Hugging Face's logo

Spaces:
chihsing
/
DrugOps
Sleeping

App Files Community
DrugOps
File size: 43,656 Bytes
af894e0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
<!DOCTYPE html>
<html lang="zh-Hant">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>DrugOps — Module 2 Ligand Enumeration</title>
<style>
@import url('https://fonts.googleapis.com/css2?family=IBM+Plex+Mono:wght@400;500;600;700;800&family=IBM+Plex+Sans:wght@300;400;500&display=swap');
:root{
  --bg:#0d0f12;--surface:#141720;--surface2:#1c2030;--border:#2a2f42;--border2:#363d55;
  --text:#e8eaf2;--text2:#8890aa;--text3:#545d78;
  --blue:#4a9eff;--blue-dim:#1a3a6e;
  --green:#3ecf8e;--green-dim:#0d3d27;
  --amber:#f5a623;--amber-dim:#3d2a08;
  --red:#f56565;--red-dim:#3d1515;
  --purple:#c084fc;--purple-dim:#2a1a40;
  --code-bg:#0a0c10;
  --mono:'IBM Plex Mono',monospace;--sans:'IBM Plex Sans',sans-serif;
}
html[data-theme="light"]{
  color-scheme:light;
  --bg:#f4f5f8;--surface:#ffffff;--surface2:#eef1f6;--border:#e2e6ef;--border2:#cdd5e4;
  --text:#141823;--text2:#4b5568;--text3:#6b7280;
  --blue:#2563eb;--blue-dim:#dbeafe;
  --green:#059669;--green-dim:#d1fae5;
  --amber:#d97706;--amber-dim:#fef3c7;
  --red:#dc2626;--red-dim:#fee2e2;
  --purple:#7c3aed;--purple-dim:#ede9fe;
  --code-bg:#e8ecf4;
}
*{box-sizing:border-box;margin:0;padding:0;}
body{background:var(--bg);color:var(--text);font-family:var(--sans);font-size:18px;min-height:100vh;}
.left{border-right:1px solid var(--border);display:flex;flex-direction:column;}

.main{padding:1.5rem 2rem;flex:1;overflow-y:auto;display:flex;flex-direction:column;gap:1.25rem;}

/* Session input (no session_id case) */
.session-input-bar{background:var(--surface);border:1px solid var(--amber);border-radius:10px;padding:1rem 1.25rem;display:flex;gap:.75rem;align-items:flex-end;}
.session-input-bar .field{flex:1;margin:0;}

/* Engine card */
.engine{background:var(--surface);border:1px solid var(--border);border-radius:12px;overflow:hidden;transition:border-color .2s;}
.engine.active{border-color:var(--border2);}
.engine.running{border-color:var(--blue);}
.engine.needs-input{border-color:var(--amber);}
.engine.done{border-color:var(--green);}
.engine.error{border-color:var(--red);}
.engine-header{padding:.875rem 1.25rem;display:flex;align-items:center;gap:.875rem;cursor:pointer;user-select:none;}
.engine-badge{font-family:var(--mono);font-size:13px;font-weight:500;padding:3px 8px;border-radius:4px;background:var(--surface2);color:var(--text3);border:1px solid var(--border);white-space:nowrap;}
.engine.active .engine-badge{background:var(--blue-dim);color:var(--blue);border-color:var(--blue);}
.engine.running .engine-badge{background:var(--blue-dim);color:var(--blue);border-color:var(--blue);animation:pulse 1.2s ease-in-out infinite;}
.engine.needs-input .engine-badge{background:var(--amber-dim);color:var(--amber);border-color:var(--amber);}
.engine.done .engine-badge{background:var(--green-dim);color:var(--green);border-color:var(--green);}
.engine.error .engine-badge{background:var(--red-dim);color:var(--red);border-color:var(--red);}
@keyframes pulse{0%,100%{opacity:1}50%{opacity:.5}}
.engine-title{font-size:18px;font-weight:500;color:var(--text);flex:1;}
.engine-subtitle{font-size:14px;color:var(--text3);}
.engine-chevron{color:var(--text3);font-size:14px;transition:transform .2s;}
.engine.open .engine-chevron{transform:rotate(180deg);}
.engine-body{display:none;border-top:1px solid var(--border);}
.engine.open .engine-body{display:block;}

/* Stage list */
.stage-list{padding:.875rem 1.25rem;display:flex;flex-direction:column;gap:.4rem;}
.stage-row{display:flex;align-items:center;gap:.625rem;padding:.4rem .625rem;border-radius:6px;background:var(--surface2);}
.stage-num{font-family:var(--mono);font-size:13px;color:var(--text3);min-width:24px;}
.stage-name{font-size:15px;color:var(--text2);flex:1;}
.stage-val{font-family:var(--mono);font-size:14px;color:var(--text);max-width:220px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;}
.stage-status{font-size:13px;font-weight:500;padding:2px 6px;border-radius:3px;white-space:nowrap;}
.s-auto{background:var(--green-dim);color:var(--green);}
.s-manual{background:var(--purple-dim);color:var(--purple);border:1px solid var(--purple);}
.s-confirm{background:var(--blue-dim);color:var(--blue);}
.s-fail{background:var(--red-dim);color:var(--red);}
.s-warn{background:var(--amber-dim);color:var(--amber);}

/* SMILES info bar */
.smiles-bar{margin:0 1.25rem .75rem;background:var(--surface2);border-radius:6px;padding:.75rem;display:flex;flex-direction:column;gap:.25rem;}
.smiles-label{font-size:13px;color:var(--text3);font-family:var(--mono);}
.smiles-val{font-family:var(--mono);font-size:14px;color:var(--text);word-break:break-all;line-height:1.6;}
.smiles-meta{font-size:14px;color:var(--text3);}
.smiles-warn{font-size:14px;color:var(--amber);margin-top:.25rem;}

