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KEHANGKEHANG
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Merge pull request #105 from ReactionMechanismGenerator/fixTrees
Fix trees
2 parents 6213eb4 + 253b662 commit 6ba1c55

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15 files changed

+4566
-4296
lines changed

15 files changed

+4566
-4296
lines changed

‎input/kinetics/families/Cyclic_Ether_Formation/groups.py‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1245,26 +1245,26 @@
12451245
L3: R3OOJ
12461246
L3: R3OOH
12471247
L4: R3OOH_SS
1248-
L4: R3OOH_SSCO
1248+
L5: R3OOH_SSCO
12491249
L4: R3OOH_SD
12501250
L4: R3OOH_DS
12511251
L3: R3OOR
12521252
L4: R3OOR_SS
1253-
L4: R3OOR_SSCO
1253+
L5: R3OOR_SSCO
12541254
L4: R3OOR_SD
12551255
L4: R3OOR_DS
12561256
L2: R4OO
12571257
L3: R4OOJ
12581258
L3: R4OOH
12591259
L4: R4OOH_SSS
1260-
L4: R4OOH_SSSCO
1260+
L5: R4OOH_SSSCO
12611261
L4: R4OOH_SSD
12621262
L4: R4OOH_SDS
12631263
L4: R4OOH_DSS
12641264
L4: R4OOH_DSD
12651265
L3: R4OOR
12661266
L4: R4OOR_SSS
1267-
L4: R4OOR_SSSCO
1267+
L5: R4OOR_SSSCO
12681268
L4: R4OOR_SSD
12691269
L4: R4OOR_SDS
12701270
L4: R4OOR_DSS
@@ -1273,7 +1273,7 @@
12731273
L3: R5OOJ
12741274
L3: R5OOH
12751275
L4: R5OOH_SSSS
1276-
L4: R5OOH_SSSSCO
1276+
L5: R5OOH_SSSSCO
12771277
L4: R5OOH_SSSD
12781278
L4: R5OOH_SSDS
12791279
L4: R5OOH_SDSS
@@ -1282,7 +1282,7 @@
12821282
L4: R5OOH_DSDS
12831283
L3: R5OOR
12841284
L4: R5OOR_SSSS
1285-
L4: R5OOR_SSSSCO
1285+
L5: R5OOR_SSSSCO
12861286
L4: R5OOR_SSSD
12871287
L4: R5OOR_SSDS
12881288
L4: R5OOR_SDSS

‎input/kinetics/families/Disproportionation/groups.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2720,13 +2720,12 @@
27202720
L2: Y_2centerbirad
27212721
L3: O2b
27222722
L3: C2b
2723-
L3: S2b
2723+
L3: S2b
27242724
L2: Y_1centerbirad
27252725
L3: CO_birad_triplet
27262726
L3: O_atom_triplet
27272727
L3: CH2_triplet
27282728
L3: NH_triplet
2729-
L2: H_rad
27302729
L2: Y_rad
27312730
L3: Ct_rad
27322731
L4: Ct_rad/Ct
@@ -2811,6 +2810,7 @@
28112810
L5: N3d_rad/N
28122811
L3: N5_rad
28132812
L4: N5d_rad
2813+
L3: H_rad
28142814
L1: XH_Rrad_birad
28152815
L2: XH_Rrad
28162816
L3: XH_s_Rrad
@@ -2852,7 +2852,7 @@
28522852
L6: C/H2/Nd_COrad
28532853
L6: C/H2/Nd_Orad
28542854
L6: C/H2/Nd_Nrad
2855-
L6: C/H2/Nd_Srad
2855+
L6: C/H2/Nd_Srad
28562856
L5: C/H2/De_Rrad
28572857
L6: C/H2/De_Csrad
28582858
L7: C/H2/De_Csrad/H/Cd

