refactored reaction recipes

modified reaction recipe actions FORM_BOND, CHANGE_BOND and
BREAK_BOND to have integers as their third variables instead of
strings

Author: goldmanm

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

@@ -12,9 +12,9 @@
 reverse = "Three_Ring_Cleavage"
 
 recipe(actions=[
-    ['CHANGE_BOND', '*1', '-1', '*2'],
-    ['FORM_BOND', '*1', 'S', '*3'],
-    ['FORM_BOND', '*2', 'S', '*3'],
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['FORM_BOND', '*1', 1, '*3'],
+    ['FORM_BOND', '*2', 1, '*3'],
     ['LOSE_PAIR', '*3', '1'],
 ])
 

input/kinetics/families/1,2-Birad_to_alkene/groups.py

@@ -12,7 +12,7 @@
 reverse = "Alkene_to_1,2-birad"
 
 recipe(actions=[
-    ['CHANGE_BOND', '*1', '1', '*2'],
+    ['CHANGE_BOND', '*1', 1, '*2'],
     ['LOSE_RADICAL', '*1', '1'],
     ['LOSE_RADICAL', '*2', '1'],
 ])

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

@@ -12,11 +12,11 @@
 reverse = "1,1_Elimination"
 
 recipe(actions=[
-    ['CHANGE_BOND', '*1', '-1', '*4'],
+    ['CHANGE_BOND', '*1', -1, '*4'],
     ['GAIN_PAIR', '*4', '1'],
-    ['BREAK_BOND', '*2', 'S', '*3'],
-    ['FORM_BOND', '*1', 'S', '*2'],
-    ['FORM_BOND', '*1', 'S', '*3'],
+    ['BREAK_BOND', '*2', 1, '*3'],
+    ['FORM_BOND', '*1', 1, '*2'],
+    ['FORM_BOND', '*1', 1, '*3'],
     ['LOSE_PAIR', '*1', '1'],
 ])
 

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

@@ -12,9 +12,9 @@
 reverse = "1,1_Elimination"
 
 recipe(actions=[
-    ['BREAK_BOND', '*2', 'S', '*3'],
-    ['FORM_BOND', '*1', 'S', '*2'],
-    ['FORM_BOND', '*1', 'S', '*3'],
+    ['BREAK_BOND', '*2', 1, '*3'],
+    ['FORM_BOND', '*1', 1, '*2'],
+    ['FORM_BOND', '*1', 1, '*3'],
     ['LOSE_PAIR', '*1', '1'],
 ])
 

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

@@ -12,8 +12,8 @@
 reverse = "1,2_S_radical_shift"
 
 recipe(actions=[
-    ['BREAK_BOND', '*1', 'S', '*2'],
-    ['FORM_BOND', '*1', 'S', '*3'],
+    ['BREAK_BOND', '*1', 1, '*2'],
+    ['FORM_BOND', '*1', 1, '*3'],
     ['GAIN_RADICAL', '*2', '1'],
     ['LOSE_RADICAL', '*3', '1'],
 ])

input/kinetics/families/1,3_Insertion_CO2/groups.py

@@ -12,10 +12,10 @@
 reverse = "1,2_Elimination_CO2"
 
 recipe(actions=[
-    ['BREAK_BOND', '*3', 'S', '*4'],
-    ['CHANGE_BOND', '*1', '-1', '*2'],
-    ['FORM_BOND', '*1', 'S', '*3'],
-    ['FORM_BOND', '*2', 'S', '*4'],
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['FORM_BOND', '*1', 1, '*3'],
+    ['FORM_BOND', '*2', 1, '*4'],
 ])
 
 entry(

input/kinetics/families/1,3_Insertion_ROR/groups.py

@@ -12,10 +12,10 @@
 reverse = "1,2_Elimination_ROR"
 
 recipe(actions=[
-    ['BREAK_BOND', '*3', 'S', '*4'],
-    ['CHANGE_BOND', '*1', '-1', '*2'],
-    ['FORM_BOND', '*1', 'S', '*3'],
-    ['FORM_BOND', '*2', 'S', '*4'],
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['FORM_BOND', '*1', 1, '*3'],
+    ['FORM_BOND', '*2', 1, '*4'],
 ])
 
 entry(

input/kinetics/families/1,3_Insertion_RSR/groups.py

@@ -12,10 +12,10 @@
 reverse = "1,2_Elimination_RSR"
 
 recipe(actions=[
-    ['BREAK_BOND', '*3', 'S', '*4'],
-    ['CHANGE_BOND', '*1', '-1', '*2'],
-    ['FORM_BOND', '*1', 'S', '*3'],
-    ['FORM_BOND', '*2', 'S', '*4'],
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['FORM_BOND', '*1', 1, '*3'],
+    ['FORM_BOND', '*2', 1, '*4'],
 ])
 
 entry(

input/kinetics/families/1,4_Cyclic_birad_scission/groups.py

@@ -12,11 +12,11 @@
 reverse = "none"
 
 recipe(actions=[
-    ['BREAK_BOND', '*2', 'S', '*3'],
+    ['BREAK_BOND', '*2', 1, '*3'],
     ['LOSE_RADICAL', '*1', '1'],
     ['LOSE_RADICAL', '*4', '1'],
-    ['CHANGE_BOND', '*1', '1', '*2'],
-    ['CHANGE_BOND', '*3', '1', '*4'],
+    ['CHANGE_BOND', '*1', 1, '*2'],
+    ['CHANGE_BOND', '*3', 1, '*4'],
 ])
 
 entry(

input/kinetics/families/1,4_Linear_birad_scission/groups.py

@@ -14,9 +14,9 @@
 recipe(actions=[
     ['LOSE_RADICAL', '*1', '1'],
     ['LOSE_RADICAL', '*4', '1'],
-    ['CHANGE_BOND', '*1', '1', '*2'],
-    ['CHANGE_BOND', '*3', '1', '*4'],
-    ['BREAK_BOND', '*2', 'S', '*3'],
+    ['CHANGE_BOND', '*1', 1, '*2'],
+    ['CHANGE_BOND', '*3', 1, '*4'],
+    ['BREAK_BOND', '*2', 1, '*3'],
 ])
 
 entry(