/* Candidate cards */
.cand-section{padding:0 1.25rem .875rem;}
.cand-label{font-family:var(--mono);font-size:13px;color:var(--amber);letter-spacing:.08em;margin-bottom:.75rem;}
.cand-grid{display:grid;grid-template-columns:repeat(auto-fill,minmax(155px,1fr));gap:8px;}
.cand-card{padding:.875rem;border:1px solid var(--border);border-radius:10px;background:var(--surface2);cursor:pointer;transition:all .15s;position:relative;}
.cand-card:hover{border-color:var(--border2);}
.cand-card.selected{border:2px solid var(--blue);background:var(--blue-dim);}
.cand-card.auto-selected{border:2px solid var(--green);background:var(--green-dim);cursor:default;}
.cand-idx{font-family:var(--mono);font-size:13px;color:var(--text3);margin-bottom:.375rem;}
.cand-state{font-size:17px;font-weight:500;color:var(--text);margin-bottom:.25rem;}
.cand-site{font-family:var(--mono);font-size:14px;color:var(--amber);margin-bottom:.375rem;}
.cand-note{font-size:14px;color:var(--text3);line-height:1.5;}
.cand-check{position:absolute;top:8px;right:8px;width:16px;height:16px;border-radius:50%;background:var(--blue);display:none;align-items:center;justify-content:center;font-size:13px;color:#fff;}
.cand-card.selected .cand-check{display:flex;}
.cand-card.auto-selected .cand-check{display:flex;background:var(--green);}
.cand-confirm-row{margin-top:.875rem;display:flex;gap:.5rem;align-items:center;}

/* Tautomer result */
.taut-result{margin:0 1.25rem .875rem;background:var(--surface2);border-radius:8px;padding:.875rem;border-left:3px solid var(--green);}
.taut-title{font-size:14px;color:var(--text3);margin-bottom:.375rem;}
.taut-smiles{font-family:var(--mono);font-size:14px;color:var(--green);word-break:break-all;line-height:1.6;}
.taut-count{font-size:14px;color:var(--text3);margin-top:.25rem;}

/* Engine C options */
.engine-opts{padding:.875rem 1.25rem;display:flex;gap:.5rem;flex-wrap:wrap;}
.engine-opt{font-family:var(--mono);font-size:14px;padding:6px 14px;border-radius:6px;border:1px solid var(--border2);background:transparent;color:var(--text2);cursor:pointer;transition:all .15s;}
.engine-opt.active{border-color:var(--blue);background:var(--blue-dim);color:var(--blue);}
.engine-opt-label{font-size:13px;color:var(--text3);align-self:center;}

/* PDBQT result */
.pdbqt-result{margin:0 1.25rem .875rem;background:var(--green-dim);border:1px solid var(--green);border-radius:8px;padding:.875rem;}
.pdbqt-title{font-family:var(--mono);font-size:13px;color:var(--green);letter-spacing:.06em;margin-bottom:.5rem;}
.pdbqt-path{font-family:var(--mono);font-size:14px;color:var(--text2);word-break:break-all;}
.pdbqt-meta{font-size:14px;color:var(--text3);margin-top:.375rem;}

/* Log */
.log-box{margin:0 1.25rem .875rem;background:var(--code-bg);border:1px solid var(--border);border-radius:6px;padding:.625rem .875rem;font-family:var(--mono);font-size:14px;color:var(--text3);max-height:130px;overflow-y:auto;line-height:1.8;}
.log-box .ok{color:var(--green);}
.log-box .warn{color:var(--amber);}
.log-box .err{color:var(--red);}
.log-box .info{color:var(--blue);}

/* Action bar */
.action-bar{padding:.875rem 1.25rem;border-top:1px solid var(--border);display:flex;gap:.625rem;align-items:center;flex-wrap:wrap;}
.btn{font-family:var(--mono);font-size:15px;font-weight:500;padding:7px 16px;border-radius:6px;border:1px solid;cursor:pointer;transition:all .15s;}
.btn:disabled{opacity:.35;cursor:not-allowed;}
.btn-primary{background:var(--blue);color:#fff;border-color:var(--blue);}
.btn-primary:hover:not(:disabled){background:#6ab3ff;}
.btn-success{background:var(--green);color:#000;border-color:var(--green);}
.btn-ghost{background:transparent;color:var(--text2);border-color:var(--border2);}
.btn-ghost:hover:not(:disabled){background:var(--surface2);}
.btn-sm{padding:4px 10px;font-size:14px;}
.action-note{font-size:14px;color:var(--text3);margin-left:auto;}

/* Connector */
.connector{display:flex;align-items:center;padding:0 1.5rem;gap:.5rem;}
.connector-line{flex:1;height:1px;background:var(--border);}
.connector-label{font-family:var(--mono);font-size:13px;color:var(--text3);}

/* Summary */
.summary-bar{background:var(--surface);border:1px solid var(--green);border-radius:12px;padding:1.25rem;display:none;}
.summary-bar.visible{display:block;}
.summary-title{font-family:var(--mono);font-size:14px;color:var(--green);letter-spacing:.08em;margin-bottom:.75rem;}
.summary-grid{display:grid;grid-template-columns:repeat(auto-fit,minmax(160px,1fr));gap:.625rem;}
.summary-item{background:var(--surface2);border-radius:6px;padding:.625rem .875rem;}
.summary-item .lbl{font-size:14px;color:var(--text3);margin-bottom:2px;}
.summary-item .val{font-family:var(--mono);font-size:15px;color:var(--text);}

/* Field */
.field{margin-bottom:0;}
.field-label{font-size:15px;color:var(--text3);margin-bottom:5px;}
.field input{width:100%;background:var(--surface2);border:1px solid var(--border2);border-radius:6px;padding:8px 10px;font-size:17px;color:var(--text);}
.field input:focus{border-color:var(--blue);outline:none;}

</style>
<link rel="stylesheet" href="../../assets/molgate.css" onerror="this.onerror=null;this.href='/assets/molgate.css'">
<link rel="stylesheet" href="../../assets/molgate_panel_scale.css" onerror="this.onerror=null;this.href='/assets/molgate_panel_scale.css'">
<link rel="stylesheet" href="../../assets/molgate_ai_sidebar.css" onerror="this.onerror=null;this.href='/assets/molgate_ai_sidebar.css'">
</head>
<body data-molgate-module="2">

