
lambda func: coot_gui.molecule_chooser_gui("Make local NCS ghosts for molecule:",
lambda imol: ncs_ghost_res_range_func(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_ncs,
"Update NCS Ghosts using Local Match",
lambda func: ncs.update_ncs_ghosts_by_local_sphere())
coot_gui.add_simple_coot_menu_menuitem(
submenu_ncs,
"NCS Jumping...",
lambda func: coot_gui.ncs_jumping_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_ncs,
"NCS ligands...",
lambda func: coot_gui.ncs_ligand_gui())
submenu = Gtk.Menu()
menuitem2 = Gtk.MenuItem("NCS matrix type...")
menuitem2.set_submenu(submenu)
submenu_ncs.append(menuitem2)
menuitem2.show()
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Accurate (SSM)",
lambda func: coot.set_ncs_matrix_type(0))
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Fast (LSQ)",
lambda func: coot.set_ncs_matrix_type(1))
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Extra Fast (LSQ, only every 2nd CA)",
lambda func: coot.set_ncs_matrix_type(2))
def add_draw_representations_menu(submenu_views):
# ---------------------------------------------------------------------
# Views/Representations
# ---------------------------------------------------------------------
#
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Undo Symmetry View",
lambda func: coot.undo_symmetry_view())
def make_ball_n_stick_func(imol, text):
bns_handle = coot.make_ball_and_stick(imol, text, 0.18, 0.3, 1)
print("handle: ", bns_handle)
global default_ball_and_stick_selection # maybe should be at the top of the file
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Ball & Stick...",
lambda func: coot_gui.generic_chooser_and_entry("Ball & Stick",
"Atom Selection:",
default_ball_and_stick_selection,
lambda imol, text: make_ball_n_stick_func(imol, text)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Add Balls to Simple Sticks",
lambda func: [set_draw_stick_mode_atoms(imol, 1) for imol in coot_utils.molecule_number_list()])
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Simple Sticks (No Balls)",
lambda func: [set_draw_stick_mode_atoms(imol, 0) for imol in coot_utils.molecule_number_list()])
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Clear Ball & Stick...",
lambda func: coot_gui.molecule_chooser_gui(
"Choose a molecule from which to clear Ball&Stick objects",
lambda imol: coot.clear_ball_and_stick(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Electrostatic Surface...",
lambda func: coot_gui.molecule_chooser_gui(
"Choose a molecule to represent as a surface..." + \
"\n" + \
"Can be SLOW",
lambda imol: coot.do_surface(imol, 1))) # shall we switch on the light too?!
def surface_func1(clipped = 0):
active_atom = active_residue()
aa_imol = active_atom[0]
aa_chain_id = active_atom[1]
aa_res_no = active_atom[2]
aa_ins_code = active_atom[3]
aa_atom_name = active_atom[4]
aa_alt_conf = active_atom[5]
central_residue = active_residue()
residues = residues_near_residue(aa_imol, central_residue[1:4], 6.0)
# no waters in surface, thanks.
# but what if they have different names?! (only HOH so far)
filtered_residues = []
for res in residues:
if (coot.residue_name(aa_imol, *res) != "HOH"):
filtered_residues.append(res)
imol_copy = coot.copy_molecule(aa_imol)
# delete the interesting residue from the copy (so that
# it is not surfaced).
coot.delete_residue(imol_copy, aa_chain_id, aa_res_no, aa_ins_code)
if clipped:
coot.do_clipped_surface(imol_copy, filtered_residues)
else:
coot.do_surface(imol_copy, 1)
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Clipped Surface Here (This Residue)",
lambda func:
surface_func1(1))
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Full Surface Around Here (This Residue)",
lambda func:
surface_func1())
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Un-Surface...",
lambda func: coot_gui.molecule_chooser_gui(
"Choose a molecule to represent conventionally...",
lambda imol: coot.do_surface(imol, 0)))
def hilight_site_func():
active_atom = active_residue()
if (active_atom):
imol = active_atom[0]
centre_residue_spec = [active_atom[1],
active_atom[2],
active_atom[3]]
coot_utils.hilight_binding_site(imol, centre_residue_spec, 230,4)
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Highlight Interesting Site (here)...",
lambda func: hilight_site_func())
def make_dot_surf_func(imol,text):
# I think a single colour is better than colour by atom
coot.set_dots_colour(imol, 0.5, 0.5, 0.5)
coot.dots_handle = dots(imol, text, text, 2, 1)
print("dots handle: ", dots_handle)
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Dotted Surface...",
lambda func: coot_gui.generic_chooser_and_entry("Surface for molecule",
"Atom Selection:", "//A/1-2",
lambda imol, text: make_dot_surf_func(imol, text)))
def clear_dot_surf_func(imol,text):
try:
n = int(text)
coot.clear_dots(imol,n)
except:
print("BL WARNING:: dots handle number shall be an integer!!")