‎input/kinetics/families/H_Abstraction/groups.py‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -533,10 +533,10 @@
533533
label = "Cd/H/OneDe",
534534
group =
535535
"""
536-
1 *1 C u0 {2,D} {3,S} {4,S}
537-
2 Cd u0 {1,D} {5,S}
538-
3 *2 H u0 {1,S}
539-
4 [Cd,Ct,Cb,CO,CS,N] u0 {1,S}
536+
1 *1 C u0 {2,D} {3,S} {4,S}
537+
2 Cd u0 {1,D} {5,S}
538+
3 *2 H u0 {1,S}
539+
4 [Cd,Ct,Cb,CO,CS,N3d,N3t,N3b,N5d,N5dd,N5t,N5b] u0 {1,S}
540540
5 R u0 {2,S}
541541
""",
542542
kinetics = None,
@@ -6678,8 +6678,8 @@
66786678
L8: O_rad/Cd\Cs_Cd\H2
66796679
L8: O_rad/Cd\Cs_Cd\H\Cs
66806680
L8: O_rad/Cd\Cs_Cd\Cs2
6681-
L6: InChI=1S/NO3/c2-1(3)4
66826681
L6: O_rad/OneDeN
6682+
L7: InChI=1S/NO3/c2-1(3)4
66836683
L3: S_rad
66846684
L4: S_pri_rad
66856685
L4: S_sec_rad

‎input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py‎

Lines changed: 21 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1079,32 +1079,34 @@
10791079
group =
10801080
"""
10811081
1 *1 Cs u0 {2,S} {3,S}
1082-
2 *2 H u0 {1,S}
1082+
2 *4 H u0 {1,S}
10831083
3 H u0 {1,S}
10841084
""",
10851085
kinetics = None,
10861086
)
10871087

10881088
entry(
10891089
index = 182,
1090-
label = "radadd_intra_csHNd",
1090+
label = "radadd_intra_csHHNd",
10911091
group =
10921092
"""
1093-
1 *1 Cs u0 {2,S} {3,S}
1094-
2 *2 H u0 {1,S}
1093+
1 *1 Cs u0 {2,S} {3,S} {4,S}
1094+
2 *4 H u0 {1,S}
10951095
3 [Cs,O] u0 {1,S}
1096+
4 H u0 {1,S}
10961097
""",
10971098
kinetics = None,
10981099
)
10991100