<div class="mg-top-bar">
  <div class="mg-toolbar">
    <button type="button" class="nav-btn" id="mgNavPrev" onclick="molgateNavPrev()" data-zh="← 上一頁" data-en="← Previous">← 上一頁</button>
    <button type="button" class="nav-btn" id="mgNavNext" onclick="molgateNavNext()" data-zh="下一頁 →" data-en="Next →">下一頁 →</button>
    <div class="theme-btns" aria-label="Theme">
      <button type="button" class="theme-btn active" data-theme="dark" onclick="setTheme('dark')" data-zh="深色" data-en="Dark">深色</button>
      <button type="button" class="theme-btn" data-theme="light" onclick="setTheme('light')" data-zh="淺色" data-en="Light">淺色</button>
    </div>
    <div class="lang-btns">
      <button type="button" class="lang-btn active" data-lang="zh" onclick="molgateSetLang('zh')">中文</button>
      <button type="button" class="lang-btn" data-lang="en" onclick="molgateSetLang('en')">EN</button>
    </div>
  </div>
</div>
<div class="mg-chrome">
  <div class="header">
    <div class="molgate-logo">
      <div class="molgate-logo-main"><span class="logo-mol">Drug</span><span class="logo-gate">Ops</span></div>
      <div class="logo-sub">CreaDrug · module-2 · ligand-enumeration</div>
    </div>
  </div>
  <div class="header-meta">
    <span class="session-pill" id="session-pill">session: —</span>
    <span class="session-pill" id="target-pill">target: —</span>
  </div>
</div>

<div class="app-shell">

<!-- ══ LEFT ══ -->
<div class="left">
  <div class="main">

  <!-- Session input bar (no session_id) -->
  <div class="session-input-bar" id="session-input-bar" style="display:none">
    <div class="field">
      <div class="field-label" data-zh="輸入 Session ID" data-en="Enter Session ID">輸入 Session ID</div>
      <input type="text" id="manual-session" placeholder="93e44ebf6158878c" style="font-family:var(--mono)">
    </div>
    <div class="field" style="flex:0.5;">
      <div class="field-label" data-zh="Target" data-en="Target">Target</div>
      <input type="text" id="manual-target" placeholder="COX2">
    </div>
    <button class="btn btn-primary btn-sm" onclick="loadSession()" data-zh="載入" data-en="Load">載入</button>
  </div>

  <!-- ENGINE B -->
  <div class="engine active open" id="engB">
    <div class="engine-header">
      <div class="engine-badge" id="badgeB">ENGINE B</div>
      <div>
        <div class="engine-title" data-zh="配體枚舉" data-en="Ligand enumeration">配體枚舉</div>
        <div class="engine-subtitle" data-zh="Stage 04 質子化 + Stage 05 互變異構" data-en="Stage 04 protonation + Stage 05 tautomer">Stage 04 質子化 + Stage 05 互變異構</div>
      </div>
    </div>
    <div class="engine-body">

      <!-- SMILES 來源顯示 -->
      <div class="smiles-bar" id="smiles-bar">
        <div class="smiles-label" data-zh="輸入 SMILES（來自 Stage 01）" data-en="Input SMILES (from Stage 01)">輸入 SMILES（來自 Stage 01）</div>
        <div class="smiles-val" id="smiles-display">—</div>
        <div class="smiles-meta" id="smiles-meta"></div>
        <div class="smiles-warn" id="smiles-warn" style="display:none"></div>
      </div>

      <div class="stage-list">
        <div class="stage-row">
          <span class="stage-num">04</span>
          <span class="stage-name" data-zh="質子化狀態（pH 7.4）" data-en="Protonation state (pH 7.4)">質子化狀態（pH 7.4）</span>
          <span class="stage-val" id="v04">—</span>
          <span class="stage-status" id="s04" style="display:none"></span>
        </div>
        <div class="stage-row">
          <span class="stage-num">05</span>
          <span class="stage-name" data-zh="互變異構（canonical）" data-en="Tautomer (canonical)">互變異構（canonical）</span>
          <span class="stage-val" id="v05">—</span>
          <span class="stage-status" id="s05" style="display:none"></span>
        </div>
      </div>

      <!-- 候選卡片區（Stage 04 需要人工選擇時顯示）-->
      <div class="cand-section" id="cand-section" style="display:none">
        <div class="cand-label" id="cand-label" data-zh="選擇質子化形態（pH 7.4）" data-en="Select protonation state (pH 7.4)">選擇質子化形態（pH 7.4）</div>
        <div class="cand-grid" id="cand-grid"></div>
        <div class="cand-confirm-row">
          <button class="btn btn-success btn-sm" id="btn-cand-confirm" onclick="confirmCandidate()" disabled data-zh="✓ 確認選擇" data-en="✓ Confirm">✓ 確認選擇</button>
          <span style="font-size:14px;color:var(--text3);" id="cand-hint" data-zh="請選擇一個形態" data-en="Please select a form">請選擇一個形態</span>
        </div>
      </div>

      <!-- Tautomer 結果 -->
      <div class="taut-result" id="taut-result" style="display:none">
        <div class="taut-title" data-zh="Canonical tautomer（Stage 05）" data-en="Canonical tautomer (Stage 05)">Canonical tautomer（Stage 05）</div>
        <div class="taut-smiles" id="taut-smiles">—</div>
        <div class="taut-count" id="taut-count"></div>
      </div>

