Fixes to H-Abstraction: Part 9

All changes were to fix parent/child relationships
*Below if I say 1C, I mean index 1 with atom type C in a adjList
rules

Add CS to 3 of C_rad/H/OneDeS (0 rules affected)
Change 3C to CS in "C_rad/H/CSS" (50 rules affected)

Add CS to 3 of "C/H/OneDe"

Change 3C to Cd in "S/H/Cd" (48 rules affected)

Change 3C to CS in "S/H/CS" (42 rules affected)

Add CS to 3 of "C/H/Cs2" (0 rules affected)
Change C to CS in 3 of "C/H/Cs2CS"

Change 1C, 3C, and 5C to Cs in "C/H/Cs2/Cs\O" (9 rules affected)

Change 2C to Cs in "C_rad/H2/Cs\H2\Cs|Cs|O" (1 rule affected)

Add CS to 4 of "C/H2/OneDeC"
-1 rule affected, slightly dangerous because it might extend a rule where
its not supposed to
-The rule is from a child node, so it probably is already
over-generalizing, we should probably consider removing/moving it at some
later point
-I left a comment on the rule to remind myself later, when I start pruning
for training reactions
Change 4C to CS in "C/H2/CSCs" (44 rules affected)

Change name of C/H3/Cs\1NonDe to C/H3/Cs\OneNonDe to make it conform to
other group names
Change 2C to Cs in "C/H3/Cs\OneNonDe" (0 rules affected)

Add CS to 2 of "S_rad/OneDe"
Change 2C to CS in "S_rad/CS" (0 rules affected)
Change 2C to Cd in "S_rad/Cd" (6 rules affected)

Change 3C to Cd in "C_rad/H/CSCs" (51 rules)

Change 1C to Cs in "CH2_triplet" (4 rules)

Added CS to 3 and 4 in "C/H/Cs" (0 rules) For its children:
Change 3C to Cd on "C/H/CdCt" (0 rules)
Change 4C to CS in "C/H/CtCS" (0 rules)
Change 3C to Cd in "C/H/CdCb" (0 rules)
Change 3C to Cd in "C/H/CdCO" (0 rules)
Change 4C to CS in "C/H/COCS" (0 rules)
Change 3C and 4C to Cd in "C/H/CdCd" (44 rules affected)
Change 3C to Cd and 4C to CS in "C/H/CdCS" (0 rules)
Change 3C and 4C to CS in "C/H/CSCS" (0 rules)
Fixes to H-Abstraction: Part 10

All changes were to fix parent/child relationships
*Below if I say 1C, I mean index 1 with atom type C in a adjList
rules

Add CS to 3 and 4 of "C/H/TwoDe" (0 rules)

Change name of "C/H3/Cs\2NonDe" to "C/H3/Cs\TwoNonDe" to conform with
other names
Change 2C to Cs in "C/H3/Cs\TwoNonDe" (0 rules)

Add CS to 4 of "CS/H/OneDe" (0 rules). For it's children:
Change 4C to CS in "CS/H/CS" (0 rules)
Change 4C to Cd in "CS/H/Cd" (44 rules affected)

Change 1C to Cs in:
-"CH2_singlet" (0 rules)
-"Cd_Cd\H\Cs|H2|Cs_pri_rad" (1 rule)

Change 2C to Cs in
-"C_rad/H2/Cs\H\Cs|Cs\O" (0 rules)
-"C/H3/Cs\H\Cs\Cs|O" (5 rules)
-"C/H3/Cs\H2\O" (0 rules)
-"C/H3/Cs\H\Cs\O" (2 rules)
-"Cd_Cd\H\Cs|H2|Cs_pri_rad" (1 rule)
-"C_rad/H/Cs\H\Cs2/O" (3 rules)

Change 3C to Cd in "CS_rad/Cd" (44 rules)
Fixes to H-Abstraction: Part 11

All changes were to fix parent/child relationships
*Below if I say 1C, I mean index 1 with atom type C in a adjList
rules

Change 2C to Cs in "C/H2/Cs\Cs2/O" (9 rules)

Change 1C to Cs and 3C to CO in "C_rad/H/CO\H/Cs\H3" (2 rules)

Add CS to 3 of "CS_rad/OneDe" (0 rules) for its child
Change 3C to CS in "CS_rad/CS" (0 rules)

Change 1C and 3C to Cs in "C/H2/Cs\H3/Cs\H3" (1 rule)

