import gi gi.require_version('Gtk', '4.0') from gi.repository import Gtk import coot import coot_gui import coot_gui_api import coot_utils import add_linked_cho def interactive_add_cho_dialog(): def dummy_func(): print("dummy_func()") pass def refine_tree_func(): with coot_utils.UsingActiveAtom(True) as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf, aa_res_spec]: refine_residues(aa_imol, glyco_tree_residues(aa_imol, aa_res_spec)) add_linked_cho.add_synthetic_pyranose_planes() add_linked_cho.use_unimodal_pyranose_ring_torsions() # button list with [label, function] buttons = [ ["Update for Current Residue", lambda _btn: dummy_func()], # dummy_func replaced later ["Refine Tree", lambda _btn: refine_tree_func()], ["Add a NAG-ASN NAG", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("NAG", "NAG-ASN")], ["Add a BETA1-4 NAG", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("NAG", "BETA1-4")], ["Add a BETA1-4 BMA", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("BMA", "BETA1-4")], ["Add an ALPHA1-2 MAN", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("MAN", "ALPHA1-2")], ["Add an ALPHA1-3 MAN", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("MAN", "ALPHA1-3")], ["Add an ALPHA2-3 MAN", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("MAN", "ALPHA2-3")], ["Add an ALPHA2-3 GAL", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("GAL", "ALPHA2-3")], ["Add an ALPHA1-6 MAN", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("MAN", "ALPHA1-6")], ["Add a BETA1-2 NAG", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("NAG", "BETA1-2")], ["Add a BETA1-4 GAL", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("GAL", "BETA1-4")], ["Add an ALPHA1-2 FUC", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("FUC", "ALPHA1-2")], ["Add an ALPHA1-3 FUC", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("FUC", "ALPHA1-3")], ["Add an ALPHA1-6 FUC", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("FUC", "ALPHA1-6")], ["Add an BETA1-6 FUL", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("FUL", "BETA1-6")], ["Add an XYP-BMA XYP", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("XYP", "XYP-BMA")], ["Add an ALPHA2-3 SIA", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("SIA", "ALPHA2-3")], ["Add an ALPHA2-6 SIA", lambda _btn: add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("SIA", "ALPHA2-6")] ] vbox = coot_gui.dialog_box_of_buttons("Add N-linked Glycan", [420, 600], buttons, "Close")[0] gui_add_linked_cho_dialog_vbox_set_rotation_centre_hook(vbox) # set the callback on the first button first_button = vbox.get_first_child() if first_button: first_button.connect("clicked", lambda _btn: gui_add_linked_cho_dialog_vbox_set_rotation_centre_hook(vbox)) # add a widget to allow the user to choose the tree type #table = Gtk.Table(3, 2, False) table = Gtk.Grid() butt_1 = Gtk.CheckButton(label = "High Mannose") butt_2 = Gtk.CheckButton(group = butt_1, label = "Hybrid (Mammal)") # butt_3 = Gtk.CheckButton(group = butt_1, label = "Hybrid (Plant)") butt_4 = Gtk.CheckButton(group = butt_1, label = "Complex (Mammal)") butt_5 = Gtk.CheckButton(group = butt_1, label = "Complex (Plant)") butt_6 = Gtk.CheckButton(group = butt_1, label = "Expert User Mode") # this is now how we do it these days. FIXME-PE # # add buttons for nice(?) layout/order # table.attach(butt_1, 0, 1, 0, 1, Gtk.EXPAND|Gtk.FILL, Gtk.EXPAND|Gtk.FILL, 0, 0) # high mannose # table.attach(butt_4, 1, 2, 0, 1, Gtk.EXPAND|Gtk.FILL, Gtk.EXPAND|Gtk.FILL, 0, 0) # complex mammal # table.attach(butt_6, 0, 1, 1, 2, Gtk.EXPAND|Gtk.FILL, Gtk.EXPAND|Gtk.FILL, 0, 0) # Expert # # table.attach(butt_3, 1, 2, 1, 2, Gtk.EXPAND|Gtk.FILL, Gtk.EXPAND|Gtk.FILL, 0, 0) # table.attach(butt_5, 1, 2, 1, 2, Gtk.EXPAND|Gtk.FILL, Gtk.EXPAND|Gtk.FILL, 0, 0) # complex plant # table.attach(butt_2, 2, 3, 0, 1, Gtk.EXPAND|Gtk.FILL, Gtk.EXPAND|Gtk.FILL, 0, 0) # hybrid mammal vbox.append(table) #vbox.reorder_child(table, 0) #vbox.reorder_child_after(table,vbox.get_first_child()) for butt in [butt_1, butt_2, butt_4, butt_5, butt_6]: butt.connect("toggled", lambda func: