Fixes to Substitution_O family

CsJ-OneDe had repeat groups.

Deleted some duplicate entries: CsJ-OneDeOsCs, CsJ-OneDeOOss, CsJ-OneDeOsOs

Fixes to O2b and C2b to become children of their parents.

Removed O_rad from groups since it is a duplicate of OsJ, a child of OJ
Fixes to intra_H_migration family

Fixes to Cs_H_out_H/CO, Cs_H_out_H/CS, Cs_H_out_H/Ct, Cs_H_out_H/Cd to
be children of their parent Cs_H_out_H/OneDe

Replacing Cs_H_out_H/OneDe definition in rules with one from groups

Replacing R3H_SS_S definition in rules with one from groups
Fixes to 2+2_cycloaddition_CO family

Fixed CH2CHO to be child of parent CO
Fixes to H-Abstraction: Part 3

-changed the comment on O/H/OneDeN;O_pri_rad rule to correct source
(checked with bbuesser)
-changed the comment on N3d/H/NonDeC;O_pri_rad rule to correct source
(checked with bbuesser)

-changed "2 C" to "2 Cd" in definition of C_rad/CSCsS to make it a
subgroup of its parent (50 rules affected)
-changed "2 C" to "2 Cd" in definition of C_rad/CdCdCs to make it a
subgroup of its parent (57 rules affected)
-changed "2 C" to "2 Cd" in definition of C_rad/CSCs2 to make it a
subgroup of its parent (51 rules affected)
-changed "2 C" to "2 Cd" in definition of C_rad/CdCs2 to make it a
subgroup of its parent(57 rules affected)
-changed "2 C" to "2 Cd"in definition of C_rad/CdCsS to make it a
subgroup of its parent(50 rules affected)
   -in rules.py replaced 265 instances of "2    C  0 {1,S} {5,D}" with "2
   Cd  0 {1,S} {5,D}" (rules for above 5 changes)

-changed "2 C" to "2 Cd" in definition of CdCOCs to make it a subgroup of
its parent  (0 rules affected)
-changed "2 C" to "2 Cs" in definition of C_rad/H2/Cs\H\Cs\Cs|O to make it
subgroup of parent (6 rules affected)
-changed "1 C" to "1 Cd" and "3 C to 3 CO" in definition of
C/H2/CO\H/Cs\H3 to make it a subgroup of parent (1 rule affected)
-changed both C atoms to Ct in definition of C2b (affects 1 rule)
Fixes to SubstitutionS family

Made SJ group more general.

Made C2b and O2b children of their parent Y_2centeradjbirad

Made CH2_triplet child of its parent Y_1centerbirad
Fixes to R_Recombination family

Fix to Ct_rad/Ct to be child of its parent Ct_rad
by changing C's to Ct's
More fixes to intra_H_migration family

Fix Cs_H_out_H/Cd group in R3H_SS_OOCs;O_rad_out;Cs_H_out_H/Cd rule
Fixes to intra_NO2_ONO_conversion family

Fix RNO2 entry in rules to match the one in groups
Fixes to 1,2-Biard_to_alkene family

Put groups into tree:
Y_12_20a
Y_12_22a
Y_12_22b
Y_12_12b
Y_12_12a
Y_12_11b
Y_12_11a
Y_12_02b
Y_12_20b
Y_12_02a
Y_12_21a
Y_12_21b
Additional fix to R_Recombination family

Added N5d_rad to tree
Fixes to 1+2_Cycloaddition family

Change elec_def in rules to be the same as in groups
Fixes to 1,3_Insertion_ROR family

Change doublebond definition in rules to match one in groups

Fix Cd/H/Nd_Cd/H/De definition so that it is child of Cd/monosub_Cd/monosub
by changing C's to Cd's

Fix Cd/H/De_Cd/H2 definition so that it is proper child of Cd/monosub_Cd/unsub
by changing C's to Cd's

Fix Cd/De2_Cd/H/De and Cd/Nd/De_Cd/H/De's definition to be children of Cd/disub_Cd/monosub
by changing C's to Cd's

Fix Cd/Nd/De_Cd/Nd2's definition to be child of Cd/disub_Cd/disub
by changing C's to Cd's

Similar changes to these groups:
Cd/H2_Cd/H/De
Cd/De2_Cd/H2
Cd/H2_Cd/De2
Cd/H/De_Cd/Nd/De
Cd/H2_Cd/Nd/De
Cd/H/De_Cd/H/Nd
Cd/Nd2_Cd/Nd/De
Cd/De2_Cd/H/Nd
Cd/Nd/De_Cd/Nd/De
Cd/NdDe_Cd/H2
Cd/H2_Cd/H/Nd
Cd/De2_Cd/Nd/De
Cd/De2_Cd/De2
Cd/Nd2_Cd/Nd2
Cd/H/De_Cd/Nd2
Cd/H/De_Cd/H/De
Cd/Nd2_Cd/De2
Cd/Nd2_Cd/H/Nd
Cd/Nd/De_Cd/De2
Cd/H/De_Cd/De2
Cd/H/Nd_Cd/Nd/De
Cd/H2_Cd/Nd2
Cd/H/Nd_Cd/H/Nd
Cd/Nd2_Cd/H/De
Cd/Nd/De_Cd/H/Nd
Cd/H/Nd_Cd/H2
Cd/De2_Cd/Nd2
Cd/Nd2_Cd/H2
Fixes to intra_OH_migration family

