1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
|
# Copyright 2007 by Bernhard Lohkamp
# Copyright 2006, 2007 by The University of York
# 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
# import gtk
# import pango
import gi
gi.require_version("Gtk", "4.0")
from gi.repository import Gtk
import time
import os
import coot
import coot_utils
import coot_gui
import coot_gui_api
import generic_objects
# put all coot svgs in the default icon set
def register_coot_icons():
import glob
# iconfactory = Gtk.IconFactory()
# stock_ids = Gtk.stock_list_ids()
pixbuf_dir = os.getenv('COOT_PIXMAPS_DIR')
if (not pixbuf_dir):
pixbuf_dir = os.path.join(coot.get_pkgdatadir_py(), "pixmaps")
patt = os.path.normpath(pixbuf_dir + '/*.svg')
coot_icon_filename_ls = glob.glob(patt)
icon_info_ls = []
for full_name in coot_icon_filename_ls:
name = os.path.basename(full_name)
icon_info_ls.append([name, full_name])
if False:
for stock_id, filename in icon_info_ls:
# print("# register icon:", stock_id, filename)
# only load image files when our stock_id is not present
if ((stock_id not in stock_ids) and not ('phenixed' in filename)):
if os.path.isfile(filename):
pixbuf = Gtk.gdk.pixbuf_new_from_file(filename)
iconset = Gtk.IconSet(pixbuf)
iconfactory.add(stock_id, iconset)
iconfactory.add_default()
# adds a SeparatorToolItem to the coot_main_toolbar (by default at the
# last position). Return the separator or False. If there is a
# separator in the last position, dont add it
#
def add_coot_toolbar_separator():
"""adds a SeparatorToolItem to the coot_main_toolbar (by default at the
last position). There is no return value currently.
"""
try:
coot_main_toolbar = coot_gui_api.main_toolbar()
except:
print("""ERROR:: coot_gui_api module not available""")
return False
# main body
toolbar_items = coot_main_toolbar.get_children()
if (type(toolbar_items[-1]) != Gtk.SeparatorToolItem):
# only add if last one is not already separator
sep = Gtk.SeparatorToolItem()
coot_main_toolbar.insert(sep, -1)
sep.show()
return sep
else:
return False
if True: # test for python
if coot_gui_api.main_toolbar():
register_coot_icons()
def activate_menuitem(widget, item):
try:
# apply(item[1])
print("in activate_menuitem(): widget", widget, "item", item)
label = item[0]
func = item[1]
func()
except KeyError as e:
print("BL INFO:: unable to execute function", item[1])
# takes list with [["item_name", func],...]
def create_show_pop_menu(item_n_funcn_list, event):
menu = Gtk.Menu()
for item in item_n_funcn_list:
item_name = item[0]
#item_func = item[1]
menuitem = Gtk.MenuItem(item_name)
menu.append(menuitem)
menuitem.connect("activate", activate_menuitem, item)
menu.show_all()
menu.popup(None, None, None, None, event.button, event.time)
def make_icons_model():
import os
import glob
stock_icon_ls = Gtk.stock_list_ids()
# coot icons
pixbuf_dir = os.getenv('COOT_PIXMAPS_DIR')
if (not pixbuf_dir):
pixbuf_dir = os.path.join(coot.get_pkgdatadir_py(), "pixmaps")
patt = os.path.normpath(pixbuf_dir + '/*.svg')
coot_icon_filename_ls = glob.glob(patt)
# model = Gtk.ListStore(Gtk.gdk.Pixbuf, str, str)
model = Gtk.ListStore(GdkPixbuf.Pixbuf, str, str)
for icon_filename in coot_icon_filename_ls:
if os.path.isfile(icon_filename):
icon = os.path.basename(icon_filename)
# pixbuf = Gtk.gdk.pixbuf_new_from_file_at_size(
pixbuf = GdkPixbuf.Pixbuf.new_from_file_at_size(icon_filename, 16, 16)
model.append([pixbuf, icon, icon_filename])
# build in default gtk icons
# icon_theme = Gtk.icon_theme_get_default()
icon_theme = Gtk.IconTheme.get_default()
for icon in stock_icon_ls:
try:
pixbuf = icon_theme.load_icon(icon, 16, Gtk.ICON_LOOKUP_USE_BUILTIN)
model.append([pixbuf, icon, None])
