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Merged
merged 21 commits into from
Jun 15, 2016
Merged

Fix trees #105

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f55608e
Add unitTest for checking sibling relationship
nyee Jun 3, 2016
b378e10
Removed all groups with a CS atomType
nyee Jun 1, 2016
b46b957
Edit adjlist for every instance of (Cds-Cd) ligand in groups.py
nyee Jun 2, 2016
cada4c6
Move a few groups around in tree due to changes from last commit
nyee Jun 3, 2016
247568d
Fixes for siblings that should be child/parent in radical.py
nyee Jun 3, 2016
febb553
Add in groups with CS atomType
nyee Jun 12, 2016
db2fae7
Set references in training reaction to None instead of empty strings
nyee Jun 13, 2016
1e91b56
Fix parent/child siblings for Disprop family
nyee Jun 13, 2016
3f84e7c
Fix Intra_RH_Add family labels
nyee Jun 13, 2016
9b9242f
More explictly define groups for Intra_R_Add families
nyee Jun 13, 2016
471a8a0
Fix sibling parent/child for intra_substitutionCS_isomerization
nyee Jun 13, 2016
434f98f
Fix sibling parent/child relationships for H_Abstraction
nyee Jun 13, 2016
f3a5a53
Fix sibling parent/child relationships for Cyclic_Ether_Formation
nyee Jun 13, 2016
28df61d
Redefine one group in intra_H_migration to fix sibling parent/child bug
nyee Jun 13, 2016
1d47b07
Fix groups in R_Addition_Multiple_Bond
nyee Jun 14, 2016
fe05136
Fix sibling child/parent bug for R_Addition_MultipleBond
nyee Jun 14, 2016
129d1e5
Clarify some groups in statmech to avoid sibling bug
nyee Jun 14, 2016
a5d14ff
Moved four groups to fix sibling child/parent in statmech
nyee Jun 14, 2016
d20fd02
Move a groups to fix sibling bug in transport
nyee Jun 14, 2016
a48a1f4
Add sibling check for transport, kinetic families, solvation, statmec…
nyee Jun 15, 2016
253b662
Fix bug with sibling check
nyee Jun 15, 2016
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12 changes: 6 additions & 6 deletions input/kinetics/families/Cyclic_Ether_Formation/groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1245,26 +1245,26 @@
L3: R3OOJ
L3: R3OOH
L4: R3OOH_SS
L4: R3OOH_SSCO
L5: R3OOH_SSCO
L4: R3OOH_SD
L4: R3OOH_DS
L3: R3OOR
L4: R3OOR_SS
L4: R3OOR_SSCO
L5: R3OOR_SSCO
L4: R3OOR_SD
L4: R3OOR_DS
L2: R4OO
L3: R4OOJ
L3: R4OOH
L4: R4OOH_SSS
L4: R4OOH_SSSCO
L5: R4OOH_SSSCO
L4: R4OOH_SSD
L4: R4OOH_SDS
L4: R4OOH_DSS
L4: R4OOH_DSD
L3: R4OOR
L4: R4OOR_SSS
L4: R4OOR_SSSCO
L5: R4OOR_SSSCO
L4: R4OOR_SSD
L4: R4OOR_SDS
L4: R4OOR_DSS
Expand All @@ -1273,7 +1273,7 @@
L3: R5OOJ
L3: R5OOH
L4: R5OOH_SSSS
L4: R5OOH_SSSSCO
L5: R5OOH_SSSSCO
L4: R5OOH_SSSD
L4: R5OOH_SSDS
L4: R5OOH_SDSS
Expand All @@ -1282,7 +1282,7 @@
L4: R5OOH_DSDS
L3: R5OOR
L4: R5OOR_SSSS
L4: R5OOR_SSSSCO
L5: R5OOR_SSSSCO
L4: R5OOR_SSSD
L4: R5OOR_SSDS
L4: R5OOR_SDSS
Expand Down
6 changes: 3 additions & 3 deletions input/kinetics/families/Disproportionation/groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2720,13 +2720,12 @@
L2: Y_2centerbirad
L3: O2b
L3: C2b
L3: S2b
L3: S2b
L2: Y_1centerbirad
L3: CO_birad_triplet
L3: O_atom_triplet
L3: CH2_triplet
L3: NH_triplet
L2: H_rad
L2: Y_rad
L3: Ct_rad
L4: Ct_rad/Ct
Expand Down Expand Up @@ -2811,6 +2810,7 @@
L5: N3d_rad/N
L3: N5_rad
L4: N5d_rad
L3: H_rad
L1: XH_Rrad_birad
L2: XH_Rrad
L3: XH_s_Rrad
Expand Down Expand Up @@ -2852,7 +2852,7 @@
L6: C/H2/Nd_COrad
L6: C/H2/Nd_Orad
L6: C/H2/Nd_Nrad
L6: C/H2/Nd_Srad
L6: C/H2/Nd_Srad
L5: C/H2/De_Rrad
L6: C/H2/De_Csrad
L7: C/H2/De_Csrad/H/Cd
Expand Down
10 changes: 5 additions & 5 deletions input/kinetics/families/H_Abstraction/groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -533,10 +533,10 @@
label = "Cd/H/OneDe",
group =
"""
1 *1 C u0 {2,D} {3,S} {4,S}
2 Cd u0 {1,D} {5,S}
3 *2 H u0 {1,S}
4 [Cd,Ct,Cb,CO,CS,N] u0 {1,S}
1 *1 C u0 {2,D} {3,S} {4,S}
2 Cd u0 {1,D} {5,S}
3 *2 H u0 {1,S}
4 [Cd,Ct,Cb,CO,CS,N3d,N3t,N3b,N5d,N5dd,N5t,N5b] u0 {1,S}
5 R u0 {2,S}
""",
kinetics = None,
Expand Down Expand Up @@ -6678,8 +6678,8 @@
L8: O_rad/Cd\Cs_Cd\H2
L8: O_rad/Cd\Cs_Cd\H\Cs
L8: O_rad/Cd\Cs_Cd\Cs2
L6: InChI=1S/NO3/c2-1(3)4
L6: O_rad/OneDeN
L7: InChI=1S/NO3/c2-1(3)4
L3: S_rad
L4: S_pri_rad
L4: S_sec_rad
Expand Down
40 changes: 21 additions & 19 deletions input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1079,32 +1079,34 @@
group =
"""
1 *1 Cs u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 H u0 {1,S}
""",
kinetics = None,
)