gui_add_linked_cho_dialog_vbox_set_rotation_centre_hook(vbox)) vbox.show() # "global" var post-set-rotation-centre-hook # BL Note:: maybe should be a global!? global post_set_rotation_centre_script def post_set_rotation_centre_script(): gui_add_linked_cho_dialog_vbox_set_rotation_centre_hook(vbox) def glyco_tree_dialog_set_button_active_state(button, glyco_id, tree_type): def glyco_id2level_number(glyco_id): return glyco_id[0] def glyco_id2prime_arm_sym(glyco_id): return glyco_id[1] def glyco_id2residue_type(glyco_id): return glyco_id[2] def glyco_id2link_type(glyco_id): return glyco_id[3] def glyco_id2paren_residue_type(glyco_id): return glyco_id[4] def glyco_id2residue_spec(glyco_id): return glyco_id[5] def get_sensitive_button_list(glyco_id, tree_type): if not isinstance(glyco_id, list): return [] else: level_number = glyco_id2level_number(glyco_id) prim_arm_sym = glyco_id2prime_arm_sym(glyco_id) residue_type = glyco_id2residue_type(glyco_id) link_type = glyco_id2link_type(glyco_id) parent_residue_type = glyco_id2paren_residue_type(glyco_id) residue_spec = glyco_id2residue_spec(glyco_id) active_button_label_ls = [] if tree_type == 'expert-user-mode': active_button_label_ls = "expert-user-mode" # ??? # ----------------------------------------------------------------------------------- # Note the trees tested here match those from (get-tree-type) which examines the button # label of the active radio button in the dialog (these are not the auto-build trees) # ------------------------------------------------------------------------------------ # BL says:: test and control the trees if tree_type == 'oligomannose': if level_number == 0: if residue_type == "ASN": active_button_label_ls = ["Add a NAG-ASN NAG"] if level_number == 1: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 NAG"] if level_number == 2: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 BMA"] if level_number == 3: if residue_type == "BMA": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN"] if level_number == 4: if residue_type == "MAN": if link_type == "ALPHA1-3": active_button_label_ls = ["Add an ALPHA1-2 MAN"] if link_type == "ALPHA1-6": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN"] if level_number == 5: if residue_type == "MAN": # active_button_label_ls is the same, so no if required? # or wrong tree branches. FIXME. if link_type == "ALPHA1-2": active_button_label_ls = ["Add an ALPHA1-2 MAN"] if link_type == "ALPHA1-6": active_button_label_ls = ["Add an ALPHA1-2 MAN"] if link_type == "ALPHA1-3": active_button_label_ls = ["Add an ALPHA1-2 MAN"] if level_number == 6: if residue_type == "MAN": if link_type == "ALPHA1-2": active_button_label_ls = ["Add an ALPHA1-3 GLC"] # inconsistencies between links here. FIXME if level_number == 7: if residue_type == "GLC": if link_type == "ALPHA1-2": active_button_label_ls = ["Add an ALPHA1-3 GLC"] if level_number == 8: if residue_type == "GLC": if link_type == "ALPHA1-2": active_button_label_ls = ["Add an ALPHA1-2 GLC"] # hybrid mammal if tree_type == 'hybrid-mammal': if level_number == 0: if residue_type == "ASN": active_button_label_ls = ["Add a NAG-ASN NAG"] if level_number == 1: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 NAG", "Add an ALPHA1-3 FUC"] if level_number == 2: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 BMA"] if level_number == 2: if residue_type == "FUC": active_button_label_ls = ["Add a BETA1-4 GAL"] if level_number == 3: if residue_type == "BMA": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN"] if level_number == 3: if residue_type == "GAL": active_button_label_ls = ["Add an ALPHA1-2 FUC"] if level_number == 4: if residue_type == "MAN": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN", "Add a BETA1-2 NAG"] if level_number == 5: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 GAL"] if level_number == 5: if residue_type == "GAL": active_button_label_ls = ["Add an ALPHA2-3 SIA", "Add an ALPHA2-6 SIA"] # hybrid plant if tree_type == 'hybrid-plant': if level_number == 0: if residue_type == "ASN": active_button_label_ls = ["Add a NAG-ASN NAG"] if level_number == 