      <div class="action-bar">
        <button class="btn btn-primary" id="btnB" onclick="runEngineB()" disabled data-zh="▶ Run Engine B" data-en="▶ Run Engine B">▶ Run Engine B</button>
        <span class="action-note" id="noteB" data-zh="載入 Session 後啟用" data-en="Load session to enable">載入 Session 後啟用</span>
      </div>
      <div class="log-box" id="logB" style="display:none"></div>
      <div class="action-bar" id="nextCHint" style="display:none;background:var(--green-dim);border:1px solid var(--green);border-radius:8px;margin:0 1.25rem .75rem;padding:.75rem 1rem;">
        <span style="font-size:15px;color:var(--green);font-family:var(--mono);" data-zh="✓ Engine B 已完成 — 請在下方 Engine C 區塊執行 ▶ Run Engine C" data-en="✓ Engine B done — run ▶ Run Engine C in Engine C below">✓ Engine B 已完成 — 請在下方 Engine C 區塊執行 ▶ Run Engine C</span>
      </div>
    </div>
  </div>

  <div class="connector">
    <div class="connector-line"></div>
    <div class="connector-label">stage_05_tautomer.json → selected_smiles</div>
    <div class="connector-line"></div>
  </div>

  <!-- ENGINE C -->
  <div class="engine open" id="engC">
    <div class="engine-header">
      <div class="engine-badge" id="badgeC">ENGINE C</div>
      <div>
        <div class="engine-title" data-zh="PDBQT 轉換" data-en="PDBQT conversion">PDBQT 轉換</div>
        <div class="engine-subtitle" data-zh="Stage 09 → ligand/ligand.pdbqt" data-en="Stage 09 → ligand/ligand.pdbqt">Stage 09 → ligand/ligand.pdbqt</div>
      </div>
    </div>
    <div class="engine-body">
      <div class="stage-list">
        <div class="stage-row">
          <span class="stage-num">09</span>
          <span class="stage-name" data-zh="配體 PDBQT 轉換（Meeko-first）" data-en="Ligand PDBQT (Meeko-first)">配體 PDBQT 轉換（Meeko-first）</span>
          <span class="stage-val" id="v09">—</span>
          <span class="stage-status" id="s09" style="display:none"></span>
        </div>
      </div>

      <!-- 引擎選擇 -->
      <div class="engine-opts">
        <span class="engine-opt-label" data-zh="引擎：" data-en="Engine:">引擎：</span>
        <button class="engine-opt active" onclick="selectEngine('meeko',this)">meeko</button>
        <button class="engine-opt" onclick="selectEngine('auto',this)">auto</button>
        <button class="engine-opt" onclick="selectEngine('obabel',this)">obabel</button>
      </div>

      <!-- PDBQT 結果 -->
      <div class="pdbqt-result" id="pdbqt-result" style="display:none">
        <div class="pdbqt-title">LIGAND.PDBQT ✓</div>
        <div class="pdbqt-path" id="pdbqt-path">—</div>
        <div class="pdbqt-meta" id="pdbqt-meta"></div>
      </div>

      <div class="action-bar">
        <button class="btn btn-primary" id="btnC" onclick="runEngineC()" disabled data-zh="▶ Run Engine C" data-en="▶ Run Engine C">▶ Run Engine C</button>
        <span class="action-note" id="noteC" data-zh="等待 Engine B 完成" data-en="Waiting for Engine B">等待 Engine B 完成</span>
      </div>
      <div class="log-box" id="logC" style="display:none"></div>
    </div>
  </div>

  <!-- Summary -->
  <div class="summary-bar" id="summary">
    <div class="summary-title" data-zh="MODULE 2 完成 ✓" data-en="MODULE 2 COMPLETE ✓">MODULE 2 完成 ✓</div>
    <div class="summary-grid">
      <div class="summary-item"><div class="lbl" data-zh="最終 SMILES" data-en="Final SMILES">最終 SMILES</div><div class="val" id="sum-smiles" style="font-size:13px;word-break:break-all;">—</div></div>
      <div class="summary-item"><div class="lbl" data-zh="Stage 04" data-en="Stage 04">Stage 04</div><div class="val" id="sum-s04">—</div></div>
      <div class="summary-item"><div class="lbl" data-zh="Stage 05" data-en="Stage 05">Stage 05</div><div class="val" id="sum-s05">—</div></div>
      <div class="summary-item"><div class="lbl">ligand.pdbqt</div><div class="val" style="color:var(--green)" data-zh="已生成" data-en="Generated">已生成</div></div>
    </div>
    <div style="margin-top:.875rem;">
      <button class="btn btn-success" onclick="goModule3()" data-zh="繼續 Module 3 →" data-en="Continue to Module 3 →">繼續 Module 3 →</button>
    </div>
  </div>

  </div><!-- main -->
</div><!-- left -->

<!-- ══ RIGHT: AI 助手（統一格式） ══ -->
<aside class="mg-ai-sidebar" id="mgAiSidebar">
  <div class="mg-ai-head">
    <h2 data-zh="170B · AI 助手" data-en="170B · AI Assistant">170B · AI 助手</h2>
    <div class="mg-ai-opts">
      <label><input type="checkbox" id="mgAiShowRaw"> <span data-zh="顯示原始串流（含思考／CoT 類文字）" data-en="Show raw stream (CoT)">顯示原始串流（含思考／CoT 類文字）</span></label>
      <label><input type="checkbox" id="mgAiStream" checked> <span data-zh="串流輸出" data-en="Stream output">串流輸出</span></label>
    </div>
  </div>
  <div class="mg-ai-scroll">
    <div class="mg-ai-static" id="mgAiStatic">
      <div class="mg-ai-hint-box" data-zh="質子化形態選擇有疑問？在此詢問 AI 關於 pH 7.4 下的主要離子形態。" data-en="Unsure about protonation state? Ask the AI about the dominant form at pH 7.4.">質子化形態選擇有疑問？在此詢問 AI 關於 pH 7.4 下的主要離子形態。</div>
      <div class="mg-ai-hint-box" id="llm-welcome" data-zh="執行 Engine B 後，我可以解釋每個質子化候選的差異與選擇建議。" data-en="After running Engine B, I can explain the differences between protonation candidates and help you choose.">執行 Engine B 後，我可以解釋每個質子化候選的差異與選擇建議。</div>
      <div class="mg-ai-ctx" id="llm-ctx">context：尚無結果</div>
    </div>
    <div class="mg-ai-messages" id="mgAiMessages" aria-live="polite"></div>
  </div>
  <div class="mg-ai-foot">
    <div class="mg-ai-input-row">
      <textarea id="mgAiInput" rows="2" placeholder="輸入訊息…（Enter 送出，Shift+Enter 換行）"></textarea>
      <button type="button" class="btn-mg-ai-send" id="mgAiSend" data-zh="送出" data-en="Send">送出</button>
    </div>
    <div class="mg-ai-actions">
      <button type="button" class="btn btn-ghost" id="mgAiStop" disabled data-zh="停止生成" data-en="Stop">停止生成</button>
      <button type="button" class="btn btn-ghost" id="mgAiClear" data-zh="清除對話" data-en="Clear chat">清除對話</button>
    </div>
    <p class="mg-ai-foot-hint">經同源後端轉發至 <strong>170B AI</strong> 推理服務。</p>
  </div>
</aside>

