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xiaoruiDongxiaoruiDong
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Merge pull request #565 from ReactionMechanismGenerator/rotor_scans
Rotor scans
2 parents 03ff129 + e118363 commit eaf7c1a

9 files changed

Lines changed: 880 additions & 1432 deletions

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‎input/kinetics/families/1,3_sigmatropic_rearrangement/groups.py‎

Lines changed: 41 additions & 133 deletions
Original file line numberDiff line numberDiff line change
@@ -81,29 +81,29 @@
8181

8282
entry(
8383
index = 3,
84-
label = "Root_Ext-2R!H-R_5R!H->C_Ext-1R!H-R",
84+
label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C",
8585
group =
8686
"""
87-
1 *2 C u0 {2,S} {3,D} {6,[S,D,T,B,Q]}
88-
2 *3 N u0 r1 {1,S} {4,S} {5,[S,D,T,B,Q]}
87+
1 *2 C u0 {2,S} {3,D}
88+
2 *3 N u0 {1,S} {4,S} {5,[S,D,T,B,Q]}
8989
3 *1 R!H u0 {1,D}
90-
4 *4 R!H u0 r1 {2,S}
91-
5 C ux r1 {2,[S,D,T,B,Q]}
92-
6 R!H ux {1,[S,D,T,B,Q]}
90+
4 *4 C u0 {2,S}
91+
5 C ux {2,[S,D,T,B,Q]}
9392
""",
9493
kinetics = None,
9594
)
9695

9796
entry(
9897
index = 4,
99-
label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C",
98+
label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C_Ext-1R!H-R",
10099
group =
101100
"""
102-
1 *2 C u0 {2,S} {3,D}
103-
2 *3 N u0 {1,S} {4,S} {5,S}
104-
3 *1 R!H u0 {1,D}
105-
4 *4 C u0 {2,S}
106-
5 C u0 {2,S}
101+
1 *2 C u0 r0 {2,S} {3,D} {6,[S,D,T,B,Q]}
102+
2 *3 N u0 r1 {1,S} {4,S} {5,S}
103+
3 *1 R!H u0 r0 {1,D}
104+
4 *4 C u0 r1 {2,S}
105+
5 C u0 r1 {2,S}
106+
6 R!H ux {1,[S,D,T,B,Q]}
107107
""",
108108
kinetics = None,
109109
)
@@ -113,11 +113,11 @@
113113
label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C_3R!H->N",
114114
group =
115115
"""
116-
1 *2 C u0 r0 {2,S} {3,D}
117-
2 *3 N u0 r1 {1,S} {4,S} {5,S}
118-
3 *1 N u0 r0 {1,D}
116+
1 *2 C u0 {2,S} {3,D}
117+
2 *3 N u0 r1 {1,S} {4,S} {5,[S,D,T,B,Q]}
118+
3 *1 N u0 {1,D}
119119
4 *4 C u0 r1 {2,S}
120-
5 C u0 r1 {2,S}
120+
5 C ux r1 {2,[S,D,T,B,Q]}
121121
""",
122122
kinetics = None,
123123
)
@@ -127,11 +127,11 @@
127127
label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C_N-3R!H->N",
128128
group =
129129
"""
130-
1 *2 C u0 r0 {2,S} {3,D}
131-
2 *3 N u0 r1 {1,S} {4,S} {5,S}
132-
3 *1 O u0 r0 {1,D}
130+
1 *2 C u0 {2,S} {3,D}
131+
2 *3 N u0 r1 {1,S} {4,S} {5,[S,D,T,B,Q]}
132+
3 *1 O u0 {1,D}
133133
4 *4 C u0 r1 {2,S}
134-
5 C u0 r1 {2,S}
134+
5 C ux r1 {2,[S,D,T,B,Q]}
135135
""",
136136
kinetics = None,
137137
)
@@ -269,7 +269,7 @@
269269
2 *3 N u0 r1 {1,S} {4,S}
270270
3 *1 N u0 r1 {1,D}
271271
4 *4 C u0 r1 {2,S} {5,D}
272-
5 [F,I,N,Br,Cl,O,P,S,Si] u0 r1 {4,D}
272+
5 [I,P,Br,Cl,O,F,N,S,Si] u0 r1 {4,D}
273273
""",
274274
kinetics = None,
275275
)
@@ -350,7 +350,7 @@
350350
2 *3 O u0 r1 {1,S} {4,S}
351351
3 *1 N u0 r1 {1,D}
352352
4 *4 C u0 r1 {2,S} {5,D}
353-
5 [F,I,N,Br,Cl,O,P,S,Si] u0 r1 {4,D}
353+
5 [I,P,Br,Cl,O,F,N,S,Si] u0 r1 {4,D}
354354
""",
355355
kinetics = None,
356356
)
@@ -390,7 +390,7 @@
390390
2 *3 R!H u0 {1,S} {4,S}
391391
3 *1 R!H u0 {1,D}
392392
4 *4 C u0 {2,S} {5,[S,D,T,B,Q]}
393-
5 R!H ux {4,[S,D,T,B,Q]}
393+
5 O ux {4,[S,D,T,B,Q]}
394394
""",
395395
kinetics = None,
396396
)
@@ -400,20 +400,6 @@
400400
label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N",
401401
group =
402402
"""
403-
1 *2 C u0 r0 {2,S} {3,D}
404-
2 *3 N u0 {1,S} {4,S}
405-
3 *1 O u0 {1,D}
406-
4 *4 C u0 {2,S} {5,[S,D,T,B,Q]}
407-
5 R!H ux {4,[S,D,T,B,Q]}
408-
""",
409-
kinetics = None,
410-
)
411-
412-
entry(
413-
index = 27,
414-
label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O",
415-
group =
416-
"""
417403
1 *2 C u0 r0 {2,S} {3,D}
418404
2 *3 N u0 {1,S} {4,S}
419405
3 *1 O u0 {1,D}
@@ -424,123 +410,51 @@
424410
)
425411