1: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 NAG", "Add an ALPHA1-3 FUC"] if level_number == 2: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 BMA"] if level_number == 2: if residue_type == "FUC": active_button_label_ls = ["Add a BETA1-4 GAL"] if level_number == 3: if residue_type == "BMA": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN", "Add an XYP-BMA XYP"] if level_number == 3: if residue_type == "GAL": active_button_label_ls = ["Add an ALPHA1-2 FUC"] # note that level-number is not enough for complete disambiguation, # we need to know we are 4 or 4' (Vliegenthart et al 1983 nomenclature). if level_number == 4: if residue_type == "MAN": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN", "Add a BETA1-2 NAG"] if level_number == 5: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 GAL"] if level_number == 5: if residue_type == "GAL": active_button_label_ls = ["Add an ALPHA2-3 SIA", "Add an ALPHA2-6 SIA"] # complex mammal # if tree_type == 'complex-mammal': if level_number == 0: if residue_type == "ASN": active_button_label_ls = ["Add a NAG-ASN NAG"] if level_number == 1: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 NAG", "Add an ALPHA1-6 FUC"] if level_number == 2: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 BMA"] if level_number == 3: if residue_type == "BMA": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN", "Add a BETA1-4 NAG"] # note that level-number is not enough for complete disambiguation, # we need to know we are 4 or 4' (Vl...? nomenclature). # if level_number == 4: if residue_type == "MAN": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN", "Add a BETA1-2 NAG"] if level_number == 5: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 GAL"] if level_number == 6: if residue_type == "GAL": active_button_label_ls = ["Add an ALPHA2-3 SIA", "Add an ALPHA2-6 SIA"] # complex plant # if tree_type == 'complex-plant': if level_number == 0: if residue_type == "ASN": active_button_label_ls = ["Add a NAG-ASN NAG"] if level_number == 1: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 NAG", "Add an ALPHA1-3 FUC", "Add an ALPHA1-6 FUC"] if level_number == 2: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 BMA"] if level_number == 3: if residue_type == "BMA": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN", "Add an XYP-BMA XYP", "Add a BETA1-4 NAG"] if level_number == 4: if residue_type == "MAN": active_button_label_ls = ["Add an ALPHA1-3 MAN", "Add an ALPHA1-6 MAN", "Add a BETA1-2 NAG"] if level_number == 5: if residue_type == "NAG": active_button_label_ls = ["Add a BETA1-4 GAL"] if level_number == 6: if residue_type == "GAL": active_button_label_ls = ["Add an ALPHA2-3 SIA", "Add an ALPHA2-6 SIA"] return active_button_label_ls # main line # l = button.get_label() active_button_label_ls = get_sensitive_button_list(glyco_id, tree_type) if (active_button_label_ls == "expert-user-mode"): button.set_sensitive(True) else: if not (l == "Update for Current Residue") and not (l == "Refine Tree"): button.set_sensitive(l in active_button_label_ls) def gui_add_linked_cho_dialog_vbox_set_rotation_centre_hook(vbox): """ vbox is the vbox of the dialog box of buttons. One of the children of the vbox is the table that contains the buttons """ def get_tree_type(): tree_type = "oligomannose" child = vbox.get_first_child() def iterate(): child = vbox.get_next_sibling() return child is not None while iterate(): if type(child) == Gtk.Table: for table_child in child: if type(table_child) == Gtk.CheckButton: if table_child.get_active(): l = table_child.get_label() # this is a bit ugly because we are testing that these strings # match button labels (set in interactive-add-cho-dialog) if l == "High Mannose": tree_type = 'oligomannose' if l == "Hybrid (Mammal)": tree_type = 'hybrid-mammal' if l == "Hybrid (Plant)": tree_type = 'hybrid-plant' if l == "Expert User Mode": tree_type = 'expert-user-mode' if l == "Complex (Mammal)": tree_type = 'complex-mammal' if l == "Complex (Plant)": tree_type = 'complex-plant' return tree_type with coot_utils.UsingActiveAtom(True) as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf, aa_res_spec]: glyco_id = coot.glyco_tree_residue_id_py(aa_imol, aa_res_spec) # Paule says: # if it was an ASP create a level-0 glyco-id for that (glyco-tree-residue-id doesn't # do that (not sure why)). if not glyco_id: rn = coot.residue_name(aa_imol, aa_chain_id, aa_res_no, aa_ins_code) if isinstance(rn, str): if rn == "ASN": glyco_id = [0, "unset", "ASN", "", "", aa_res_spec] if isinstance(glyco_id, list): tree_type = get_tree_type() for child in vbox: if (type(child) == Gtk.Button): glyco_tree_dialog_set_button_active_state(child, glyco_id, tree_type) return True return False # There is some graphics to the validation here, so keep it in the graphics part # wont be missed in the non-grpahical part for now, I think (BL that is). # this has to be at the top level for reasons that I don't understand # (python function scoping) - I'll just put it down to python being shit as usual. # def glyco_validation_dialog_set_go_to_residue(imol, residue_spec): rc = residue_centre(imol, res_spec_utils.residue_spec_to_chain_id(residue_spec), res_spec_utils.residue_spec_to_res_no(residue_spec), '') coot.set_rotation_centre(*rc) def load_privateer_dictionary(): if os.path.exists("privateer-lib.cif"): coot.read_cif_dictionary("privateer-lib.cif") coot.set_refine_with_torsion_restraints(1) class glyco_validate: def run_privateer(self, imol, glyco_tree_residues, hklin_fn, fp_col, sigfp_col, pdbin_fn, privateer_log): if coot.is_valid_model_molecule(imol): args = ['-mtzin', hklin_fn, '-colin-fo', fp_col+','+sigfp_col, '-pdbin', pdbin_fn] # using'-mode', 'ccp4i2' makes a file with no residue nambers (afaics) coot_utils.popen_command("privateer", args, [], privateer_log, False) def make_privateer_validation_info(self, imol, fp_col, sigfp_col, glyco_tree_residues): imol_map = coot.imol_refinement_map() if len(glyco_tree_residues) > 0: d = coot_utils.get_directory("coot-ccp4") spid = str(os.getpid()) fn_pdb = "coot-privateer-" + spid + ".pdb" fn_log = "coot-privateer-" + spid + ".log" privateer_pdb = os.path.join(d, fn_pdb) privateer_log = os.path.join(d, fn_log) hklin_fn = coot.mtz_file_name(imol_map); coot.write_pdb_file(imol, privateer_pdb) self.run_privateer(imol, glyco_tree_residues, hklin_fn, fp_col, sigfp_col, privateer_pdb, privateer_log) pvi = self.parse_privateer_log(privateer_log, imol, glyco_tree_residues) return pvi else: return [] # return a list of residues with privateer validation info # def parse_privateer_log(self, log_file_name, imol, glyco_tree_residues): print('parse_privateer_log', log_file_name, imol, glyco_tree_residues) pvi = [] f = open(log_file_name) lines = f.readlines() f.close() for line in lines: l = line.rstrip() if len(l) > 10: if l[:4] == 'coot': words = l.split() if len(words) > 12: for r in glyco_tree_residues: rn = residue_name_by_spec(imol, r) try: res_id = rn + "-" + res_spec_utils.residue_spec_to_chain_id(r) + \ '-' + str(coot_utils.residue_spec_to_res_no(r)) # print "res_id", res_id if words[1] == res_id: # print words[12] , yes or check new_item = (r, words) pvi.append(new_item) except TypeError as e: print(e) print("parsed", log_file_name) return pvi def make_validation_dialog(self, imol, privateer_validation_info): print("make_validation_dialog", privateer_validation_info) buttons = [] for vi in privateer_validation_info: residue_spec = vi[0] words = vi[1] state = words[12] if state == "yes": state = " OK " # label spacing button_text = words[1] + " Q=" + words[3] + " RSCC=" + words[6] + \ " Cnf=" + words[8] + " " + state # string->function? Hideous func = "glyco_validation_dialog_set_go_to_residue(" + str(imol) + "," + \ str(residue_spec) + ")" button = [button_text, func] buttons.append(button) if len(buttons) > 0: button = ["Load Privateer Dictionary", "load_privateer_dictionary()"] buttons.append(button) coot_gui.dialog_box_of_buttons("Privateer Validation", (400, 220), buttons, " Close ") def validation_dialog(self): active_atom = coot.active_residue_py() try: imol = active_atom[0] active_residue = active_atom[:4] glyco_tree_residues = coot.glyco_tree_residues_py(imol, active_residue) print('imol', imol) print('active_residue', active_residue) print('glyco_tree_residues', glyco_tree_residues) fp_col='FP' sigfp_col='SIGFP' pvi = self.make_privateer_validation_info(imol, fp_col, sigfp_col, glyco_tree_residues) # print "validation_dialog()", pvi if len(pvi) > 0: # now make a gui self.make_validation_dialog(imol, pvi) except KeyError as e: print(e) # no active atom except TypeError as e: print(e) def auto_delete_residues_internal(self, imol, glyco_tree_residues): fp_col='FP' sigfp_col='SIGFP' pvi = self.make_privateer_validation_info(imol, fp_col, sigfp_col, glyco_tree_residues) for res_info in pvi: print("test", res_info) res_status = res_info[1][12] if res_status == 'check' or res_status == 'no': coot_utils.delete_residue_by_spec(imol, res_info[0]) def auto_delete_residues(self): try: active_atom = coot.active_residue_py() imol = active_atom[0] active_residue = active_atom[:4] glyco_tree_residues = coot.glyco_tree_residues_py(imol, active_residue) self.auto_delete_residues_internal(imol, glyco_tree_residues) except TypeError as e: print(e) # graphics... def add_module_carbohydrate_gui(): menu = coot_gui.attach_module_menu_button("Glyco") coot_gui.add_simple_action_to_menu( menu, "N-linked Glycan Addition...","interactive_add_cho_dialog", lambda _simple_action, _two: interactive_add_cho_dialog()) def add_multi_carbo_link_func(link_list): with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: add_linked_cho.multi_add_linked_residue(aa_imol, [aa_chain_id, aa_res_no, aa_ins_code], link_list) def set_default_cho_b_factor_func(): with coot_utils.UsingActiveAtom(True) as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf, aa_res_spec]: residues = coot.residues_near_residue_py(aa_imol, aa_res_spec, 10) imol_region = coot.new_molecule_by_residue_specs(aa_imol, residues) # BL says:: why not do a new mol by sphere selection?! m = coot.median_temperature_factor(imol_region) coot.close_molecule(imol_region) if coot_utils.isNumber(m): new_m = m* 1.55 coot.set_default_temperature_factor_for_new_atoms(new_m) s = "New Temperature Factor set to " + str(new_m) coot.info_dialog(s) coot_gui.add_simple_action_to_menu( menu, "Set Default N-linked CHO Atoms B-factor","set_default_cho_b_factor", lambda _simple_action, _two: set_default_cho_b_factor_func() ) coot_gui.add_simple_action_to_menu( menu, "N-link add NAG, NAG, BMA","multi_carbo_link_NAG_NAG_BMA", lambda _simple_action, _two: add_multi_carbo_link_func([["NAG", "NAG-ASN"], ["NAG", "BETA1-4"], ["BMA", "BETA1-4"]])) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add a ASN-NAG NAG", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("NAG", "NAG-ASN")) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add a BETA1-4 NAG", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("NAG", "BETA1-4")) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add a BETA1-4 BMA", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("BMA", "BETA1-4")) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add an ALPHA1-2 MAN", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("MAN", "ALPHA1-2")) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add an ALPHA1-3 MAN", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("MAN", "ALPHA1-3")) # we should do this only if we are sitting on an SIA. # Attaching a SIA to a MAN (i.e. reverse order) would be a # good test too... # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add an ALPHA2-3 MAN", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("MAN", "ALPHA2-3")) # # same consideration as above # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add an ALPHA2-3 GAL", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("GAL", "ALPHA2-3")) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add an ALPHA1-6 MAN", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("MAN", "ALPHA1-6")) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add an ALPHA1-3 FUC", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("FUC", "ALPHA1-3")) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add an ALPHA1-6 FUC", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("FUC", "ALPHA1-6")) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Add