</div><!-- app-shell -->

<script>
const LANG = {cur:'zh'};
const STATE = {
  session_id: null,
  engineBRunning: false,
  engineBDone: false,
  target: '',
  smiles: '',
  drug_label: '',
  selectedEngine: 'meeko',
  selectedCandIdx: null,
  candidates: [],
  finalSmiles: '',
};

// ── 初始化：從 URL 讀 session ──────────────────────
window.addEventListener('DOMContentLoaded', () => {
  const params = new URLSearchParams(window.location.search);
  const sid = params.get('session');
  const tgt = params.get('target');
  if (sid) {
    STATE.session_id = sid;
    STATE.target = tgt || '';
    loadSessionData(sid);
  } else {
    document.getElementById('session-input-bar').style.display = 'flex';
    document.getElementById('noteB').textContent = L('noSession');
  }
});

// ── i18n ─────────────────────────────────────────
const T = {
  zh: {
    noSession:'請先輸入 Session ID',
    sessionLoaded:'Session 載入成功',
    sessionErr:'Session 載入失敗',
    runB:'執行中...',
    auto1:'自動通過（唯一候選）',
    needSelect:'需要人工選擇',
    confirm2:'請確認（預選第一個）',
    candConfirmed:'已選定',
    tautAuto:'自動（canonical）',
    runCNote:'就緒，點擊執行',
    waitB:'等待 Engine B 完成',
    pdbqtDone:'PDBQT 生成完成',
    engineBDone:'Engine B 完成',
    engineBAgain:'↻ 重新執行 Engine B',
    nextEngineC:'✓ Engine B 已完成 — 請執行下方 Engine C',
    engineCDone:'Engine C 完成',
    gemmaCtx: (s,m) => `context：${s} | ${m} Da`,
    llmB: (n) => `Engine B 完成，找到 ${n} 個質子化候選。${n > 2 ? '需要人工選擇。' : '已自動通過。'}有問題可以問我。`,
    llmC: 'Engine C 完成，ligand.pdbqt 已生成。Module 2 全部完成。',
    noSession_input:'請輸入 Session ID 和 Target',
    stereoWarn: (c,e) => `⚠ 未定義手性中心：${c} 個，未定義 E/Z：${e} 個`,
  },
  en: {
    noSession:'Please enter a Session ID first',
    sessionLoaded:'Session loaded',
    sessionErr:'Failed to load session',
    runB:'Running...',
    auto1:'Auto pass (single candidate)',
    needSelect:'Manual selection required',
    confirm2:'Please confirm (first pre-selected)',
    candConfirmed:'Selected',
    tautAuto:'Auto (canonical)',
    runCNote:'Ready, click to run',
    waitB:'Waiting for Engine B',
    pdbqtDone:'PDBQT generated',
    engineBDone:'Engine B complete',
    engineBAgain:'↻ Re-run Engine B',
    nextEngineC:'✓ Engine B done — run Engine C below',
    engineCDone:'Engine C complete',
    gemmaCtx: (s,m) => `context: ${s} | ${m} Da`,
    llmB: (n) => `Engine B done. ${n} protonation candidate(s) found. ${n > 2 ? 'Manual selection needed.' : 'Auto-passed.'} Ask me anything.`,
    llmC: 'Engine C done. ligand.pdbqt generated. Module 2 complete.',
    noSession_input:'Please enter Session ID and Target',
    stereoWarn: (c,e) => `⚠ Undefined stereocenters: ${c}, undefined E/Z: ${e}`,
  },
};
function L(key, ...args) {
  const t = T[LANG.cur][key];
  return typeof t === 'function' ? t(...args) : (t || key);
}

function setLang(l) {
  LANG.cur = l;
  document.querySelectorAll('.lang-btn').forEach(b =>
    b.classList.toggle('active', (l==='zh'&&b.textContent==='中文')||(l==='en'&&b.textContent==='EN')));
  document.querySelectorAll('[data-zh]').forEach(el => {
    const t = el.getAttribute('data-'+l);
    if (!t) return;
    if (el.tagName==='INPUT') el.placeholder = t;
    else el.textContent = t;
  });
  molgateAiSetPlaceholder('輸入訊息…（Enter 送出，Shift+Enter 換行）', 'Message… (Enter send, Shift+Enter newline)');
}

function setTheme(t) {
  document.documentElement.setAttribute('data-theme', t);
  document.querySelectorAll('.theme-btn').forEach(b =>
    b.classList.toggle('active', b.getAttribute('data-theme') === t));
}

