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import gi
gi.require_version('Gtk', '4.0')
from gi.repository import Gtk
import coot
import coot_gui_api
import coot_utils
import coot_gui
def chain_refine(imol, ch_id):
residue_list = coot_utils.residues_in_chain(imol, ch_id)
coot.refine_residues_py(imol, residue_list)
# this might be a coot_gui function now
def coot_menubar_menu(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 add_module_refine():
menu_refine = coot_menubar_menu("Refine")
def all_atom_refine_func():
active_atom = coot.active_residue_py()
if active_atom:
imol = active_atom[0]
residue_list = coot_utils.all_residues(imol)
coot.refine_residues_py(imol, residue_list)
def chain_refine_func():
active_atom = coot.active_residue_py()
if active_atom:
imol = active_atom[0]
ch_id = active_atom[1]
chain_refine(imol, ch_id)
def refine_active_fragment_func():
active_atom = coot.active_residue_py()
if active_atom:
imol = active_atom[0]
ch_id = active_atom[1]
residue_list = coot.linked_residues_py(res_spec, imol, 1.7)
coot.refine_residues_py(imol, residue_list)
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "All-atom Refine", lambda arg: all_atom_refine_func())
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "Chain Refine", lambda arg: chain_refine_func())
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "Refine Fragment", lambda arg: chain_refine_func())
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "Contact Dots On", lambda arg: coot.set_do_coot_probe_dots_during_refine(1))
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "Contact Dots Off", lambda arg: coot.set_do_coot_probe_dots_during_refine(0))
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "Rotamer Markup On", lambda arg: coot.set_show_intermediate_atoms_rota_markup(1))
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "Rotamer Markup Off", lambda arg: coot.set_show_intermediate_atoms_rota_markup(0))
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "Refine Rotamers On", lambda arg: coot.set_refine_rotamers(1))
coot_gui.add_simple_coot_menu_menuitem(menu_refine, "Refine Rotamers Off", lambda arg: coot.set_refine_rotamers(0))
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