426412
entry(
427-
index = 28,
428-
label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O_Ext-4R!H-R",
429-
group =
430-
"""
431-
1 *2 C u0 r0 {2,S} {3,D}
432-
2 *3 N u0 {1,S} {4,S}
433-
3 *1 O u0 {1,D}
434-
4 *4 C u0 {2,S} {5,D} {6,[S,D,T,B,Q]}
435-
5 O u0 r0 {4,D}
436-
6 R!H ux {4,[S,D,T,B,Q]}
437-
""",
438-
kinetics = None,
439-
)
440-
441-
entry(
442-
index = 29,
443-
label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O_Ext-1R!H-R",
413+
index = 27,
414+
label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_Ext-1R!H-R",
444415
group =
445416
"""
446417
1 *2 C u0 r0 {2,S} {3,D} {6,[S,D,T,B,Q]}
447-
2 *3 N u0 {1,S} {4,S}
448-
3 *1 O u0 {1,D}
449-
4 *4 C u0 {2,S} {5,[S,D,T,B,Q]}
418+
2 *3 N u0 r0 {1,S} {4,S}
419+
3 *1 O u0 r0 {1,D}
420+
4 *4 C u0 r0 {2,S} {5,[S,D,T,B,Q]}
450421
5 O ux {4,[S,D,T,B,Q]}
451422
6 R!H ux {1,[S,D,T,B,Q]}
452423
""",
453424
kinetics = None,
454425
)
455426