// ── Engine toggle ─────────────────────────────────
function toggleEngine(id) {
  document.getElementById(id).classList.toggle('open');
}

function setEngineState(id, state) {
  const el = document.getElementById(id);
  el.classList.remove('active','running','needs-input','done','error');
  if (state) el.classList.add(state);
  const badge = document.getElementById(id==='engB'?'badgeB':'badgeC');
  const prefix = id==='engB' ? 'ENGINE B' : 'ENGINE C';
  const labels = {active:'READY',running:'RUNNING...',
    'needs-input':'ACTION NEEDED',done:'DONE ✓',error:'ERROR'};
  badge.textContent = state ? `${prefix} · ${labels[state]||state}` : prefix;
}

function setStage(vid, sid, val, cls, txt) {
  document.getElementById(vid).textContent = val;
  const s = document.getElementById(sid);
  s.className = 'stage-status ' + cls;
  s.textContent = txt;
  s.style.display = '';
}

function appendLog(id, msg, cls='') {
  const b = document.getElementById(id);
  b.style.display = '';
  const d = document.createElement('div');
  if (cls) d.className = cls;
  d.textContent = msg;
  b.appendChild(d);
  b.scrollTop = b.scrollHeight;
}

function sleep(ms) { return new Promise(r=>setTimeout(r,ms)); }

// ── Session 載入 ──────────────────────────────────
async function loadSession() {
  const sid = document.getElementById('manual-session').value.trim();
  const tgt = document.getElementById('manual-target').value.trim().toUpperCase();
  if (!sid || !tgt) { alert(L('noSession_input')); return; }
  STATE.session_id = sid;
  STATE.target = tgt;
  await loadSessionData(sid);
}

async function loadSessionData(sid) {
  try {
    const r = await fetch(`/api/session/${sid}/stage01`);
    if (!r.ok) {
      const err = await r.json();
      molgateAiNotify(`❌ ${err.error || L('sessionErr')}`);
      return;
    }
    const data = await r.json();
    STATE.smiles = data.canonical_smiles || '';
    STATE.drug_label = data.drug_label || '';
    if (!STATE.target) STATE.target = data.target || '';

    // Update UI
    document.getElementById('session-input-bar').style.display = 'none';
    document.getElementById('session-pill').textContent = `session: ${sid.slice(0,8)}...`;
    document.getElementById('target-pill').textContent = `target: ${STATE.target}`;

    // SMILES bar
    document.getElementById('smiles-display').textContent = STATE.smiles;
    const meta = [];
    if (data.mol_weight) meta.push(`MW: ${data.mol_weight} Da`);
    if (STATE.drug_label) meta.push(STATE.drug_label);
    if (STATE.target) meta.push(STATE.target);
    document.getElementById('smiles-meta').textContent = meta.join(' · ');

    // Stereo warning
    const nc = data.n_undefined_chiral_centers || 0;
    const ne = data.n_undefined_ez_bonds || 0;
    if (nc > 0 || ne > 0) {
      const w = document.getElementById('smiles-warn');
      w.textContent = L('stereoWarn', nc, ne);
      w.style.display = '';
    }

    // Enable Engine B (unless already completed — restore handles that)
    const restored = await restoreModule2Progress(sid);
    if (!restored) {
      document.getElementById('btnB').disabled = false;
      document.getElementById('noteB').textContent = L('sessionLoaded');
      setEngineState('engB', 'active');
    }

    molgateAiNotify(`Session ${sid.slice(0,8)}... 載入完成。SMILES: ${STATE.smiles.slice(0,40)}...`);
    document.getElementById('llm-ctx').textContent = L('gemmaCtx', STATE.target, data.mol_weight||'?');
  } catch(e) {
    molgateAiNotify(`❌ ${L('sessionErr')}: ${e}`);
  }
}

async function restoreModule2Progress(sid) {
  try {
    const [r4resp, r5resp, r9check] = await Promise.all([
      fetch(`/api/session/${sid}/stage04`),
      fetch(`/api/session/${sid}/stage05`),
      fetch(`/api/session/${sid}/status`),
    ]);
    if (!r4resp.ok || !r5resp.ok) return false;
    const r4 = await r4resp.json();
    const r5 = await r5resp.json();
    handleEngineBResult(r4, r5);
    STATE.engineBDone = true;
    document.getElementById('btnB').disabled = false;
    setBtnBLabel(false);
    document.getElementById('noteB').textContent = L('nextEngineC');
    document.getElementById('nextCHint').style.display = 'flex';
    if (r9check.ok) {
      const st = await r9check.json();
      const s9 = st.stages?.stage_09;
      if (s9 && s9 !== 'unknown') {
        document.getElementById('btnC').disabled = false;
        setEngineState('engC', 'done');
        document.getElementById('noteC').textContent = L('pdbqtDone');
      }
    }
    return true;
  } catch (e) {
    return false;
  }
}

function setBtnBLabel(running) {
  const btn = document.getElementById('btnB');
  if (running) {
    btn.textContent = L('runB');
    return;
  }
  btn.textContent = STATE.engineBDone ? L('engineBAgain') : (LANG.cur === 'zh' ? '▶ Run Engine B' : '▶ Run Engine B');
}

// ── Engine B ──────────────────────────────────────
async function runEngineB() {
  if (STATE.engineBRunning) return;
  STATE.engineBRunning = true;
  document.getElementById('btnB').disabled = true;
  setBtnBLabel(true);
  setEngineState('engB', 'running');
  document.getElementById('logB').style.display = '';
  if (!STATE.engineBDone) document.getElementById('logB').innerHTML = '';
  document.getElementById('nextCHint').style.display = 'none';

  let finalResult = null;
  try {
    const resp = await fetch('/api/module2/engineB/run', {
      method: 'POST',
      headers: {'Content-Type':'application/json'},
      body: JSON.stringify({session_id: STATE.session_id, target: STATE.target}),
    });
    if (!resp.ok) {
      const err = await resp.json().catch(() => ({}));
      appendLog('logB', `❌ ${err.error || resp.statusText}`, 'err');
      setEngineState('engB', 'error');
      return;
    }

    const reader = resp.body.getReader();
    const decoder = new TextDecoder();
    let buffer = '';

    while (true) {
      const {done, value} = await reader.read();
      if (done) break;
      buffer += decoder.decode(value, {stream:true});
      const lines = buffer.split('\n');
      buffer = lines.pop();
      for (const line of lines) {
        if (!line.startsWith('data:')) continue;
        try {
          const msg = JSON.parse(line.slice(5).trim());
          if (msg.log !== undefined) {
            const cls = msg.log.includes('✓') ? 'ok' :
                        msg.log.includes('⚠') ? 'warn' :
                        msg.log.includes('❌') ? 'err' : '';
            appendLog('logB', msg.log, cls);
          }
          if (msg.status) finalResult = msg;
        } catch(e) {}
      }
    }