except:
pass
return model
def icon_selection_combobox(model):
combobox = Gtk.ComboBox()
combobox.set_wrap_width(10)
combobox.set_model(model)
crpx = Gtk.CellRendererPixbuf()
#crt = Gtk.CellRendererText()
combobox.pack_start(crpx, False)
combobox.add_attribute(crpx, 'pixbuf', 0)
combobox.show_all()
return combobox
def make_toolbar_button_gui():
def delete_event(*args):
window.destroy()
return False
def go_function(*args):
save_toolbuttons_qm = save_button.get_active()
# print "do something, maybe, save state", save_toolbuttons_qm
# iterate thru the widgets and get the state of check button and icon combobox
frames = frame_vbox.get_children()
for frame in frames:
inner_vbox = frame.get_children()[0]
hboxes = inner_vbox.get_children()
for hbox in hboxes:
left_hbox, right_hbox = hbox.get_children()
check_button, description = left_hbox.get_children()
label, combobox = right_hbox.get_children()
model = combobox.get_model()
button_label = check_button.get_label()
if (check_button.get_active()):
# make new button
iter = combobox.get_active_iter()
icon = None
if (iter):
icon, icon_stock, icon_filename = model.get(
iter, 0, 1, 2)
# print "icon", icon, icon_stock, icon_filename
if (icon_stock):
icon = icon_stock
toolbar_ls = list_of_toolbar_functions()
for group in toolbar_ls:
group_name = group[0]
group_items = group[1:len(group)]
for item in group_items:
if (len(item) > 0):
check_button_label = item[0]
callback_function = item[1]
description = item[2]
toggle_button_item = False
use_button_item = False
# is this foolproof? We assume an icon on i3
if len(item) > 4:
toggle_button_item = item[4]
if len(item) > 5:
use_button_item = item[5]
if (check_button_label == button_label):
new_toolbutton = coot_gui.coot_toolbar_button(button_label,
callback_function,
icon_name=icon,
tooltip=description,
toggle_button=toggle_button_item,
use_button=use_button_item)
# save
if save_toolbuttons_qm:
save_toolbar_to_init_file(button_label,
callback_function,
icon=icon,
tooltip=description,
toggle_button=toggle_button_item,
use_button=use_button_item)
break
else:
# remove an existing button?
# check if the button is in the existing button list
for toolbar in coot_gui.toolbar_label_list():
if (button_label == toolbar[0]):
coot_gui_api.main_toolbar().remove(toolbar[1])
# remove from save
remove_toolbar_from_init_file(button_label)
window.destroy()
return False
def save_function(*args):
print("Save me")
window = Gtk.Window()
window.set_title("Toolbar Selection")
window.set_default_size(800, 450)
scrolled_win = Gtk.ScrolledWindow()
# scrolled_win.set_policy(Gtk.POLICY_AUTOMATIC, Gtk.POLICY_ALWAYS)
vbox = Gtk.VBox(False, 2)
frame_vbox = Gtk.VBox(False, 2)
h_sep = Gtk.HSeparator()
buttons_hbox = Gtk.HBox(False, 2)
cancel_button = Gtk.Button(" Cancel ")
go_button = Gtk.Button(" Apply ")
save_button = Gtk.CheckButton(" Save to preferences?")
save_button.set_active(True)
icon_model = make_icons_model()
toolbar_ls = list_of_toolbar_functions()
for group in toolbar_ls:
group_name = group[0]
group_items = group[1:len(group)]
inner_vbox = Gtk.VBox(False, 2)
# frame = Gtk.Frame(group_name)
frame = Gtk.Frame()
frame.add(inner_vbox)
for item in group_items:
if (len(item) > 0):
suggested_icon = False
check_button_label = item[0]
callback_function = item[1]
description = item[2]
if (len(item) > 3):
suggested_icon = item[3]
def check_button_callback(*args):
# print "check button toggled"
# we actually dont do anything and check later for the status?
pass
hbox = Gtk.HBox(False, 0)
left_hbox = Gtk.HBox(False, 0)
right_hbox = Gtk.HBox(False, 0)
check_button = Gtk.CheckButton(check_button_label)
label = Gtk.Label(description)
icon_label = Gtk.Label("Add icon?")