11001101
entry(
11011102
index = 183,
1102-
label = "radadd_intra_csHDe",
1103+
label = "radadd_intra_csHHDe",
11031104
group =
11041105
"""
1105-
1 *1 Cs u0 {2,S} {3,S}
1106-
2 *2 H u0 {1,S}
1106+
1 *1 Cs u0 {2,S} {3,S} {4,S}
1107+
2 *4 H u0 {1,S}
11071108
3 [Cd,Ct,Cb,CO] u0 {1,S}
1109+
4 H u0 {1,S}
11081110
""",
11091111
kinetics = None,
11101112
)
@@ -1115,7 +1117,7 @@
11151117
group =
11161118
"""
11171119
1 *1 Cs u0 {2,S} {3,S} {4,S}
1118-
2 *2 H u0 {1,S}
1120+
2 *4 H u0 {1,S}
11191121
3 [Cs,O] u0 {1,S}
11201122
4 [Cs,O] u0 {1,S}
11211123
""",
@@ -1128,7 +1130,7 @@
11281130
group =
11291131
"""
11301132
1 *1 Cs u0 {2,S} {3,S} {4,S}
1131-
2 *2 H u0 {1,S}
1133+
2 *4 H u0 {1,S}
11321134
3 [Cs,O] u0 {1,S}
11331135
4 [Cd,Ct,Cb,CO] u0 {1,S}
11341136
""",
@@ -1141,7 +1143,7 @@
11411143
group =
11421144
"""
11431145
1 *1 Cs u0 {2,S} {3,S} {4,S}
1144-
2 *2 H u0 {1,S}
1146+
2 *4 H u0 {1,S}
11451147
3 [Cd,Ct,Cb,CO] u0 {1,S}
11461148
4 [Cd,Ct,Cb,CO] u0 {1,S}
11471149
""",
@@ -1174,7 +1176,7 @@
11741176
group =
11751177
"""
11761178
1 *1 Cd u0 {2,S} {3,S}
1177-
2 *2 H u0 {1,S}
1179+
2 *4 H u0 {1,S}
11781180
3 R u0 {1,S}
11791181
""",
11801182
kinetics = None,
@@ -1186,7 +1188,7 @@
11861188
group =
11871189
"""
11881190
1 *1 Cd u0 {2,S} {3,S}
1189-
2 *2 H u0 {1,S}
1191+
2 *4 H u0 {1,S}
11901192
3 H u0 {1,S}
11911193
""",
11921194
kinetics = None,
@@ -1198,7 +1200,7 @@
11981200
group =
11991201
"""
12001202
1 *1 Cd u0 {2,S} {3,S}
1201-
2 *2 H u0 {1,S}
1203+
2 *4 H u0 {1,S}
12021204
3 [Cs,O] u0 {1,S}
12031205
""",
12041206
kinetics = None,
@@ -1210,7 +1212,7 @@
12101212
group =
12111213
"""
12121214
1 *1 Cd u0 {2,S} {3,S}
1213-
2 *2 H u0 {1,S}
1215+
2 *4 H u0 {1,S}
12141216
3 [Cd,Ct,Cb,CO] u0 {1,S}
12151217
""",
12161218
kinetics = None,
@@ -1222,7 +1224,7 @@
12221224
group =
12231225
"""
12241226
1 *1 Cd u0 {2,S} {3,D}
1225-
2 *2 H u0 {1,S}
1227+
2 *4 H u0 {1,S}
12261228
3 Cd u0 {1,D}
12271229
""",
12281230
kinetics = None,
@@ -1234,7 +1236,7 @@
12341236
group =
12351237
"""
12361238
1 *1 CO u0 {2,S} {3,D}
1237-
2 *2 H u0 {1,S}
1239+
2 *4 H u0 {1,S}
12381240
3 O u0 {1,D}
12391241
""",
12401242
kinetics = None,
@@ -1246,7 +1248,7 @@
12461248
group =
12471249
"""
12481250
1 *1 Ct u0 {2,S} {3,T}
1249-
2 *2 H u0 {1,S}
1251+
2 *4 H u0 {1,S}
12501252
3 Ct u0 {1,T}
12511253
""",
12521254
kinetics = None,
@@ -1324,8 +1326,8 @@
13241326
L1: radadd_intra
13251327
L2: radadd_intra_cs
13261328
L3: radadd_intra_cs2H
1327-
L3: radadd_intra_csHNd
1328-
L3: radadd_intra_csHDe
1329+
L4: radadd_intra_csHHNd
1330+
L4: radadd_intra_csHHDe
13291331
L3: radadd_intra_csNdNd
13301332
L3: radadd_intra_csNdDe
13311333
L3: radadd_intra_csDeDe

‎input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py‎

Lines changed: 21 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -2548,32 +2548,34 @@
25482548
group =
25492549
"""
25502550
1 *1 Cs u0 {2,S} {3,S}
2551-
2 *2 H u0 {1,S}
2551+
2 *4 H u0 {1,S}
25522552
3 H u0 {1,S}
25532553
""",
25542554
kinetics = None,
25552555
)
25562556

25572557
entry(
25582558
index = 182,
2559-
label = "radadd_intra_csHNd",
2559+
label = "radadd_intra_csHHNd",
25602560
group =
25612561
"""
2562-
1 *1 Cs u0 {2,S} {3,S}
2563-
2 *2 H u0 {1,S}
2562+
1 *1 Cs u0 {2,S} {3,S} {4,S}
2563+
2 *4 H u0 {1,S}
25642564
3 [Cs,O] u0 {1,S}
2565+
4 H u0 {1,S}
25652566
""",
25662567
kinetics = None,
25672568
)
25682569