456427
entry(
457-
index = 30,
458-
label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_N-5R!H->O",
459-
group =
460-
"""
461-
1 *2 C u0 r0 {2,S} {3,D}
462-
2 *3 N u0 r0 {1,S} {4,S}
463-
3 *1 O u0 r0 {1,D}
464-
4 *4 C u0 r0 {2,S} {5,D}
465-
5 N ux {4,D}
466-
""",
467-
kinetics = None,
468-
)
469-
470-
entry(
471-
index = 31,
428+
index = 28,
472429
label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N",
473430
group =
474431
"""
475-
1 *2 C u0 r0 {2,S} {3,D}
476-
2 *3 O u0 {1,S} {4,S}
477-
3 *1 N u0 {1,D}
478-
4 *4 C u0 {2,S} {5,[S,D,T,B,Q]}
479-
5 R!H u0 {4,[S,D,T,B,Q]}
480-
""",
481-
kinetics = None,
482-
)
483-
484-
entry(
485-
index = 32,
486-
label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_5R!H->N",
487-
group =
488-
"""
489432
1 *2 C u0 r0 {2,S} {3,D}
490433
2 *3 O u0 {1,S} {4,S}
491434
3 *1 N u0 {1,D}
492435
4 *4 C u0 {2,S} {5,[S,D,T,B,Q]}
493-
5 N u0 {4,[S,D,T,B,Q]}
494-
""",
495-
kinetics = None,
496-
)
497-
498-
entry(
499-
index = 33,
500-
label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_5R!H->N_Ext-4R!H-R",
501-
group =
502-
"""
503-
1 *2 C u0 r0 {2,S} {3,D}
504-
2 *3 O u0 {1,S} {4,S}
505-
3 *1 N u0 {1,D}
506-
4 *4 C u0 {2,S} {5,[S,D,T,B,Q]} {6,[S,D,T,B,Q]}
507-
5 N u0 r0 {4,[S,D,T,B,Q]}
508-
6 R!H ux {4,[S,D,T,B,Q]}
509-
""",
510-
kinetics = None,
511-
)
512-
513-
entry(
514-
index = 34,
515-
label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_N-5R!H->N",
516-
group =
517-
"""
518-
1 *2 C u0 r0 {2,S} {3,D}
519-
2 *3 O u0 {1,S} {4,S}
520-
3 *1 N u0 {1,D}
521-
4 *4 C u0 {2,S} {5,D}
522-
5 O u0 {4,D}
436+
5 O ux {4,[S,D,T,B,Q]}
523437
""",
524438
kinetics = None,
525439
)
526440

527441
entry(
528-
index = 35,
529-
label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_N-5R!H->N_Ext-1R!H-R",
442+
index = 29,
443+
label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_Ext-1R!H-R",
530444
group =
531445
"""
532446
1 *2 C u0 r0 {2,S} {3,D} {6,[S,D,T,B,Q]}
533-
2 *3 O u0 {1,S} {4,S}
534-
3 *1 N u0 {1,D}
535-
4 *4 C u0 {2,S} {5,D}
536-
5 O u0 r0 {4,D}
447+
2 *3 O u0 r0 {1,S} {4,S}
448+
3 *1 N u0 r0 {1,D}
449+
4 *4 C u0 r0 {2,S} {5,[S,D,T,B,Q]}
450+
5 O ux {4,[S,D,T,B,Q]}
537451
6 R!H ux {1,[S,D,T,B,Q]}
538452
""",
539453
kinetics = None,
540454
)
541455

542456
entry(
543-
index = 36,
457+
index = 30,
544458
label = "Root_N-1R!H-inRing_2R!H->C",
545459
group =
546460
"""
@@ -553,7 +467,7 @@
553467
)
554468

555469
entry(
556-
index = 37,
470+
index = 31,
557471
label = "Root_N-1R!H-inRing_N-2R!H->C",
558472
group =
559473
"""
@@ -570,8 +484,8 @@
570484
L1: Root
571485
L2: Root_Ext-2R!H-R
572486
L3: Root_Ext-2R!H-R_5R!H->C
573-
L4: Root_Ext-2R!H-R_5R!H->C_Ext-1R!H-R
574487
L4: Root_Ext-2R!H-R_5R!H->C_4R!H->C
488+
L5: Root_Ext-2R!H-R_5R!H->C_4R!H->C_Ext-1R!H-R
575489
L5: Root_Ext-2R!H-R_5R!H->C_4R!H->C_3R!H->N
576490
L5: Root_Ext-2R!H-R_5R!H->C_4R!H->C_N-3R!H->N
577491
L4: Root_Ext-2R!H-R_5R!H->C_N-4R!H->C
@@ -594,15 +508,9 @@
594508
L2: Root_N-1R!H-inRing
595509
L3: Root_N-1R!H-inRing_Ext-4R!H-R
596510
L4: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N
597-
L5: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O
598-
L6: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O_Ext-4R!H-R
599-
L6: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O_Ext-1R!H-R
600-
L5: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_N-5R!H->O
511+
L5: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_Ext-1R!H-R
601512
L4: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N
602-
L5: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_5R!H->N
603-
L6: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_5R!H->N_Ext-4R!H-R
604-
L5: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_N-5R!H->N
605-
L6: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_N-5R!H->N_Ext-1R!H-R
513+
L5: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_Ext-1R!H-R
606514
L3: Root_N-1R!H-inRing_2R!H->C
607515
L3: Root_N-1R!H-inRing_N-2R!H->C
608516
"""

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