intra_RH_Add_Exocyclic accessibility

-rearrangement of entries to meet accessibility tests
-combination of radadd_intra_cddouble and radadd_intra_cdsingle branches into one branch
-fixed radadd_intra and it’s sub-entries
-added *4 labels/appropriate hydrogens to match backbone properly
-removed a Ct from radadd_intra_Ct to allow connection to backbone

Author: mjohnson541

input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py

@@ -43,7 +43,8 @@
     label = "radadd_intra",
     group = 
 """
-1 *1 R!H u0
+1 *1 R!H u0 {2,S}
+2 *4 H u0 {1,S}
 """,
     kinetics = None,
 )
@@ -1151,7 +1152,8 @@
     label = "radadd_intra_cs",
     group = 
 """
-1 *1 Cs u0
+1 *1 Cs u0 {2,S}
+2 *4 H u0 {1,S}
 """,
     kinetics = None,
 )
@@ -1162,7 +1164,7 @@
     group = 
 """
 1 *1 Cs u0 {2,S} {3,S}
-2    H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    H  u0 {1,S}
 """,
     kinetics = None,
@@ -1174,7 +1176,7 @@
     group = 
 """
 1 *1 Cs     u0 {2,S} {3,S} {4,S}
-2    H      u0 {1,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
 4    H      u0 {1,S}
 """,
@@ -1187,7 +1189,7 @@
     group = 
 """
 1 *1 Cs            u0 {2,S} {3,S} {4,S}
-2    H             u0 {1,S}
+2 *4 H             u0 {1,S}
 3    [Cd,Ct,Cb,CO] u0 {1,S}
 4    H             u0 {1,S}
 """,
@@ -1200,7 +1202,7 @@
     group = 
 """
 1 *1 Cs     u0 {2,S} {3,S} {4,S}
-2    H      u0 {1,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
 4    [Cs,O] u0 {1,S}
 """,
@@ -1213,7 +1215,7 @@
     group = 
 """
 1 *1 Cs            u0 {2,S} {3,S} {4,S}
-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}
 """,
@@ -1226,7 +1228,7 @@
     group = 
 """
 1 *1 Cs            u0 {2,S} {3,S} {4,S}
-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}
 """,
@@ -1238,7 +1240,8 @@
     label = "radadd_intra_O",
     group = 
 """
-1 *1 O u0
+1 *1 O u0 {2,S}
+2 *4 H u0 {1,S}
 """,
     kinetics = None,
 )
@@ -1248,7 +1251,8 @@
     label = "radadd_intra_Cb",
     group = 
 """
-1 *1 Cb u0
+1 *1 Cb u0 {2,S}
+2 *4 H u0 {1,S}
 """,
     kinetics = None,
 )
@@ -1259,7 +1263,7 @@
     group = 
 """
 1 *1 Cd u0 {2,S} {3,S}
-2    H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    R  u0 {1,S}
 """,
     kinetics = None,
@@ -1271,7 +1275,7 @@
     group = 
 """
 1 *1 Cd u0 {2,S} {3,S}
-2    H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    H  u0 {1,S}
 """,
     kinetics = None,
@@ -1283,7 +1287,7 @@
     group = 
 """
 1 *1 Cd     u0 {2,S} {3,S}
-2    H      u0 {1,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
 """,
     kinetics = None,
@@ -1295,7 +1299,7 @@
     group = 
 """
 1 *1 Cd            u0 {2,S} {3,S}
-2    H             u0 {1,S}
+2 *4 H             u0 {1,S}
 3    [Cd,Ct,Cb,CO] u0 {1,S}
 """,
     kinetics = None,
@@ -1306,9 +1310,9 @@
     label = "radadd_intra_cddouble",
     group = 
 """
-1 *1 Cd u0 {2,S} {3,D}
-2    H  u0 {1,S}
-3    Cd u0 {1,D}
+1 *1 Cd  u0 {2,S} {3,D}
+2 *4 H   u0 {1,S}
+3    R!H u0 {1,D}
 """,
     kinetics = None,
 )
@@ -1319,7 +1323,7 @@
     group = 
 """
 1 *1 CO u0 {2,S} {3,D}
-2    H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    O  u0 {1,D}
 """,
     kinetics = None,
@@ -1330,9 +1334,8 @@
     label = "radadd_intra_Ct",
     group = 
 """
-1 *1 Ct u0 {2,S} {3,T}
-2    H  u0 {1,S}
-3    Ct u0 {1,T}
+1 *1 Ct u0 {2,S}
+2 *4 H  u0 {1,S}
 """,
     kinetics = None,
 )
@@ -1356,8 +1359,8 @@
     L2: R6
         L3: R6_RSR
             L4: R6_SSR
-                L5: R6_SSS
                 L5: R6_SSM
+                L5: R6_SSS
             L4: R6_DSR
                 L5: R6_DSS
                 L5: R6_DSM
@@ -1404,23 +1407,23 @@
 L1: multiplebond_intra
     L2: doublebond_intra
         L3: doublebond_intra_2H
-            L4: doublebond_intra_2H_pri
-            L4: doublebond_intra_2H_secNd
             L4: doublebond_intra_2H_secDe
+            L4: doublebond_intra_2H_secNd
+            L4: doublebond_intra_2H_pri
     L2: triplebond_intra
         L3: triplebond_intra_H
     L2: double_bond_intra
-        L3: double_bond_intra_H
-        L3: double_bond_intra_Nd
         L3: double_bond_intra_De
+        L3: double_bond_intra_Nd
+        L3: double_bond_intra_H
 L1: radadd_intra
     L2: radadd_intra_cs
-        L3: radadd_intra_cs2H
-            L4: radadd_intra_csHHNd
-            L4: radadd_intra_csHHDe
         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