an XYP-BMA XYP", # lambda _simple_action, _two: # add_linked_cho.add_linked_residue_with_extra_restraints_to_active_residue("XYP", "XYP-BMA")) # the mode in the function call now takes take of this # coot_gui.add_simple_coot_menu_menuitem( # menu, "Auto Fit & Refine On for Link Addition", # lambda _simple_action, _two: coot.set_add_linked_residue_do_fit_and_refine(1)) # coot_gui.add_simple_coot_menu_menuitem( # menu, "Auto Fit & Refine Off for Link Addition", # lambda _simple_action, _two: coot.set_add_linked_residue_do_fit_and_refine(0)) def add_oligo_tree_func(oligo_tree): with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: coot.make_backup(aa_imol) # switch backup off?! add_linked_cho.add_linked_residue_tree(aa_imol, [aa_chain_id, aa_res_no, aa_ins_code], oligo_tree) coot_gui.add_simple_action_to_menu( menu, "Add High Mannose","add_high_mannose", lambda _simple_action, _two: add_oligo_tree_func(add_linked_cho.oligomannose_tree())) coot_gui.add_simple_action_to_menu( menu, "Add Hybrid (Mammal)","add_hybrid_mammal", lambda _simple_action, _two: add_oligo_tree_func(add_linked_cho.hybrid_mammal_tree())) # in practice, no one will be doing this. # coot_gui.add_simple_action_to_menu( # menu, "Add Hybrid (Plant)", # lambda _simple_action, _two: add_oligo_tree_func(add_linked_cho.hybrid_plant_derived_tree())) coot_gui.add_simple_action_to_menu( menu, "Add Complex (Mammal)","add_complex_mammal", lambda _simple_action, _two: add_oligo_tree_func(add_linked_cho.complex_mammal_tree())) coot_gui.add_simple_action_to_menu( menu, "Add Complex (Plant)","add_complex_plant", lambda _simple_action, _two: add_oligo_tree_func(add_linked_cho.complex_plant_tree())) coot_gui.add_simple_action_to_menu( menu, "Delete All Carbohydrate","delete_all_cho", lambda _simple_action, _two: add_linked_cho.delete_all_cho()) def torsion_fit_this_func(refine = False): with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: centre_residue = [aa_chain_id,aa_res_no, aa_ins_code] coot.multi_residue_torsion_fit(aa_imol, [centre_residue], 30000) if refine: with AutoAccept(): refine_residues(aa_imol, [centre_residue]) def torsion_fit_this_and_neighbours_func(refine = False): with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: centre_residue = [aa_chain_id,aa_res_no, aa_ins_code] residues = coot.residues_near_residue_py(aa_imol, centre_residue, 1.9) residues.append(centre_residue) coot.multi_residue_torsion_fit(aa_imol, residues, 30000) if refine: with AutoAccept(): refine_residues(aa_imol, [centre_residue]) coot_gui.add_simple_action_to_menu( menu, "Torsion Fit this residue","torsion_fit_this", lambda _simple_action, _two: torsion_fit_this_func()) # coot_gui.add_simple_action_to_menu( # menu, "Torsion Fit This Residue and Neighbours", # lambda _simple_action, _two: torsion_fit_this_and_neighbours_func()) coot_gui.add_simple_action_to_menu( menu, "Torsion Fit & Refine this residue","torsion_fit_refine_this", lambda _simple_action, _two: torsion_fit_this_func(True)) coot_gui.add_simple_action_to_menu( menu, "Add synthetic pyranose plane restraints","add_synthetic_pyranose_planes", lambda _simple_action, _two: add_linked_cho.add_synthetic_pyranose_planes()) coot_gui.add_simple_action_to_menu( menu, "Use Unimodal ring torsion restraints","use_unimodal_pyranose_ring_torsions", lambda _simple_action, _two: add_linked_cho.use_unimodal_pyranose_ring_torsions()) # This should probably become a checkbox?? # note: this is duplicated in Restraints coot_gui.add_simple_action_to_menu( menu, "Display Extra Restraints","cho__display_extra_restraints", lambda _simple_action, _two: coot_utils.using_active_atom(set_show_extra_restraints, "aa_imol", 1)) coot_gui.add_simple_action_to_menu( menu, "Undisplay Extra Restraints","cho__undisplay_extra_restraints", lambda _simple_action, _two: coot_utils.using_active_atom(set_show_extra_restraints, "aa_imol", 0)) coot_gui.add_simple_action_to_menu( menu, "Extract this Tree","new_molecule_from_this_glyco_tree", lambda _simple_action, _two: add_linked_cho.new_molecule_from_this_glyco_tree())