Change 2C and 3C to Cs in "C_rad/O/Cs/Cs\Cs" (1 rule)

Change 2C to Cs in "C/H3/Cs\H2\Cs" (1 rule)

Add CS to 3 of "Cd_rad/OneDe" (0 rules). For it's children:
Change 3C to CS in "Cd_rad/CS" (51 rules)
Change 3C to Cd in "Cd_rad/Cd"(57 rules)

Change 3C to Cd in "C/H/Cs2Cd" (44 rules)
Fixes to H-Abstraction: Part 12

All changes were to fix parent/child relationships
*Below if I say 1C, I mean index 1 with atom type C in a adjList
rules

Change 3C to Cd in "C_rad/H/CdS' (50 rules)

Add CS to 3 and N in 4 of "C_rad/H/OneDe" (0 rules). For its child:
Change 3C to Cd in "C_rad/H/OneDeN" (0 rules)

Last of children/parent fixes
Fixes to 1,3_Insertion_ROR

All changes were to fix parent/child relationships
*Below if I say 1C, I mean index 1 with atom type C in a adjList
rules

Change 1C and 2C to Cd in "Thiophene2" (1 rule affected)
Change 1C and 2C to Cd in "Thiophene3" (1 rule affected)
Fixes to H-Abstraction: Part 13

"Cd/H/NonDeN" and "Cd/H/N" share the same definition. After examining it,
it appears one is supposed to have a NonDeN and the other is supposed to
be DeN. Although I am not entirely sure if nitrogen with lone pairs should
be considered non-delocalized I have settled on the following solution:
-Change 4N to {N3s,N5s} in "Cd/H/NonDeN" (0 rules affected)
-Change "Cd/H/N" name to "Cd/H/DeN"	(0 rules affected)
-Change 4N to {N3d,N3t,N3b,N5d,N5dd,N5t,N5b} (0 rules affected)

"N3s_rad/H2" and "NH2_rad" share the same definition. "N3s_rad/H2" is not
in the tree, so it seems to be an accidental duplicate.
-Delete the group "N3s_rad/H2"
-Replace "N3s_rad/H2" with "NH2_rad" in the name of 5 rules

"N3s/H2/OneDeN" and "N3s/H2/OneDe" share the same definition. The latter
should include all delocalized groups. For now I have just added carbons
-Change 4{N3d,N5d} to {Cd,Cdd,Ct,CO,CS,N3d,N5d} (0 rules)

-Delete group "N3_atom_quartet" because it seems to overlap with the
group" N_atom_quartet" (Doesn't really make sense to call a tri-radical N
atom N3 or N5)
-Replace rule "N3_atom_quartet" with "N_atom_quartet" in 1 rule

-Delete group "CX_H_or_Xrad_H_Xbirad_Hrad". The definition made no sense
with the name, it did not appear in the tree, and it had no rules. Seemed
like some leftover mistake.

-"N_birad_H" does not appear in the tree. There are two very similar
groups: "NH_triplet_H" and "NH_singlet_H", which are the same as
"N_birad_H", but specify the spin state. Additionally there are 5 rules
which use "N_birad_H". After checking all the sources of the rules, it
seems quite likely that NH is in the lower energy triplet state (1 source
directly states this assumption in its theoretical calculation, the other
rules were all derived by experiment
-Changed "N_birad_H" to "NH_triplet_H" in 5 rules
-deleted group "N_birad_H"

Add Cd to 3 of "N3d/H/NonDe" to make it fit child/parent relationship with
"N3d/H/NonDeC" (0 rules affected)

Add CO to 3 of "N3d/H/OneDe" to make it fit child/parent relationship with
""N3d/H/OneDeC"(0 rules)
Change name "N3d/H/OneDeC" to "N3d/H/OneDeCO" based on the source of its
rules (they should probably be a training reaction)
In "N3d/H/OneDeCO" change 3{Cd,Ct,Cb} to CO (6 rules affected)

The definition of "C/H/NonDeC" doesn't make much sense.
C/H/NonDeC
1 *1 C        0 {2,S} {3,S} {4,S} {5,S}
2 *2 H        0 {1,S}
3    {Cs,O,S} 0 {1,S}
4    {Cs,O,S} 0 {1,S}
5    {Cs,O,S} 0 {1,S}

Based on its position on the tree I think it should be just "C/H/NonDe":
-Change the name from "C/H/NonDeC" to "C/H/NonDe"
-Add N to 3, 4, and 5 (0 rules affected)