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Unimol accessibility #167

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merged 16 commits into from
Mar 2, 2017
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Merged

Unimol accessibility #167

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64add53
Remove extra files leftover from messy rebase
nyee Feb 24, 2017
0f2a45f
Add lone pairs to group in solvation/abraham.py
nyee Mar 1, 2017
b3a41ef
Fixes to radical.py for entryAccessibility
nyee Feb 27, 2017
d8d2841
1,2_shiftS accessibility
mjohnson541 Feb 17, 2017
b69d1a9
Birad_recombination accessibility
mjohnson541 Feb 17, 2017
24f7e06
Cyclic_Ether_Formation accessibility
mjohnson541 Feb 21, 2017
4de6185
intra_H_mirgration accessibility
mjohnson541 Feb 21, 2017
0394fbf
intra_OH_migration accessibility
mjohnson541 Feb 21, 2017
91b79ba
Intra_R_Add_ExoTetCyclic accessibility
mjohnson541 Feb 21, 2017
07f2930
Intra_RH_Add_Endocyclic accessibility
mjohnson541 Feb 21, 2017
12b5544
intra_RH_Add_Exocyclic accessibility
mjohnson541 Feb 21, 2017
d861503
ketoenol accessibility
mjohnson541 Feb 21, 2017
69852f5
intra_substitutionCS_cyclization accessibility
mjohnson541 Feb 21, 2017
98288a0
intra_substitutionCS_isomerization accessibility
mjohnson541 Feb 21, 2017
ca42452
intra_substitutionS_cyclization accessibility
mjohnson541 Feb 21, 2017
225c107
intra_substitutionS_isomerization accessibility
mjohnson541 Feb 21, 2017
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125 changes: 63 additions & 62 deletions input/kinetics/families/1,2_shiftS/groups.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1553,25 +1553,24 @@
L2: CJ-Ss
L3: CdsJ-Ss
L3: CsJ-Ss
L4: CsJ-SsHH
L4: CsJ-SsCsH
L4: CsJ-SsCsCs
L4: CsJ-SsSsH
L4: CsJ-SsSsSs
L4: CsJ-SsCsSs
L4: CsJ-SsOneDe
L5: CsJ-SsOneDeH
L6: CsJ-SsCdH
L5: CsJ-SsOneDeCs
L6: CsJ-SsCdCs
L5: CsJ-SsOneDeSs
L6: CsJ-SsCdSs
L5: CsJ-SsOneDeH
L6: CsJ-SsCdH
L4: CsJ-SsSsSs
L4: CsJ-SsCsSs
L4: CsJ-SsCsCs
L4: CsJ-SsCsH
L4: CsJ-SsSsH
L4: CsJ-SsHH
L2: SJ-Ss
L1: C-Ss
L2: Cb-Ss
L2: Ct-Ss
L2: Cds-Ss
L3: Cds-SsH
L3: Cds-SsCs
L3: Cds-SsCt
L3: Cds-SsCb
Expand All @@ -1580,8 +1579,8 @@