entry(
index = 182,
label = "radadd_intra_csHNd",
label = "radadd_intra_csHHNd",
group =
"""
1 *1 Cs u0 {2,S} {3,S}
2 *2 H u0 {1,S}
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *4 H u0 {1,S}
3 [Cs,O] u0 {1,S}
4 H u0 {1,S}
""",
kinetics = None,
)

entry(
index = 183,
label = "radadd_intra_csHDe",
label = "radadd_intra_csHHDe",
group =
"""
1 *1 Cs u0 {2,S} {3,S}
2 *2 H u0 {1,S}
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *4 H u0 {1,S}
3 [Cd,Ct,Cb,CO] u0 {1,S}
4 H u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -1115,7 +1117,7 @@
group =
"""
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cs,O] u0 {1,S}
4 [Cs,O] u0 {1,S}
""",
Expand All @@ -1128,7 +1130,7 @@
group =
"""
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cs,O] u0 {1,S}
4 [Cd,Ct,Cb,CO] u0 {1,S}
""",
Expand All @@ -1141,7 +1143,7 @@
group =
"""
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cd,Ct,Cb,CO] u0 {1,S}
4 [Cd,Ct,Cb,CO] u0 {1,S}
""",
Expand Down Expand Up @@ -1174,7 +1176,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 R u0 {1,S}
""",
kinetics = None,
Expand All @@ -1186,7 +1188,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 H u0 {1,S}
""",
kinetics = None,
Expand All @@ -1198,7 +1200,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cs,O] u0 {1,S}
""",
kinetics = None,
Expand All @@ -1210,7 +1212,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cd,Ct,Cb,CO] u0 {1,S}
""",
kinetics = None,
Expand All @@ -1222,7 +1224,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,D}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 Cd u0 {1,D}
""",
kinetics = None,
Expand All @@ -1234,7 +1236,7 @@
group =
"""
1 *1 CO u0 {2,S} {3,D}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 O u0 {1,D}
""",
kinetics = None,
Expand All @@ -1246,7 +1248,7 @@
group =
"""
1 *1 Ct u0 {2,S} {3,T}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 Ct u0 {1,T}
""",
kinetics = None,
Expand Down Expand Up @@ -1324,8 +1326,8 @@
L1: radadd_intra
L2: radadd_intra_cs
L3: radadd_intra_cs2H
L3: radadd_intra_csHNd
L3: radadd_intra_csHDe
L4: radadd_intra_csHHNd
L4: radadd_intra_csHHDe
L3: radadd_intra_csNdNd
L3: radadd_intra_csNdDe
L3: radadd_intra_csDeDe
Expand Down
40 changes: 21 additions & 19 deletions input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -2548,32 +2548,34 @@
group =
"""
1 *1 Cs u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 H u0 {1,S}
""",
kinetics = None,
)

