Merge pull request #115 from ReactionMechanismGenerator/N-unforbidden

In the forbidden groups of many kinetic families N was so far treated as having similar valance as C or Si.

This was now fixed generally by deleting "N" from the "birad_singlet" and "quadrad_singlet" forbidden groups, and by adding a new “N_birad_singlet” forbidden group.

The following families were changed: Disproportionation, H_Abstraction, Intra_H_migration, Intra_R_Add_Endocyclic, Intra_R_Add_Exocyclic, Intra_R_Add_ExoTetcyclic, Substitution_O, SubstitutionS

Removed many other forbidden groups because they seemed to be redundant after we switched to the new adjList format.

Author: connie

input/kinetics/families/1+2_Cycloaddition/groups.py

@@ -747,16 +747,3 @@
 """
 )
 
-forbidden(
-    label = "birad_triplet",
-    group = 
-"""
-1 *3 R!H u2
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-

input/kinetics/families/1,2_Insertion_CO/groups.py

@@ -821,16 +821,3 @@
 """
 )
 
-forbidden(
-    label = "birad_triplet",
-    group = 
-"""
-1 *1 R!H u2
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-

input/kinetics/families/1,2_Insertion_carbene/groups.py

@@ -820,16 +820,3 @@
 """
 )
 
-forbidden(
-    label = "birad_triplet",
-    group = 
-"""
-1 *1 R!H u2
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-

input/kinetics/families/Disproportionation/groups.py

@@ -2956,19 +2956,6 @@
 """,
 )
 
-forbidden(
-    label = "OS_birad_singlet",
-    group = 
-"""
-1 *1 [O,S] u0 p3
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
 forbidden(
     label = "O_Orad",
     group = 
@@ -2988,7 +2975,7 @@
     label = "XH_birad_singlet",
     group = 
 """
-1 *3 [C,N,Si] u0 p1 {2,[S,D,T]}
+1 *3 [C,Si] u0 p1 {2,[S,D,T]}
 2 *2 R!H      ux {1,[S,D,T]} {3,S}
 3 *4 H        u0 {2,S}
 """,
@@ -3003,7 +2990,7 @@
     label = "XH_quadrad_singlet",
     group = 
 """
-1 *3 [C,N,Si] u0 p2 {2,[S,D,T]}
+1 *3 [C,Si] u0 p2 {2,[S,D,T]}
 2 *2 R!H      ux {1,[S,D,T]} {3,S}
 3 *4 H        u0 {2,S}
 """,
@@ -3015,23 +3002,12 @@
 )
 
 forbidden(
-    label = "birad_singlet",
+    label = "XH_N_birad_singlet",
     group = 
 """
-1 *1 [C,N,Si] u0 p1
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
-forbidden(
-    label = "quadrad_singlet",
-    group = 
-"""
-1 *1 [C,N,Si] u0 p2
+1 *3 N u0 p2 {2,[S,D]}
+2 *2 R!H      ux {1,[S,D]} {3,S}
+3 *4 H        u0 {2,S}
 """,
     shortDesc = u"""""",
     longDesc = 

input/kinetics/families/H_Abstraction/groups.py

@@ -6859,32 +6859,6 @@
 """
 )
 
-forbidden(
-    label = "OS_birad_singlet",
-    group = 
-"""
-1 *3 [O,S] u0 p3
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
-forbidden(
-    label = "birad_singlet",
-    group = 
-"""
-1 *3 [C,N,Si] u0 p1
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
 forbidden(
     label = "disprop1",
     group = 
@@ -6972,16 +6946,3 @@
 """,
 )
 
-forbidden(
-    label = "quadrad_singlet",
-    group = 
-"""
-1 *3 [C,N,Si] u0 p2
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-

input/kinetics/families/Intra_R_Add_Endocyclic/groups.py

@@ -2626,32 +2626,6 @@
 """
 )
 
-forbidden(
-    label = "OS_birad_singlet",
-    group = 
-"""
-1 *1 [O,S] u0 p3
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
-forbidden(
-    label = "birad_singlet",
-    group = 
-"""
-1 *1 [C,N,Si] u0 p1
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
 forbidden(
     label = "bond31",
     group = 
@@ -2680,16 +2654,3 @@
 """,
 )
 
-forbidden(
-    label = "quadrad_singlet",
-    group = 
-"""
-1 *1 [C,N,Si] u0 p2
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-

input/kinetics/families/Intra_R_Add_ExoTetCyclic/groups.py

@@ -3155,32 +3155,6 @@
 """
 )
 
-forbidden(
-    label = "OS_birad_singlet",
-    group = 
-"""
-1 *1 [O,S] u0 p3
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
-forbidden(
-    label = "birad_singlet",
-    group = 
-"""
-1 *1 [C,N,Si] u0 p1
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
 forbidden(
     label = "bond21",
     group = 
@@ -3195,16 +3169,3 @@
 """,
 )
 
-forbidden(
-    label = "quadrad_singlet",
-    group = 
-"""
-1 *1 [C,N,Si] u0 p2
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-

input/kinetics/families/Intra_R_Add_Exocyclic/groups.py

@@ -2931,32 +2931,6 @@
 """
 )
 
-forbidden(
-    label = "OS_birad_singlet",
-    group = 
-"""
-1 *1 [O,S] u0 p3
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
-forbidden(
-    label = "birad_singlet",
-    group = 
-"""
-1 *1 [C,N,Si] u0 p1
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
 forbidden(
     label = "bond21",
     group = 
@@ -2984,16 +2958,3 @@
 """,
 )
 
-forbidden(
-    label = "quadrad_singlet",
-    group = 
-"""
-1 *1 [C,N,Si] u0 p2
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-

input/kinetics/families/R_Addition_CSm/groups.py

@@ -709,20 +709,6 @@
 """
 )
 
-forbidden(
-    label = "CSm_triplet",
-    group = 
-"""
-1 *1 C u2 p0 {2,D}
-2    S u0 p2 {1,D}
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
 forbidden(
     label = "O2_birad",
     group = 

input/kinetics/families/R_Addition_MultipleBond/groups.py

@@ -17741,45 +17741,6 @@
 """,
 )
 
-forbidden(
-    label = "OS_birad_singlet",
-    group = 
-"""
-1 *3 [O,S] u0 p3
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
-forbidden(
-    label = "birad_singlet",
-    group = 
-"""
-1 *3 [C,N,Si] u0 p1
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
-forbidden(
-    label = "quadrad_singlet",
-    group = 
-"""
-1 *3 [C,N,Si] u0 p2
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
-
 # forbidden(
 #     label = "benzene_doublebond",
 #     group =