L3: Cds-SsSs
L3: Cds-SsCd
L3: Cds-SsC=S
L3: Cds-SsH
L2: C=S-Ss
L3: C=S-SsH
L3: C=S-SsCs
L3: C=S-SsCt
L3: C=S-SsCb
Expand All @@ -1590,66 +1589,17 @@
L3: C=S-SsSs
L3: C=S-SsCd
L3: C=S-SsC=S
L3: C=S-SsH
L2: Cs-Ss
L3: Cs-SsHHH
L3: Cs-SsCsHH
L3: Cs-SsCsCsH
L3: Cs-SsCsCsCs
L3: Cs-SsOsHH
L3: Cs-SsOsCsH
L3: Cs-SsOsCsCs
L3: Cs-SsOsOsH
L3: Cs-SsOsOsCs
L3: Cs-SsOsOsOs
L3: Cs-SsSsHH
L3: Cs-SsSsCsH
L3: Cs-SsSsCsCs
L3: Cs-SsSsSsH
L3: Cs-SsSsSsCs
L3: Cs-SsSsSsSs
L3: Cs-SsOneDe
L4: Cs-SsOneDeHH
L5: Cs-SsCtHH
L5: Cs-SsCbHH
L5: Cs-SsCOHH
L5: Cs-SsCdHH
L5: Cs-SsC=SHH
L4: Cs-SsOneDeCsH
L5: Cs-SsCtCsH
L5: Cs-SsCbCsH
L5: Cs-SsCOCsH
L5: Cs-SsCdCsH
L5: Cs-SsC=SCsH
L4: Cs-SsOneDeOsH
L4: Cs-SsOneDeSsH
L4: Cs-SsOneDeCsCs
L5: Cs-SsCtCsCs
L5: Cs-SsCbCsCs
L5: Cs-SsCOCsCs
L5: Cs-SsCdCsCs
L5: Cs-SsC=SCsCs
L4: Cs-SsOneDeOsCs
L4: Cs-SsOneDeSsCs
L4: Cs-SsOneDeOsOs
L4: Cs-SsOneDeOsSs
L4: Cs-SsOneDeSsSs
L3: Cs-SsThreeDe
L3: Cs-SsTwoDe
L4: Cs-SsTwoDeH
L5: Cs-SsCtCtH
L5: Cs-SsCtCbH
L5: Cs-SsCtCOH
L5: Cs-SsCbCbH
L5: Cs-SsCbCOH
L5: Cs-SsCOCOH
L5: Cs-SsCdCtH
L5: Cs-SsCdCbH
L5: Cs-SsCdCOH
L5: Cs-SsCtC=SH
L5: Cs-SsCbC=SH
L5: Cs-SsCOC=SH
L5: Cs-SsCdCdH
L5: Cs-SsCdC=SH
L5: Cs-SsC=SC=SH
L4: Cs-SsTwoDeCs
L5: Cs-SsCtCtCs
L5: Cs-SsCtCbCs
Expand All @@ -1668,7 +1618,58 @@
L5: Cs-SsC=SC=SCs
L4: Cs-SsTwoDeOs
L4: Cs-SsTwoDeSs
L3: Cs-SsThreeDe
L4: Cs-SsTwoDeH
L5: Cs-SsCtCtH
L5: Cs-SsCtCbH
L5: Cs-SsCtCOH
L5: Cs-SsCbCbH
L5: Cs-SsCbCOH
L5: Cs-SsCOCOH
L5: Cs-SsCdCtH
L5: Cs-SsCdCbH
L5: Cs-SsCdCOH
L5: Cs-SsCtC=SH
L5: Cs-SsCbC=SH
L5: Cs-SsCOC=SH
L5: Cs-SsCdCdH
L5: Cs-SsCdC=SH
L5: Cs-SsC=SC=SH
L3: Cs-SsOneDe
L4: Cs-SsOneDeCsCs
L5: Cs-SsCtCsCs
L5: Cs-SsCbCsCs
L5: Cs-SsCOCsCs
L5: Cs-SsCdCsCs
L5: Cs-SsC=SCsCs
L4: Cs-SsOneDeOsCs
L4: Cs-SsOneDeSsCs
L4: Cs-SsOneDeOsOs
L4: Cs-SsOneDeOsSs
L4: Cs-SsOneDeSsSs
L4: Cs-SsOneDeOsH
L4: Cs-SsOneDeSsH
L4: Cs-SsOneDeCsH
L5: Cs-SsCtCsH
L5: Cs-SsCbCsH
L5: Cs-SsCOCsH
L5: Cs-SsCdCsH
L5: Cs-SsC=SCsH
L4: Cs-SsOneDeHH
L5: Cs-SsCtHH
L5: Cs-SsCbHH
L5: Cs-SsCOHH
L5: Cs-SsCdHH
L5: Cs-SsC=SHH
L3: Cs-SsCsCsH
L3: Cs-SsOsOsH
L3: Cs-SsOsCsH
L3: Cs-SsSsSsH
L3: Cs-SsSsCsH
L3: Cs-SsOsHH
L3: Cs-SsCsHH
L3: Cs-SsSsHH
L3: Cs-SsHHH