entry(
index = 182,
label = "radadd_intra_csHNd",
label = "radadd_intra_csHHNd",
group =
"""
1 *1 Cs u0 {2,S} {3,S}
2 *2 H u0 {1,S}
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *4 H u0 {1,S}
3 [Cs,O] u0 {1,S}
4 H u0 {1,S}
""",
kinetics = None,
)

entry(
index = 183,
label = "radadd_intra_csHDe",
label = "radadd_intra_csHHDe",
group =
"""
1 *1 Cs u0 {2,S} {3,S}
2 *2 H u0 {1,S}
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *4 H u0 {1,S}
3 [Cd,Ct,Cb,CO] u0 {1,S}
4 H u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -2584,7 +2586,7 @@
group =
"""
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cs,O] u0 {1,S}
4 [Cs,O] u0 {1,S}
""",
Expand All @@ -2597,7 +2599,7 @@
group =
"""
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cs,O] u0 {1,S}
4 [Cd,Ct,Cb,CO] u0 {1,S}
""",
Expand All @@ -2610,7 +2612,7 @@
group =
"""
1 *1 Cs u0 {2,S} {3,S} {4,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cd,Ct,Cb,CO] u0 {1,S}
4 [Cd,Ct,Cb,CO] u0 {1,S}
""",
Expand Down Expand Up @@ -2643,7 +2645,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 R u0 {1,S}
""",
kinetics = None,
Expand All @@ -2655,7 +2657,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 H u0 {1,S}
""",
kinetics = None,
Expand All @@ -2667,7 +2669,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cs,O] u0 {1,S}
""",
kinetics = None,
Expand All @@ -2679,7 +2681,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,S}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 [Cd,Ct,Cb,CO] u0 {1,S}
""",
kinetics = None,
Expand All @@ -2691,7 +2693,7 @@
group =
"""
1 *1 Cd u0 {2,S} {3,D}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 Cd u0 {1,D}
""",
kinetics = None,
Expand All @@ -2703,7 +2705,7 @@
group =
"""
1 *1 CO u0 {2,S} {3,D}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 O u0 {1,D}
""",
kinetics = None,
Expand All @@ -2715,7 +2717,7 @@
group =
"""
1 *1 Ct u0 {2,S} {3,T}
2 *2 H u0 {1,S}
2 *4 H u0 {1,S}
3 Ct u0 {1,T}
""",
kinetics = None,
Expand Down Expand Up @@ -2886,8 +2888,8 @@
L1: radadd_intra
L2: radadd_intra_cs
L3: radadd_intra_cs2H
L3: radadd_intra_csHNd
L3: radadd_intra_csHDe
L4: radadd_intra_csHHNd
L4: radadd_intra_csHHDe
L3: radadd_intra_csNdNd
L3: radadd_intra_csNdDe
L3: radadd_intra_csDeDe
Expand Down
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