icon_combobox = icon_selection_combobox(icon_model)
button_icon = False
all_toolbar_labels = [x[0]
for x in coot_gui.toolbar_label_list()]
if (check_button_label in all_toolbar_labels):
check_button.set_active(True)
# now try to get the icon
try:
ls = coot_gui.toolbar_label_list()
button_icon = ls[all_toolbar_labels.index(
check_button_label)][1].get_stock_id()
except:
# no icon found
pass
if (not button_icon):
button_icon = suggested_icon
# set the icon
if (button_icon):
for index in range(len(icon_model)):
icon_iter = icon_model.get_iter(index)
stock_id = icon_model.get_value(icon_iter, 1)
if (stock_id == button_icon):
icon_combobox.set_active_iter(icon_iter)
break
left_hbox.append(check_button)
left_hbox.pack_end(label, True, True, 3)
right_hbox.append(icon_label)
right_hbox.append(icon_combobox)
hbox.append(left_hbox)
hbox.pack_end(right_hbox, False, False, 3)
inner_vbox.append(hbox)
check_button.connect("toggled", check_button_callback)
frame_vbox.append(frame)
frame_vbox.set_border_width(3)
scrolled_win.add_with_viewport(frame_vbox)
buttons_hbox.append(go_button)
buttons_hbox.append(cancel_button)
vbox.append(scrolled_win)
vbox.append(h_sep)
vbox.append(save_button)
vbox.append(buttons_hbox)
cancel_button.connect("clicked", delete_event)
go_button.connect("clicked", go_function)
save_button.connect("toggled", save_function)
window.add(vbox)
window.show_all()
# simple GUI to remove a toolbar
def remove_toolbar_button_gui():
def remove_toolbar_button(entry_text):
print("remove button", entry_text)
for toolbar_child in coot_main_toolbar.get_children():
if (type(toolbar_child) == Gtk.ToolButton or
type(toolbar_child) == Gtk.ToggleToolButton):
button_label = toolbar_child.get_label()
if (button_label == entry_text):
coot_main_toolbar.remove(toolbar_child)
remove_toolbar_from_init_file(button_label)
break
coot_gui.generic_single_entry("Remove toolbar button",
"button label",
"Remove",
remove_toolbar_button)
# GUI to add user-defined toolbars
# uses Assistant or a simple GUI, depending on PyGTK version
def add_toolbar_button_gui():
major, minor, micro = Gtk.pygtk_version
if (major >= 2 and minor >= 10):
# have assistant
print("BL DEBUG:: run assistant")
add_toolbar_button_assistant()
else:
# no assistant available -> simple GUI
add_toolbar_button_simple_gui()
print("BL DEBUG:: no assistant, so simple GUI")
def toolbar_hide_text():
coot_main_toolbar.set_style(Gtk.TOOLBAR_ICONS)
def toolbar_show_text():
coot_main_toolbar.set_style(Gtk.TOOLBAR_BOTH_HORIZ)
####################################
# an assistant to add a toolbutton #
####################################
def add_toolbar_button_assistant():
def cb_close(assistant):
assi.destroy()
return False
def cb_name_entry_key_press(entry, event):
assi.set_page_complete(entry.get_parent(),
len(entry.get_text()) > 0)
def cb_func_entry_key_press(entry, event):
assi.set_page_complete(entry.get_parent(),
len(entry.get_text()) > 0)
def cb_entry_key_press(entry, event):
assi.set_page_complete(entry.get_parent(),
len(entry.get_text()) > 0)
def cb_apply(assistant):
name_str = name_entry.get_text()
func_str = func_entry.get_text()
save_qm = radiobutton_yes.get_active()
icon_iter = icon_combobox.get_active_iter()
icon = None
if (icon_iter):
icon, icon_stock, icon_filename = icon_model.get(
icon_iter, 0, 1, 2)
if (icon_stock):
icon = icon_stock
coot_gui.coot_toolbar_button(name_str, func_str, icon)
if (save_qm):
save_toolbar_to_init_file(name_str, func_str, icon)
assi = Gtk.Assistant()
assi.set_title("Toolbutton Assistant")
assi.connect('delete_event', cb_close)
assi.connect('close', cb_close)
assi.connect('cancel', cb_close)
assi.connect('apply', cb_apply)
# Construct page 0 (enter the button name)
vbox = Gtk.VBox(False, 5)
vbox.set_border_width(5)
vbox.show()
assi.append_page(vbox)
assi.set_page_title(vbox, 'Create a new Coot toolbutton')
assi.set_page_type(vbox, Gtk.ASSISTANT_PAGE_CONTENT)
label = Gtk.Label(
"Please enter the name for the new toolbutton...")