    if (finalResult && finalResult.status === 'complete') {
      const r4 = finalResult.result?.stage04 || {};
      const r5 = finalResult.result?.stage05 || {};
      if (!finalResult.result?.stage04 || !finalResult.result?.stage05) {
        await restoreModule2Progress(STATE.session_id);
      } else {
        handleEngineBResult(r4, r5);
      }
    } else if (finalResult && finalResult.status === 'error') {
      setEngineState('engB', 'error');
      appendLog('logB', `❌ Engine B 結束碼 ${finalResult.result?.returncode ?? '?'}`, 'err');
    } else {
      const restored = await restoreModule2Progress(STATE.session_id);
      if (!restored) {
        setEngineState('engB', 'error');
        appendLog('logB', LANG.cur === 'zh' ? '❌ 未收到完成狀態，請重試' : '❌ No completion status — please retry', 'err');
      }
    }
  } catch (e) {
    setEngineState('engB', 'error');
    appendLog('logB', `❌ ${e}`, 'err');
  } finally {
    STATE.engineBRunning = false;
    if (!STATE.engineBDone) {
      document.getElementById('btnB').disabled = false;
      setBtnBLabel(false);
    }
  }
}

function handleEngineBResult(r4, r5) {
  const candidates = r4.candidates || [];
  const status4 = r4.status || '';
  STATE.candidates = candidates;
  STATE.finalSmiles = r5.selected_smiles || r4.selected_smiles || '';

  // Stage 04
  if (status4 === 'AUTO') {
    setStage('v04','s04', candidates[0]?.slice(0,20)+'...', 's-auto', 'AUTO');
    STATE.selectedCandIdx = 0;
  } else if (status4 === 'CONFIRM' && candidates.length === 2) {
    setStage('v04','s04', `${candidates.length} 個候選`, 's-confirm', 'CONFIRM');
    renderCandidates(candidates, false);
    STATE.selectedCandIdx = 0;
    document.querySelectorAll('.cand-card')[0]?.classList.add('selected');
    document.getElementById('btn-cand-confirm').disabled = false;
    document.getElementById('cand-hint').textContent = candidates.length + ' ' + L('confirm2');
    setEngineState('engB', 'needs-input');
    return;
  } else if (status4 === 'MANUAL') {
    setStage('v04','s04', `${candidates.length} 個候選`, 's-manual', 'ACTION NEEDED');
    renderCandidates(candidates, true);
    setEngineState('engB', 'needs-input');
    molgateAiNotify(L('llmB', candidates.length));
    return;
  }

  // Stage 05
  handleTautomerResult(r5);
}

function renderCandidates(candidates, needManual) {
  const grid = document.getElementById('cand-grid');
  const section = document.getElementById('cand-section');
  grid.innerHTML = '';

  candidates.forEach((smi, i) => {
    const info = parseCandidateInfo(smi, i);
    const card = document.createElement('div');
    card.className = 'cand-card' + (!needManual && i===0 ? ' selected' : '');
    card.innerHTML = `
      <div class="cand-check">✓</div>
      <div class="cand-idx">形態 ${i}</div>
      <div class="cand-state">${info.chargeLabel}</div>
      <div class="cand-site">${info.site}</div>
      <div class="cand-note">${info.note}</div>
    `;
    card.onclick = () => selectCand(i, card);
    grid.appendChild(card);
  });
  section.style.display = '';
  document.getElementById('cand-label').textContent =
    needManual ? L('needSelect') : L('confirm2');
}

function parseCandidateInfo(smi, idx) {
  // 簡化解析：偵測質子化位置
  const hasNH = (smi.match(/\[NH\+\]/g)||[]).length;
  const hasNeg = (smi.match(/\[O-\]/g)||[]).length;
  const hasPos = (smi.match(/\[N\+\]/g)||[]).length + (smi.match(/\[NH\+\]/g)||[]).length +
                 (smi.match(/\[NH2\+\]/g)||[]).length;
  const totalCharge = hasPos - hasNeg;

  let chargeLabel, site, note;
  if (totalCharge === 0) {
    chargeLabel = idx===0 ? '中性（主要形態）' : '中性';
    site = '未帶電';
    note = 'pH 7.4 中性形態';
  } else if (totalCharge > 0) {
    chargeLabel = `+${totalCharge} 質子化`;
    site = smi.includes('[NH+]') ? 'N-H⁺ 帶電' :
           smi.includes('[N+]')  ? 'N⁺ 四級銨' : 'N 帶電';
    note = `pKa 接近 7.4，部分質子化`;
  } else {
    chargeLabel = `${totalCharge} 去質子化`;
    site = smi.includes('[O-]') ? '-COO⁻ 羧酸根' : 'O⁻ 帶電';
    note = 'pH 7.4 去質子化形態';
  }
  return {chargeLabel, site, note};
}

function selectCand(idx, el) {
  document.querySelectorAll('.cand-card').forEach(c => c.classList.remove('selected'));
  el.classList.add('selected');
  STATE.selectedCandIdx = idx;
  document.getElementById('btn-cand-confirm').disabled = false;
  document.getElementById('cand-hint').textContent = `已選：形態 ${idx}`;
}

async function confirmCandidate() {
  document.getElementById('cand-section').style.display = 'none';
  document.getElementById('btn-cand-confirm').disabled = true;
  const selected = STATE.candidates[STATE.selectedCandIdx];
  setStage('v04','s04', selected.slice(0,20)+'...', 's-manual', 'MANUAL');
  STATE.finalSmiles = selected;