25692570
entry(
25702571
index = 183,
2571-
label = "radadd_intra_csHDe",
2572+
label = "radadd_intra_csHHDe",
25722573
group =
25732574
"""
2574-
1 *1 Cs u0 {2,S} {3,S}
2575-
2 *2 H u0 {1,S}
2575+
1 *1 Cs u0 {2,S} {3,S} {4,S}
2576+
2 *4 H u0 {1,S}
25762577
3 [Cd,Ct,Cb,CO] u0 {1,S}
2578+
4 H u0 {1,S}
25772579
""",
25782580
kinetics = None,
25792581
)
@@ -2584,7 +2586,7 @@
25842586
group =
25852587
"""
25862588
1 *1 Cs u0 {2,S} {3,S} {4,S}
2587-
2 *2 H u0 {1,S}
2589+
2 *4 H u0 {1,S}
25882590
3 [Cs,O] u0 {1,S}
25892591
4 [Cs,O] u0 {1,S}
25902592
""",
@@ -2597,7 +2599,7 @@
25972599
group =
25982600
"""
25992601
1 *1 Cs u0 {2,S} {3,S} {4,S}
2600-
2 *2 H u0 {1,S}
2602+
2 *4 H u0 {1,S}
26012603
3 [Cs,O] u0 {1,S}
26022604
4 [Cd,Ct,Cb,CO] u0 {1,S}
26032605
""",
@@ -2610,7 +2612,7 @@
26102612
group =
26112613
"""
26122614
1 *1 Cs u0 {2,S} {3,S} {4,S}
2613-
2 *2 H u0 {1,S}
2615+
2 *4 H u0 {1,S}
26142616
3 [Cd,Ct,Cb,CO] u0 {1,S}
26152617
4 [Cd,Ct,Cb,CO] u0 {1,S}
26162618
""",
@@ -2643,7 +2645,7 @@
26432645
group =
26442646
"""
26452647
1 *1 Cd u0 {2,S} {3,S}
2646-
2 *2 H u0 {1,S}
2648+
2 *4 H u0 {1,S}
26472649
3 R u0 {1,S}
26482650
""",
26492651
kinetics = None,
@@ -2655,7 +2657,7 @@
26552657
group =
26562658
"""
26572659
1 *1 Cd u0 {2,S} {3,S}
2658-
2 *2 H u0 {1,S}
2660+
2 *4 H u0 {1,S}
26592661
3 H u0 {1,S}
26602662
""",
26612663
kinetics = None,
@@ -2667,7 +2669,7 @@
26672669
group =
26682670
"""
26692671
1 *1 Cd u0 {2,S} {3,S}
2670-
2 *2 H u0 {1,S}
2672+
2 *4 H u0 {1,S}
26712673
3 [Cs,O] u0 {1,S}
26722674
""",
26732675
kinetics = None,
@@ -2679,7 +2681,7 @@
26792681
group =
26802682
"""
26812683
1 *1 Cd u0 {2,S} {3,S}
2682-
2 *2 H u0 {1,S}
2684+
2 *4 H u0 {1,S}
26832685
3 [Cd,Ct,Cb,CO] u0 {1,S}
26842686
""",
26852687
kinetics = None,
@@ -2691,7 +2693,7 @@
26912693
group =
26922694
"""
26932695
1 *1 Cd u0 {2,S} {3,D}
2694-
2 *2 H u0 {1,S}
2696+
2 *4 H u0 {1,S}
26952697
3 Cd u0 {1,D}
26962698
""",
26972699
kinetics = None,
@@ -2703,7 +2705,7 @@
27032705
group =
27042706
"""
27052707
1 *1 CO u0 {2,S} {3,D}
2706-
2 *2 H u0 {1,S}
2708+
2 *4 H u0 {1,S}
27072709
3 O u0 {1,D}
27082710
""",
27092711
kinetics = None,
@@ -2715,7 +2717,7 @@
27152717
group =
27162718
"""
27172719
1 *1 Ct u0 {2,S} {3,T}
2718-
2 *2 H u0 {1,S}
2720+
2 *4 H u0 {1,S}
27192721
3 Ct u0 {1,T}
27202722
""",
27212723
kinetics = None,
@@ -2886,8 +2888,8 @@
28862888
L1: radadd_intra
28872889
L2: radadd_intra_cs
28882890
L3: radadd_intra_cs2H
2889-
L3: radadd_intra_csHNd
2890-
L3: radadd_intra_csHDe
2891+
L4: radadd_intra_csHHNd
2892+
L4: radadd_intra_csHHDe
28912893
L3: radadd_intra_csNdNd
28922894
L3: radadd_intra_csNdDe
28932895
L3: radadd_intra_csDeDe

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