label.set_line_wrap(True)
label.show()
vbox.append(label)
name_entry = Gtk.Entry()
name_entry.connect("key-press-event", cb_name_entry_key_press)
name_entry.show()
vbox.pack_end(name_entry)
# check if name exists!!!!
# Construct page 1 (enter the function)
vbox = Gtk.VBox(False, 5)
vbox.set_border_width(5)
vbox.show()
assi.append_page(vbox)
assi.set_page_title(vbox, 'Set the function')
assi.set_page_type(vbox, Gtk.ASSISTANT_PAGE_CONTENT)
label = Gtk.Label(
"Please enter the python function... (e.g. fitting.refine_active_residue())")
label.set_line_wrap(True)
label.show()
vbox.append(label)
func_entry = Gtk.Entry()
func_entry.connect("key-press-event", cb_func_entry_key_press)
func_entry.show()
vbox.append(func_entry)
# add advanced option? FIXME (for callable func and args!?)
#adv_button = Gtk.Button("Advanced options...")
# adv_button.show()
#vbox.append(adv_button)
# Construct page 2 (save?)
vbox = Gtk.VBox(False, 5)
vbox.set_border_width(5)
vbox.show()
assi.append_page(vbox)
assi.set_page_title(vbox, 'Save to preferences?')
assi.set_page_type(vbox, Gtk.ASSISTANT_PAGE_CONTENT)
label = Gtk.Label(
"Do you want to save the button in your preferences?")
label.set_line_wrap(True)
label.show()
vbox.append(label)
radiobutton_yes = Gtk.RadioButton(None, "Yes")
radiobutton_no = Gtk.RadioButton(radiobutton_yes, "No")
radiobutton_yes.set_active(True)
radiobutton_yes.show()
radiobutton_no.show()
vbox.append(radiobutton_yes)
vbox.append(radiobutton_no)
assi.set_page_complete(radiobutton_yes.get_parent(), True)
# Construct page 3 (select icon)
vbox = Gtk.VBox(False, 5)
vbox.set_border_width(5)
vbox.show()
assi.append_page(vbox)
assi.set_page_title(vbox, 'Select an icon')
assi.set_page_type(vbox, Gtk.ASSISTANT_PAGE_CONTENT)
label = Gtk.Label("Please select an icon or leave as it is...")
label.set_line_wrap(True)
label.show()
vbox.append(label)
hbox = Gtk.HBox(False, 5)
icon_model = make_icons_model()
icon_combobox = icon_selection_combobox(icon_model)
icon_combobox.show()
hbox.show()
hbox.append(icon_combobox)
vbox.pack_end(hbox)
assi.set_page_complete(label.get_parent(), True)
# Final page
# As this is the last page needs to be of page_type
# Gtk.ASSISTANT_PAGE_CONFIRM or Gtk.ASSISTANT_PAGE_SUMMARY
label = Gtk.Label('Thanks for using the toolbutton assistent!')