  // 讀取 Stage 05 結果（已寫入）
  try {
    const r = await fetch(`/api/session/${STATE.session_id}/status`);
    const data = await r.json();
    // stage05 已由 engine B 寫入
    const r5resp = await fetch(`/api/session/${STATE.session_id}/stage05`);
    if (r5resp.ok) {
      const r5 = await r5resp.json();
      handleTautomerResult(r5);
    } else {
      finishEngineB();
    }
  } catch(e) {
    finishEngineB();
  }
}

function handleTautomerResult(r5) {
  if (!r5 || !r5.selected_smiles) { finishEngineB(); return; }
  STATE.finalSmiles = r5.selected_smiles;
  setStage('v05','s05', r5.selected_smiles.slice(0,20)+'...', 's-auto', r5.status||'AUTO');
  document.getElementById('taut-smiles').textContent = r5.selected_smiles;
  document.getElementById('taut-count').textContent =
    `${r5.tautomer_count||1} 個互變異構體 · 選定 canonical`;
  document.getElementById('taut-result').style.display = '';
  finishEngineB();
}

function finishEngineB() {
  STATE.engineBDone = true;
  setEngineState('engB', 'done');
  document.getElementById('btnB').disabled = false;
  setBtnBLabel(false);
  document.getElementById('noteB').textContent = L('nextEngineC');
  document.getElementById('nextCHint').style.display = 'flex';
  document.getElementById('btnC').disabled = false;
  document.getElementById('noteC').textContent = L('runCNote');
  setEngineState('engC', 'active');
  document.getElementById('engC').classList.add('open');
  molgateAiNotify(L('llmB', STATE.candidates.length));
}

// ── Engine C ──────────────────────────────────────
function selectEngine(name, el) {
  STATE.selectedEngine = name;
  document.querySelectorAll('.engine-opt').forEach(b => b.classList.remove('active'));
  el.classList.add('active');
}

async function runEngineC() {
  document.getElementById('btnC').disabled = true;
  setEngineState('engC', 'running');
  document.getElementById('logC').style.display = '';
  document.getElementById('logC').innerHTML = '';

  const resp = await fetch('/api/module2/engineC/run', {
    method: 'POST',
    headers: {'Content-Type':'application/json'},
    body: JSON.stringify({
      session_id: STATE.session_id,
      target: STATE.target,
      engine: STATE.selectedEngine,
    }),
  });

  const reader = resp.body.getReader();
  const decoder = new TextDecoder();
  let buffer = '';
  let finalResult = null;

  while (true) {
    const {done, value} = await reader.read();
    if (done) break;
    buffer += decoder.decode(value, {stream:true});
    const lines = buffer.split('\n');
    buffer = lines.pop();
    for (const line of lines) {
      if (!line.startsWith('data:')) continue;
      try {
        const msg = JSON.parse(line.slice(5).trim());
        if (msg.log !== undefined) {
          const cls = msg.log.includes('✓') ? 'ok' :
                      msg.log.includes('⚠') ? 'warn' :
                      msg.log.includes('❌') ? 'err' : '';
          appendLog('logC', msg.log, cls);
        }
        if (msg.status) finalResult = msg;
      } catch(e) {}
    }
  }

  if (finalResult && finalResult.status === 'complete') {
    const r = finalResult.result || {};
    const s9 = r.stage09 || {};
    setStage('v09','s09', s9.engine||STATE.selectedEngine, 's-auto', 'AUTO');
    if (r.pdbqt_exists) {
      document.getElementById('pdbqt-path').textContent = r.pdbqt_path || '—';
      document.getElementById('pdbqt-meta').textContent =
        `引擎：${s9.engine||STATE.selectedEngine} · ${s9.atom_count||'?'} 原子`;
      document.getElementById('pdbqt-result').style.display = '';
    }
    setEngineState('engC', 'done');
    showSummary(s9);
    molgateAiNotify(L('llmC'));
  } else {
    setEngineState('engC', 'error');
    document.getElementById('btnC').disabled = false;
  }
}

function showSummary(s9) {
  document.getElementById('sum-smiles').textContent = STATE.finalSmiles;
  document.getElementById('sum-s04').textContent =
    STATE.candidates.length > 1 ? 'MANUAL' : 'AUTO';
  document.getElementById('sum-s05').textContent = 'AUTO';
  document.getElementById('summary').classList.add('visible');
}

function goModule3() {
  var qs = 'session=' + encodeURIComponent(STATE.session_id) + '&target=' + encodeURIComponent(STATE.target || '');
  window.location.href = (window.molgateModuleUrl ? window.molgateModuleUrl(3, qs) : ('/module/3?' + qs));
}

// ── Stage 05 API ──────────────────────────────────
// 加一個讀取 stage05 的 helper endpoint（server 需支援）
// 若 server 未實作，confirmCandidate 會直接 finishEngineB
</script>
<script src="../../assets/molgate.js" onerror="this.onerror=null;this.src='/molgate_ui_shared.js'"></script>
<script src="../../assets/molgate_ai_sidebar.js" onerror="this.onerror=null;this.src='/assets/molgate_ai_sidebar.js'"></script>
<script>
window.LANG = LANG;
molgateAiBind({
  panelKey: 'm2',
  systemPrompt: () => LANG.cur === 'zh'
    ? '你是 DrugOps Module 2 助手，協助解釋質子化候選、tautomer 與 ligand 準備。請用繁體中文（台灣）回答。'
    : 'You are the DrugOps Module 2 assistant for protonation, tautomers, and ligand prep. Reply in Traditional Chinese (Taiwan) unless asked otherwise.',
  extraMessages: () => {
    const parts = [];
    if (STATE.smiles) parts.push({ role: 'system', content: 'SMILES: ' + STATE.smiles });
    if (STATE.target) parts.push({ role: 'system', content: 'Target: ' + STATE.target });
    if (STATE.session_id) parts.push({ role: 'system', content: 'Session: ' + STATE.session_id });
    if (STATE.candidates && STATE.candidates.length) {
      parts.push({ role: 'system', content: 'Protonation candidates: ' + JSON.stringify(STATE.candidates) });
    }
    return parts;
  },
});
</script>
</body>
</html>