diff --git a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py index eba8023729..4f7f2bbe60 100644 --- a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py +++ b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py @@ -2,16 +2,22 @@ # encoding: utf-8 name = "Intra_RH_Add_Endocyclic/groups" -shortDesc = u"" -longDesc = u""" +shortDesc = "" +longDesc = """ """ -template(reactants=["Rn"], products=["RnCycle"], ownReverse=False) +template(reactants=["Root"], products=["RnCycle"], ownReverse=False) reverse = "Ring_Open+H_Migration" - reversible = True + +reactantNum = 1 + +productNum = 1 + +autoGenerated = True + recipe(actions=[ ['BREAK_BOND', '*1', 1, '*4'], ['FORM_BOND', '*1', 1, '*3'], @@ -23,1303 +29,60 @@ entry( index = 0, - label = "Rn", - group = "OR{R4, R5, R6, R7}", - kinetics = None, -) - -entry( - index = 1, - label = "multiplebond_intra", - group = -""" -1 *2 C u0 {2,D} -2 *3 C u0 {1,D} -""", - kinetics = None, -) - -entry( - index = 2, - label = "radadd_intra", + label = "Root", group = """ 1 *1 R!H u0 {2,S} 2 *4 H u0 {1,S} +3 *2 R!H u0 {4,D} +4 *3 R!H u0 {3,D} """, kinetics = None, ) -entry( - index = 3, - label = "R4", - group = -""" -1 *1 R!H u0 {2,S} {3,[S,D,T,B]} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,[S,D,T,B]} {4,S} -4 *2 C u0 {3,S} {5,D} -5 *3 C u0 {4,D} -""", - kinetics = None, -) - -entry( - index = 4, - label = "R4_S", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *2 C u0 {3,S} {5,D} -5 *3 C u0 {4,D} -""", - kinetics = None, -) - -entry( - index = 5, - label = "R4_D", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *2 C u0 {3,S} {5,D} -5 *3 C u0 {4,D} -""", - kinetics = None, -) - -entry( - index = 6, - label = "R4_T", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *2 C u0 {3,S} {5,D} -5 *3 C u0 {4,D} -""", - kinetics = None, -) - -entry( - index = 7, - label = "R4_B", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *2 C u0 {3,S} {5,D} -5 *3 C u0 {4,D} -""", - kinetics = None, -) - -entry( - index = 8, - label = "R5", - group = "OR{R5_SS, R5_SD, R5_DS, R5_ST, R5_TS, R5_SB, R5_BS}", - kinetics = None, -) - -entry( - index = 9, - label = "R5_SS", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *2 C u0 {4,S} {6,D} -6 *3 C u0 {5,D} -""", - kinetics = None, -) - -entry( - index = 10, - label = "R5_SD", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,D} -4 *6 R!H u0 {3,D} {5,S} -5 *2 C u0 {4,S} {6,D} -6 *3 C u0 {5,D} -""", - kinetics = None, -) - -entry( - index = 11, - label = "R5_DS", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *2 C u0 {4,S} {6,D} -6 *3 C u0 {5,D} -""", - kinetics = None, -) - -entry( - index = 12, - label = "R5_ST", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,S} {4,T} -4 *6 Ct u0 {3,T} {5,S} -5 *2 C u0 {4,S} {6,D} -6 *3 C u0 {5,D} -""", - kinetics = None, -) - -entry( - index = 13, - label = "R5_TS", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *2 C u0 {4,S} {6,D} -6 *3 C u0 {5,D} -""", - kinetics = None, -) - -entry( - index = 14, - label = "R5_SB", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,S} {4,B} -4 *6 Cb u0 {3,B} {5,S} -5 *2 C u0 {4,S} {6,D} -6 *3 C u0 {5,D} -""", - kinetics = None, -) - -entry( - index = 15, - label = "R5_BS", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *2 C u0 {4,S} {6,D} -6 *3 C u0 {5,D} -""", - kinetics = None, -) - -entry( - index = 16, - label = "R6", - group = "OR{R6_RSR, R6_SMS, R6_SBB, R6_BBS}", - kinetics = None, -) - -entry( - index = 17, - label = "R6_RSR", - group = -""" -1 *1 R!H u0 {2,S} {3,[S,D,T,B]} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,[S,D,T,B]} {4,S} -4 *6 R!H u0 {3,S} {5,[S,D,T,B]} -5 *7 R!H u0 {4,[S,D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 18, - label = "R6_SSR", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 R!H u0 {3,S} {5,[S,D,T,B]} -5 *7 R!H u0 {4,[S,D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 19, - label = "R6_SSM", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[S,D,T,B]} -5 *7 [Cd,Ct,Cb] u0 {4,[S,D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 20, - label = "R6_SSS", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *7 R!H u0 {4,S} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 21, - label = "R6_DSR", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 R!H u0 {3,S} {5,[S,D,T,B]} -5 *7 R!H u0 {4,[S,D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 22, - label = "R6_DSS", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *7 R!H u0 {4,S} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 23, - label = "R6_DSM", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[D,T,B]} -5 *7 [Cd,Ct,Cb] u0 {4,[D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 24, - label = "R6_TSR", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 R!H u0 {3,S} {5,[S,D,T,B]} -5 *7 R!H u0 {4,[S,D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 25, - label = "R6_TSS", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *7 R!H u0 {4,S} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 26, - label = "R6_TSM", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[D,T,B]} -5 *7 [Cd,Ct,Cb] u0 {4,[D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 27, - label = "R6_BSR", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 R!H u0 {3,S} {5,[S,D,T,B]} -5 *7 R!H u0 {4,[S,D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 28, - label = "R6_BSS", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *7 R!H u0 {4,S} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 29, - label = "R6_BSM", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[D,T,B]} -5 *7 [Cd,Ct,Cb] u0 {4,[D,T,B]} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 30, - label = "R6_SMS", - group = +tree( """ -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 [Cd,Ct,Cb] u0 {1,S} {4,[D,T,B]} -4 *6 [Cd,Ct,Cb] u0 {3,[D,T,B]} {5,S} -5 *7 R!H u0 {4,S} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, -) - -entry( - index = 31, - label = "R6_SBB", - group = +L1: Root """ -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,S} {4,B} -4 *6 Cbf u0 {3,B} {5,B} -5 *7 Cb u0 {4,B} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} -""", - kinetics = None, ) -entry( - index = 32, - label = "R6_BBS", +forbidden( + label = "R3_rad", group = """ -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cbf u0 {1,B} {4,B} -4 *6 Cb u0 {3,B} {5,S} -5 *7 R!H u0 {4,S} {6,S} -6 *2 C u0 {5,S} {7,D} -7 *3 C u0 {6,D} +1 *1 R!H u0 p0 c0 {2,S} +2 *4 H u0 p0 c0 {1,S} +3 *2 R!H u0 p0 c0 {4,D} +4 *3 R!H u0 p0 c0 {3,D} {5,S} +5 R!H u1 p0 c0 {4,S} """, - kinetics = None, -) - -entry( - index = 33, - label = "R7", - group = "OR{R7_RSSR, R7_RSMS, R7_SMSR, R7_BBSR, R7_RSBB, R7_SBBS}", - kinetics = None, -) - -entry( - index = 34, - label = "R7_RSSR", - group = + shortDesc = """""", + longDesc = """ -1 *1 R!H u0 {2,S} {3,[S,D,T,B]} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,[S,D,T,B]} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,[S,D,T,B]} -6 *7 R!H u0 {5,[S,D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} +Prevent R3 from being connected to a radical. +As an example, it prevents the reactant from this reaction from matching the template. +rsmi: [C:1](=[C:2]([C:3]([C:4]([C:5](=[C:6]([C:7]([H:17])[H:18])[H:16])[H:15])([H:13])[H:14])([H:11])[H:12])[H:10])([H:8])[H:9] +psmi: [C:1]1([H:9])=[C:2]([H:10])[C:3]([H:11])([H:12])[C:4]([H:13])([H:14])[C:5]([H:8])([H:15])[C:6]1([C:7]([H:17])[H:18])[H:16] """, - kinetics = None, ) -entry( - index = 35, - label = "R7_SSSR", +forbidden( + label = "R3_rad_rev", group = """ -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,[S,D,T,B]} -6 *7 R!H u0 {5,[S,D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} +1 *1 R!H u0 p0 c0 {2,S} +2 *3 R!H u0 p0 c0 {1,S} {3,S} {4,S} +3 R!H u1 p0 c0 {2,S} +4 *2 R!H u0 p0 c0 {2,S} {5,S} +5 *4 H u0 p0 c0 {4,S} """, - kinetics = None, -) - -entry( - index = 36, - label = "R7_SSSS", - group = + shortDesc = """""", + longDesc = """ -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} +Prevent R3 from being connected to a radical. +As an example, it prevents the product from this reaction from matching the template. +rsmi: [C:1](=[C:2]([C:3]([C:4]([C:5](=[C:6]([C:7]([H:17])[H:18])[H:16])[H:15])([H:13])[H:14])([H:11])[H:12])[H:10])([H:8])[H:9] +psmi: [C:1]1([H:9])=[C:2]([H:10])[C:3]([H:11])([H:12])[C:4]([H:13])([H:14])[C:5]([H:8])([H:15])[C:6]1([C:7]([H:17])[H:18])[H:16] """, - kinetics = None, -) - -entry( - index = 37, - label = "R7_SSSM", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 [Cd,Ct,Cb] u0 {4,S} {6,[D,T,B]} -6 *7 [Cd,Ct,Cb] u0 {5,[D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 38, - label = "R7_DSSR", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,[S,D,T,B]} -6 *7 R!H u0 {5,[S,D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 39, - label = "R7_DSSS", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 40, - label = "R7_DSSM", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 [Cd,Ct,Cb] u0 {4,S} {6,[D,T,B]} -6 *7 [Cd,Ct,Cb] u0 {5,[D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 41, - label = "R7_TSSR", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,[S,D,T,B]} -6 *7 R!H u0 {5,[S,D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 42, - label = "R7_TSSS", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 43, - label = "R7_TSSM", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 [Cd,Ct,Cb] u0 {4,S} {6,[D,T,B]} -6 *7 [Cd,Ct,Cb] u0 {5,[D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 44, - label = "R7_BSSR", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,[S,D,T,B]} -6 *7 R!H u0 {5,[S,D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 45, - label = "R7_BSSS", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 R!H u0 {4,S} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 46, - label = "R7_BSSM", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 R!H u0 {3,S} {5,S} -5 *8 [Cd,Ct,Cb] u0 {4,S} {6,[D,T,B]} -6 *7 [Cd,Ct,Cb] u0 {5,[D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 47, - label = "R7_RSMS", - group = -""" -1 *1 R!H u0 {2,S} {3,[S,D,T,B]} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,[S,D,T,B]} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[D,T,B]} -5 *8 [Cd,Ct,Cb] u0 {4,[D,T,B]} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 48, - label = "R7_SSMS", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[D,T,B]} -5 *8 [Cd,Ct,Cb] u0 {4,[D,T,B]} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 49, - label = "R7_DSMS", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[D,T,B]} -5 *8 [Cd,Ct,Cb] u0 {4,[D,T,B]} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 50, - label = "R7_TSMS", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[D,T,B]} -5 *8 [Cd,Ct,Cb] u0 {4,[D,T,B]} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 51, - label = "R7_BSMS", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 [Cd,Ct,Cb] u0 {3,S} {5,[D,T,B]} -5 *8 [Cd,Ct,Cb] u0 {4,[D,T,B]} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 52, - label = "R7_SMSR", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 [Cd,Ct,Cb] u0 {1,S} {4,[D,T,B]} -4 *6 [Cd,Ct,Cb] u0 {3,[D,T,B]} {5,S} -5 *8 R!H u0 {4,S} {6,[S,D,T,B]} -6 *7 R!H u0 {5,[S,D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 53, - label = "R7_SMSS", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 [Cd,Ct,Cb] u0 {1,S} {4,[D,T,B]} -4 *6 [Cd,Ct,Cb] u0 {3,[D,T,B]} {5,S} -5 *8 R!H u0 {4,S} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 54, - label = "R7_SMSM", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 [Cd,Ct,Cb] u0 {1,S} {4,[D,T,B]} -4 *6 [Cd,Ct,Cb] u0 {3,[D,T,B]} {5,S} -5 *8 [Cd,Ct,Cb] u0 {4,S} {6,[D,T,B]} -6 *7 [Cd,Ct,Cb] u0 {5,[D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 55, - label = "R7_BBSR", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cbf u0 {1,B} {4,B} -4 *6 Cb u0 {3,B} {5,S} -5 *8 R!H u0 {4,S} {6,[S,D,T,B]} -6 *7 R!H u0 {5,[S,D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 56, - label = "R7_BBSS", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cbf u0 {1,B} {4,B} -4 *6 Cb u0 {3,B} {5,S} -5 *8 R!H u0 {4,S} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 57, - label = "R7_BBSM", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cbf u0 {1,B} {4,B} -4 *6 Cb u0 {3,B} {5,S} -5 *8 [Cd,Ct,Cb] u0 {4,S} {6,[D,T,B]} -6 *7 [Cd,Ct,Cb] u0 {5,[D,T,B]} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 58, - label = "R7_RSBB", - group = -""" -1 *1 R!H u0 {2,S} {3,[S,D,T,B]} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,[S,D,T,B]} {4,S} -4 *6 Cb u0 {3,S} {5,B} -5 *8 Cbf u0 {4,B} {6,B} -6 *7 Cb u0 {5,B} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 59, - label = "R7_SSBB", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 R!H u0 {1,S} {4,S} -4 *6 Cb u0 {3,S} {5,B} -5 *8 Cbf u0 {4,B} {6,B} -6 *7 Cb u0 {5,B} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 60, - label = "R7_DSBB", - group = -""" -1 *1 R!H u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 *5 Cd u0 {1,D} {4,S} -4 *6 Cb u0 {3,S} {5,B} -5 *8 Cbf u0 {4,B} {6,B} -6 *7 Cb u0 {5,B} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 61, - label = "R7_TSBB", - group = -""" -1 *1 R!H u0 {2,S} {3,T} -2 *4 H u0 {1,S} -3 *5 Ct u0 {1,T} {4,S} -4 *6 Cb u0 {3,S} {5,B} -5 *8 Cbf u0 {4,B} {6,B} -6 *7 Cb u0 {5,B} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 62, - label = "R7_BSBB", - group = -""" -1 *1 R!H u0 {2,S} {3,B} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,B} {4,S} -4 *6 Cb u0 {3,S} {5,B} -5 *8 Cbf u0 {4,B} {6,B} -6 *7 Cb u0 {5,B} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 63, - label = "R7_SBBS", - group = -""" -1 *1 R!H u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 *5 Cb u0 {1,S} {4,B} -4 *6 Cbf u0 {3,B} {5,B} -5 *8 Cb u0 {4,B} {6,S} -6 *7 R!H u0 {5,S} {7,S} -7 *2 C u0 {6,S} {8,D} -8 *3 C u0 {7,D} -""", - kinetics = None, -) - -entry( - index = 64, - label = "doublebond_intra_2H", - group = -""" -1 *2 C u0 {2,D} -2 *3 C u0 {1,D} {3,S} {4,S} -3 H u0 {2,S} -4 H u0 {2,S} -""", - kinetics = None, -) - -entry( - index = 65, - label = "doublebond_intra_2H_secDe", - group = -""" -1 *2 C u0 {2,D} {3,S} -2 *3 C u0 {1,D} {4,S} {5,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 H u0 {2,S} -5 H u0 {2,S} -""", - kinetics = None, -) - -entry( - index = 66, - label = "doublebond_intra_2H_secNd", - group = -""" -1 *2 C u0 {2,D} {3,S} -2 *3 C u0 {1,D} {4,S} {5,S} -3 [Cs,O,S] u0 {1,S} -4 H u0 {2,S} -5 H u0 {2,S} -""", - kinetics = None, -) - -entry( - index = 67, - label = "doublebond_intra_2H_pri", - group = -""" -1 *2 C u0 {2,D} {3,S} -2 *3 C u0 {1,D} {4,S} {5,S} -3 H u0 {1,S} -4 H u0 {2,S} -5 H u0 {2,S} -""", - kinetics = None, -) - -entry( - index = 68, - label = "radadd_intra_cs", - group = -""" -1 *1 Cs u0 {2,S} -2 *4 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 69, - label = "radadd_intra_csNdNd", - group = -""" -1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *4 H u0 {1,S} -3 [Cs,O,S2s] u0 {1,S} -4 [Cs,O,S2s] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 70, - label = "radadd_intra_csNdDe", - group = -""" -1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *4 H u0 {1,S} -3 [Cs,O,S2s] u0 {1,S} -4 [Cd,Ct,Cb,CO,CS] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 71, - label = "radadd_intra_csDeDe", - group = -""" -1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *4 H u0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 [Cd,Ct,Cb,CO,CS] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 72, - label = "radadd_intra_cs2H", - group = -""" -1 *1 Cs u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 73, - label = "radadd_intra_csHHNd", - group = -""" -1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *4 H u0 {1,S} -3 [Cs,O,S2s] u0 {1,S} -4 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 74, - label = "radadd_intra_csHHDe", - group = -""" -1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *4 H u0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 75, - label = "radadd_intra_O", - group = -""" -1 *1 O u0 {2,S} -2 *4 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 76, - label = "radadd_intra_Cb", - group = -""" -1 *1 Cb u0 {2,S} -2 *4 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 77, - label = "radadd_intra_cdsingle", - group = -""" -1 *1 Cd u0 {2,S} {3,S} -2 *4 H u0 {1,S} -3 R u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 78, - label = "radadd_intra_cddouble", - group = -""" -1 *1 Cd u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 R!H u0 {1,D} -""", - kinetics = None, -) - -entry( - index = 79, - label = "radadd_intra_CO", - group = -""" -1 *1 CO u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 O u0 {1,D} -""", - kinetics = None, -) - -entry( - index = 80, - label = "radadd_intra_Ct", - group = -""" -1 *1 Ct u0 {2,S} -2 *4 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 81, - label = "radadd_intra_CS", - group = -""" -1 *1 CS u0 {2,S} {3,D} -2 *4 H u0 {1,S} -3 S u0 {1,D} -""", - kinetics = None, -) - -tree( -""" -L1: Rn - L2: R4 - L3: R4_S - L3: R4_D - L3: R4_T - L3: R4_B - L2: R5 - L3: R5_SS - L3: R5_SD - L3: R5_DS - L3: R5_ST - L3: R5_TS - L3: R5_SB - L3: R5_BS - L2: R6 - L3: R6_RSR - L4: R6_SSR - L5: R6_SSM - L5: R6_SSS - L4: R6_DSR - L5: R6_DSS - L5: R6_DSM - L4: R6_TSR - L5: R6_TSS - L5: R6_TSM - L4: R6_BSR - L5: R6_BSS - L5: R6_BSM - L3: R6_SMS - L3: R6_SBB - L3: R6_BBS - L2: R7 - L3: R7_RSSR - L4: R7_SSSR - L5: R7_SSSS - L5: R7_SSSM - L4: R7_DSSR - L5: R7_DSSS - L5: R7_DSSM - L4: R7_TSSR - L5: R7_TSSS - L5: R7_TSSM - L4: R7_BSSR - L5: R7_BSSS - L5: R7_BSSM - L3: R7_RSMS - L4: R7_SSMS - L4: R7_DSMS - L4: R7_TSMS - L4: R7_BSMS - L3: R7_SMSR - L4: R7_SMSS - L4: R7_SMSM - L3: R7_BBSR - L4: R7_BBSS - L4: R7_BBSM - L3: R7_RSBB - L4: R7_SSBB - L4: R7_DSBB - L4: R7_TSBB - L4: R7_BSBB - L3: R7_SBBS -L1: multiplebond_intra - L2: doublebond_intra_2H - L3: doublebond_intra_2H_secDe - L3: doublebond_intra_2H_secNd - L3: doublebond_intra_2H_pri -L1: radadd_intra - L2: radadd_intra_cs - L3: radadd_intra_csNdNd - L3: radadd_intra_csNdDe - L3: radadd_intra_csDeDe - L3: radadd_intra_cs2H - L4: radadd_intra_csHHNd - L4: radadd_intra_csHHDe - L2: radadd_intra_O - L2: radadd_intra_Cb - L2: radadd_intra_cdsingle - L2: radadd_intra_cddouble - L2: radadd_intra_CO - L2: radadd_intra_Ct - L2: radadd_intra_CS -""" ) diff --git a/input/kinetics/families/Intra_RH_Add_Endocyclic/rules.py b/input/kinetics/families/Intra_RH_Add_Endocyclic/rules.py index 6ca231b3f8..a2e152dd6b 100644 --- a/input/kinetics/families/Intra_RH_Add_Endocyclic/rules.py +++ b/input/kinetics/families/Intra_RH_Add_Endocyclic/rules.py @@ -7,13 +7,13 @@ """ entry( - index = 807, - label = "Rn;multiplebond_intra;radadd_intra", + index = 0, + label = "Root", kinetics = ArrheniusEP( A = (1e+10, 's^-1'), n = 0, alpha = 0, - E0 = (5, 'kcal/mol'), + E0 = (20, 'kcal/mol'), Tmin = (300, 'K'), Tmax = (1500, 'K'), ), diff --git a/input/kinetics/families/Intra_RH_Add_Endocyclic/training/reactions.py b/input/kinetics/families/Intra_RH_Add_Endocyclic/training/reactions.py index a2a968778b..71fb6fb2e8 100644 --- a/input/kinetics/families/Intra_RH_Add_Endocyclic/training/reactions.py +++ b/input/kinetics/families/Intra_RH_Add_Endocyclic/training/reactions.py @@ -2,8 +2,8 @@ # encoding: utf-8 name = "Intra_RH_Add_Endocyclic/training" -shortDesc = u"Reaction kinetics used to generate rate rules" -longDesc = u""" +shortDesc = "Reaction kinetics used to generate rate rules" +longDesc = """ Put kinetic parameters for specific reactions in this file to use as a training set for generating rate rules to populate this kinetics family. """