label.set_line_wrap(True)
label.show()
assi.append_page(label)
assi.set_page_title(label, 'Finish')
assi.set_page_complete(label, True)
assi.set_page_type(label, Gtk.ASSISTANT_PAGE_CONFIRM)
assi.show()
def add_toolbar_button_simple_gui():
print("add_toolbar_button_simple_gui() has been removed for now")
pass
# save this for reference
def add_toolbar_button_simple_gui_old():
def button_func(*args):
# dummy dont need to do anythin here
pass
def do_func(*args):
name_str = args[0]
func_str = args[1]
save_qm = args[2]
icon_iter = icon_combobox.get_active_iter()
icon = None
if (icon_iter):
icon, icon_stock, icon_filename = icon_model.get(
icon_iter, 0, 1, 2)
if (icon_stock):
icon = icon_stock
coot_gui.coot_toolbar_button(name_str, func_str, icon)
if (save_qm):
save_toolbar_to_init_file(name_str, func_str, icon)
entry_widget = coot_gui.generic_double_entry("Button Name:", "Python Function:",
"test", "centre_of_mass(0)",
"Save to Preferences?", button_func,
"Create", do_func,
return_widget=True)
hbox = Gtk.HBox(True, 0)
label = Gtk.Label("Icon:")
icon_model = make_icons_model()
icon_combobox = icon_selection_combobox(icon_model)
hbox.append(label)
hbox.append(icon_combobox)
children = entry_widget.get_children()
vbox = children[0]
vbox.append(hbox)
vbox.reorder_child(hbox, 3)
hbox.show_all()
def show_pop_up_menu(widget, event):
if event.button == 3:
create_show_pop_menu([["Manage Buttons", make_toolbar_button_gui],
["Add a user-defined Button", add_toolbar_button_gui],
["Remove a Button", remove_toolbar_button_gui],
["Hide Text (only icons)", toolbar_hide_text],
["Show Text", toolbar_show_text]],
event)
coot_main_toolbar = coot_gui_api.main_toolbar()
# remove this for now.
# coot_main_toolbar.connect("button-press-event", show_pop_up_menu)
# save a toolbar button to ~/.coot-preferences/coot_toolbuttons.py
#
def save_toolbar_to_init_file(button_label, callback_function,
icon=None, tooltip=None,
toggle_button=False, use_button=False):
# so far only for string
save_str = "coot_toolbar_button(\"" + button_label + "\", "
if type(callback_function) is StringType:
save_str += ("\"" + callback_function + "\"")
else:
# no lists yet. FIXME
save_str += (callback_function.__name__)
if icon:
save_str += (", icon_name=\"" + str(icon) + "\"")
if tooltip:
save_str += (", tooltip=\"" + str(tooltip) + "\"")
if toggle_button:
save_str += (", toggle_button=" + str(toggle_button))
if use_button:
save_str += (", use_button=" + str(use_button))
save_str += ")"
home = os.getenv('HOME')
if (not home and os.name == 'nt'):
home = os.getenv('COOT_HOME')
if not home:
print("BL ERROR:: could not find a home directory")
else:
filename = os.path.join(
home, ".coot-preferences", "coot_toolbuttons.py")
coot_utils.remove_line_containing_from_file(["coot_toolbar_button", button_label],
filename)
coot_utils.save_string_to_file(save_str, filename)
# remove a toolbar from ~/.coot-preferences/coot_toolbuttons.py
#
def remove_toolbar_from_init_file(button_label):
home = os.getenv('HOME')
if (not home and os.name == 'nt'):
home = os.getenv('COOT_HOME')
if not home:
print("BL ERROR:: could not find a home directory")
else:
filename = os.path.join(
home, ".coot-preferences", "coot_toolbuttons.py")
remove_str_ls = ["coot_toolbar_button", button_label]
if (os.path.isfile(filename)):
coot_utils.remove_line_containing_from_file(
remove_str_ls, filename)