"""
)

128 changes: 16 additions & 112 deletions input/kinetics/families/Birad_recombination/groups.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -432,7 +432,7 @@
)

entry(
index = 28,
index = 82,
label = "O_rad",
group =
"""
Expand All @@ -442,7 +442,7 @@
)

entry(
index = 29,
index = 83,
label = "S_rad",
group =
"""
Expand All @@ -451,50 +451,6 @@
kinetics = None,
)

entry(
index = 30,
label = "Cd_rad_out",
group =
"""
1 *1 C u1 {2,D}
2 [C,O,S] u0 {1,D}
""",
kinetics = None,
)

entry(
index = 31,
label = "Cd_rad_out_C",
group =
"""
1 *1 C u1 {2,D}
2 C u0 {1,D}
""",
kinetics = None,
)

entry(
index = 32,
label = "Cd_rad_out_O",
group =
"""
1 *1 C u1 {2,D}
2 O u0 {1,D}
""",
kinetics = None,
)

entry(
index = 33,
label = "Cd_rad_out_S",
group =
"""
1 *1 C u1 {2,D}
2 S u0 {1,D}
""",
kinetics = None,
)

entry(
index = 34,
label = "Cdsingle_rad_out",
Expand Down Expand Up @@ -763,50 +719,6 @@
kinetics = None,
)

entry(
index = 57,
label = "Cdpri_rad_out",
group =
"""
1 *2 C u1 {2,D}
2 [C,O,S] u0 {1,D}
""",
kinetics = None,
)

entry(
index = 58,
label = "Cdpri_rad_out_C",
group =
"""
1 *2 C u1 {2,D}
2 C u0 {1,D}
""",
kinetics = None,
)

entry(
index = 59,
label = "Cdpri_rad_out_O",
group =
"""
1 *2 C u1 {2,D}
2 O u0 {1,D}
""",
kinetics = None,
)

entry(
index = 60,
label = "Cdpri_rad_out_S",
group =
"""
1 *2 C u1 {2,D}
2 S u0 {1,D}
""",
kinetics = None,
)

entry(
index = 61,
label = "Cdsinglepri_rad_out",
Expand Down Expand Up @@ -1088,21 +1000,11 @@
L1: Y_rad_out
L2: O_rad
L2: S_rad
L2: Cd_rad_out
L3: Cd_rad_out_C
L3: Cd_rad_out_O
L3: Cd_rad_out_S
L2: Cdsingle_rad_out
L3: CdsingleH_rad_out
L3: CdsingleND_rad_out
L3: CdsingleDe_rad_out
L3: CdsingleND_rad_out
L3: CdsingleH_rad_out
L2: C_rad_out_single
L3: C_rad_out_2H
L3: C_rad_out_1H
L4: C_rad_out_H/NonDeC
L4: C_rad_out_H/NonDeO
L4: C_rad_out_H/NonDeS
L4: C_rad_out_H/OneDe
L3: C_rad_out_noH
L4: C_rad_out_NonDe
L5: C_rad_out_Cs2
Expand All @@ -1113,24 +1015,20 @@
L5: C_rad_out_OneDe/O
L5: C_rad_out_OneDe/S
L4: C_rad_out_TwoDe
L3: C_rad_out_1H
L4: C_rad_out_H/NonDeC
L4: C_rad_out_H/NonDeO
L4: C_rad_out_H/NonDeS
L4: C_rad_out_H/OneDe
L3: C_rad_out_2H
L1: Ypri_rad_out
L2: Opri_rad
L2: Spri_rad
L2: Cdpri_rad_out
L3: Cdpri_rad_out_C
L3: Cdpri_rad_out_O
L3: Cdpri_rad_out_S
L2: Cdsinglepri_rad_out
L3: CdsinglepriH_rad_out
L3: CdsinglepriND_rad_out
L3: CdsinglepriDe_rad_out
L2: Cpri_rad_out_single
L3: Cpri_rad_out_2H
L3: Cpri_rad_out_1H
L4: Cpri_rad_out_H/NonDeC
L4: Cpri_rad_out_H/NonDeO
L4: Cpri_rad_out_H/NonDeS
L4: Cpri_rad_out_H/OneDe
L3: Cpri_rad_out_noH
L4: Cpri_rad_out_NonDe
L5: Cpri_rad_out_Cs2
Expand All @@ -1141,6 +1039,12 @@
L5: Cpri_rad_out_OneDe/O
L5: Cpri_rad_out_OneDe/S
L4: Cpri_rad_out_TwoDe
L3: Cpri_rad_out_1H
L4: Cpri_rad_out_H/NonDeC
L4: Cpri_rad_out_H/NonDeO
L4: Cpri_rad_out_H/NonDeS
L4: Cpri_rad_out_H/OneDe
L3: Cpri_rad_out_2H
"""
)

Expand Down
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