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Clear Surface Dots...",
lambda func: coot_gui.generic_chooser_and_entry("Molecule with Dotted Surface",
"Dots Handle Number:", "0",
lambda imol, text: clear_dot_surf_func(imol, text)))
def limit_model_disp_func(text):
try:
f = float(text)
if f < 0.1:
coot.set_model_display_radius(0, 10)
else:
coot.set_model_display_radius(1, f)
except:
coot.set_model_display_radius(0, 10)
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Limit Model Display Radius...",
lambda func: coot_gui.generic_single_entry("Display Radius Limit (0 for \'no limit\') ",
# "15.0" ;; maybe this should be the map radius
# BL says:: I think it should be the current one
str(coot.get_map_radius()),
"Set: ",
lambda text: limit_model_disp_func(text)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"HOLE...",
lambda func: test_hole.hole_ify())
coot_gui.add_simple_coot_menu_menuitem(
submenu_representation,
"Label All CAs...",
lambda func: coot_gui.molecule_chooser_gui("Choose a molecule to label",
lambda imol: coot_utils.label_all_CAs(imol)))
#---------------------------------------------------------------------
# 3D annotations
#---------------------------------------------------------------------
submenu = Gtk.Menu()
menuitem2 = Gtk.MenuItem("3D Annotations...")
menuitem2.set_submenu(submenu)
submenu_representation.append(menuitem2)
menuitem2.show()
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Annotate position...",
lambda func: coot_gui.generic_single_entry("Annotation: ", "",
"Make Annotation",
lambda txt: coot_utils.add_annotation_here(txt)))
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Save Annotations...",
lambda func: coot_gui.generic_single_entry("Save Annotations",
"coot_annotations.py",
" Save ",
lambda file_name: coot_utils.save_annotations(file_name)))
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Load Annotations...",
lambda func: coot_gui.generic_single_entry("Load Annotations",
"coot_annotations.py",
" Load ",
lambda file_name: coot_utils.load_annotations(file_name)))
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Remove annotation here",
lambda func: coot_utils.remove_annotation_here())
coot_gui.add_simple_coot_menu_menuitem(
submenu,
"Remove annotation near click",
lambda func: coot_utils.remove_annotation_at_click())
def add_draw_views_menu(submenu_views):
coot_gui.add_simple_coot_menu_menuitem(
submenu_views,
"Add View...",
lambda func: coot_gui.view_saver_gui())
# BL says:: maybe check if number at some point
coot_gui.add_simple_coot_menu_menuitem(
submenu_views,
"Add a Spin View...",
lambda func: coot_gui.generic_double_entry("Number of Steps",
"Number of Degrees (total)", "3600", "360",
False, False, #check button text and callback
" Add Spin ",
lambda text_1, text_2: coot.add_spin_view("Spin", int(text_1), float(text_2))))
coot_gui.add_simple_coot_menu_menuitem(
submenu_views,
"Views Panel...",
lambda func: coot_gui.views_panel_gui())
coot_gui.add_simple_coot_menu_menuitem(
submenu_views,
"Play Views",
lambda func: list(map(eval,["go_to_first_view(1)",
"time.sleep(1)", "play_views()"])))
# BL says:: maybe check if number at some point
coot_gui.add_simple_coot_menu_menuitem(
submenu_views, "Set Views Play Speed...",
lambda func: coot_gui.generic_single_entry("Set Views Play Speed",
str(coot.views_play_speed()), " Set it ",
lambda text: coot.set_views_play_speed(float(text))))
coot_gui.add_simple_coot_menu_menuitem(
submenu_views, "Save Views...",
lambda func: coot_gui.generic_single_entry("Save Views",
"coot-views.py", " Save ",
lambda txt: coot.save_views(txt)))
def add_calculate_pisa_menu(submenu_pisa):
# ---------------------------------------------------------------------
# PISA Interface and Assemblies
# ---------------------------------------------------------------------
coot_gui.add_simple_coot_menu_menuitem(
submenu_pisa, "PISA Assemblies...",
lambda func:
coot_gui.molecule_chooser_gui("Choose molecule for PISA assembly analysis",
lambda imol:
parse_pisa_xml.pisa_assemblies(imol)))
coot_gui.add_simple_coot_menu_menuitem(
submenu_pisa, "PISA Interfaces...",
lambda func:
coot_gui.molecule_chooser_gui("Choose molecule for PISA interface analysis",
lambda imol:
parse_pisa_xml.pisa_interfaces(imol)))
#---------------------------------------------------------------------
# Run those functions to populate the menus
#---------------------------------------------------------------------
add_calculate_modules_menu(submenu_modules)
add_calculate_maps_menu(submenu_maps)
add_calculate_modelling_menu(submenu_modelling)
add_calculate_ncs_menu(submenu_ncs)
add_edit_settings_menu(submenu_settings)
add_draw_representations_menu(submenu_representation)
add_draw_views_menu(submenu_views)
add_calculate_pisa_menu(submenu_pisa)
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