# returns a list with pre-defined toolbar-functions (stock-id is optional,
# so are a few others - almost consistent with order in coot_gui.coot_toolbar_button
# function)
# format:
# [[Group1,[toolbarname1, callbackfunction1, description1],
# [toolbarname2, callbackfunction2, description2(tooltip),
# stock-id2, toggle_button, use_button],...],
# [Group2]....]
# OBS: callbackfunction is a string! not any more exclusively
#
def list_of_toolbar_functions():
ls = [["Display",
["Stereo/Mono", "stereo_mono_toggle()",
"Toggle between Stereo and Mono view", "stereo-view.svg"],
["Side-by-side/Mono", "side_by_side_stereo_mono_toggle()",
"Toggle between Side-by-Side Stereo and Mono view", "stereo-view.svg"],
["Zalman Stereo/mono", "zalman_stereo_mono_toggle()",
"Toggle between Zalman Stereo and Mono view", "stereo-view.svg"],
["Swap Stereo", "switch_stereo_sides()",
"Change left and right stereo image", "undo-1.svg"],
["Full screen", coot_utils.toggle_full_screen,
"Switch between full screen and window mode", "gtk-fullscreen",
True, True],
['Hydrogens', coot_gui.toggle_hydrogen_display,
"Toggle to show (or not) hydrogens",
"delete.svg", True, True],
],
["Refinement",
["Sphere Refine", "sphere_refine()", "RSR around active residue",
"reset-view.svg"],
["Sphere Refine +", "sphere_refine_plus()",
"RSR around active residue +/- 1 residue", "reset-view.svg"],
["Repeat Refine Zone", "repeat_refine_zone()",
"Repeat (so that I don't need to click the atoms again)", "rrz.svg"],
["Tandem Refine", "refine_tandem_residues()",
"Refine a tandem 7-residue range", "something.svg"],
["Sphere Regularization", "sphere_regularize()",
"Regularize around active residue", "reset-view.svg"],
["Sphere Regularization +", "sphere_regularize_plus()",
"Regularize around active residue +/- 1 residue", "reset-view.svg"],
["Refine residue", "refine_active_residue()", "RSR active residue"],
["Reset B", "reset_b_factor_active_residue()",
"Reset the B-Factor of active Residue"],
["Add Alt Conf", "altconf()", "Add alternative conformation",
"add-alt-conf.svg"],
["Change Alt Conf Occ", "select_atom_alt_conf_occ_gui()",
"Change occupancies for alternative conformations", "add-alt-conf.svg"],
["Edit BB", "setup_backbone_torsion_edit(1)",
"Edit Backbone Torsion Angle", "flip-peptide.svg"],
['Torsion Gen.',
"setup_torsion_general(1)", "Torsion General (after O function)", "edit-chi.svg"],
['Backrub Rotamers', coot_gui.toggle_backrub_rotamers,
"Toggle use (or not) of backrub rotamers",
"auto-fit-rotamer.svg", True, True],
['Cis<->Trans',
"do_cis_trans_conversion_setup(1)", "Convert peptide: cis->trans or trans->cis", "flip-peptide.svg"],
["Run Refmac", "wrapped_create_run_refmac_dialog()", "Launch Refmac for Refinement", "azerbaijan.svg"]],
["Validation",
["Update Atom Overlaps", coot_gui.atom_overlaps_for_this_model, "Update the Atom Overlap representation", "auto-fit-rotamer.svg"],
["Interactive dots", generic_objects.toggle_interactive_probe_dots,
"Show dots after refinement and for chi/rotamer changes",
"probe-clash.svg", True, True],
["Local generic_objects.probe dots", "probe_local_sphere_active_atom()",
"Show generic_objects.probe dots for active atom in 4A radius.",
"probe-clash.svg"]
],
["Building",
["Choose Undo Molecule", "show_set_undo_molecule_chooser()",
"Choose Undo Molecule", "undo-1.svg"],
["Ligand Builder", "start_ligand_builder_gui()", "Ligand Builder",
"go-to-ligand.svg"],
["Split Water", "split_active_water()", "Split water in two and refine",
"add-water.svg"],
["Find Waters", "wrapped_create_find_waters_dialog()",
"Find water molecules in map", "add-water.svg"],
["Build NA", "find_nucleic_acids_local(6.0)",
"Find nucleic acids locally using Cootilus", "dna.svg"]
],
["NMR", []],
["EM", []],
["Sidechains/Alignment", []]]
return ls
# to make combobox
#coot_toolbar_combobox("MC restraints", ["no","aH","bS"], [set_secondary_structure_restraints_type], tooltip="Change refinement restraints for secondary structure")
|