Make Y_rad_out more general by allowing
all C, not just Cd and Cs.  It should be ok with any carbon group
that has a radical.
Fixes to H-Abstraction: Part 4

Found using databaseTester
*Below if I say 1C, I mean index 1 with atom type C in a adjList

Change C to Ct in "C_methane;C2b" rule

Change 1C to 1Cs and 3C to 3CO in "C/H2/CO\H/Cs\H3;C_rad/H2/Cs\H\Cs\Cs|O"
rule

Remove "Orad_H": was duplicate with "OH_rad_H", appeared in 0 rules and
did not appear in tree

Change O to Os in "O2b" (21 rules affected)

Change 1C to 1Cs in "C/H2/Cd\H_Cd\H2/Cs\H3" (2 rules affected)

Change 5C to 5CS in "C/H3/CS" (44 rules affected)

Change 5{Cd,Ct,Cb,CO} to 5{Cd,Ct,Cb,CO,CS} in "C/H3/OneDe" to make above
("C/H3/CS") proper child (0 rules)

Change 2Cd to 2Cdd in "N3d_rad/OneDeCdd_O" (3 rules affected)

Change 2Cd to 2Cdd in "N3d_rad/OneDeC" to make above
("N3d_rad/OneDeCdd_O") proper child (0 rules)

Change 2Cd to 2{Cd,Cdd} in "N3d_rad/OneDe" to make above
("N3d_rad/OneDe") proper child (0 rules)

Change 5C to 5Cd in "C/H3/Cd" (51 rules affected)

Three children for above group "C/H3/Cd", change C to Cd in them as well
-"C/H3/Cd\H_Cd\H2;H_rad" (6 rules),
-"C/H3/Cd\H_Cd\H\Cs" (3 rules),
-"C/H3/Cd\Cs_Cd\H2" (7 rules)

Change 2C to 2Cs in "C/H3/Cs\H3" (2 rules affected)
Fixes to H-Abstraction Part 5

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 3O to 3Od in "N3d/H/NonDeO" (6 rules affected)

change 4C to 4Cd in "C/H2/CdS" (44 rules affected)

change 1C, 2C, 4C, and 5O to Cs or Os in "C_rad/H/Cs\H\Cs\O/Cs" (1 rule
affected)

change 5C to 5Cd in "C/H2/CtCS" (0 rules affected)

change 3C to 3Cd in "C_rad/COCSCs" (0 rules affected)

change 3C to 3Cd in "C_rad/CdCdCs" (57 rules affected)

-remove "Orad_H": was duplicate with "OH_rad_H", appeared in 0 rules and
did not appear in tree
More fixes to 1,3_Insertion_ROR family

Fixes to entries in rules that don't match their groups

Fixes to Cd/H/S_Cd/H/Cd and Cd/H/Cd_Cd/H/S changing C's to Cd's
so that they are children of their parents
Fixes to H-Abstraction: Part 6

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

For the following children of C_rad/H/NonDeC: change C to Cs
-"C_rad/H/Cs\H3/Cs\H3" (2 rules affected)
-"C_rad/H/Cs\H2\Cs/Cs\H2\O" (1 rules affected)
-"C_rad/H/Cs\H2\Cs|O/Cs" (1 rule affected)

Change 1C to Cs in "Cd_Cd\H\Cs_rad/Cs" (1 rule affected)

Changed 2C and 3C to Cs in "C_rad/H/Cs\H2\Cs|H2|Cs/O" (1 rule affected)

Added N to 4 in "Cd/H/OneDe" (0 rules affected)

For the following children of "C_rad/Cs": change C to Cd (no rules for any
of them)
-2C to Cd in "C_rad/CdCtCs"
-3C to Cd in "C_rad/CtCSCs"
-2C to Cd in "C_rad/CdCbCs"
-3C to Cd in "C_rad/CbCSCs"
-2C and 3C in "C_rad/CdCSCs"
-2C and 3C in "C_rad/CSCSCs"

Change 4C to Cd in "Cd/H/CS" (44 rules affected)

Change 3C to Cs in "O_rad/Cs\H2\Cs|H|Cs2" (3 rules affected)

Change 2C to Cs in "C_rad/H2/Cs\Cs2\O" (1 rule affected)

Change 4C to Cd in "C_rad/H/COCS" (0 rules affected)

Change 4C to Cd in "Cd/H/Cd" (44 rules affected)
Fixes to H-Abstraction: Part 7

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 4 of "C/H2/OneDe" (0 rules affected)
Add CS to 4 of "C/H2/OneDeS" (0 rules affected):
Change 4C to CS in "C/H2/CSS" (44 rules affected)

Add CS to 3 of "C/H/CsS" (0 rules affected):
Change 4C to Cd in "C/H/CdCsS" (0 rules affected)
Change 3C to CS in "C/H/CSCsS" (88 rules affected)

Add N to 2 pf "Cd_H" (0 rules affected)

Change 2C to Cs in "C_rad/H2/Cs\H3" (2 rules affected)

Change 4C to Cd in "C/H/CbCS" (0 rules affected)

Change 4C to Cd in "C/H2/CdCt" (0 rules affected)

Change 4C to Cd in "C/H2/CdCs" (44 rules affected)

Change 3C to Cd in "C/H2/Cd\H_Cd\H2/Cs\H3" (2 rules affected)
Fixes to H-Abstraction: Part 8

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 4 and 5 of "C/H2/TwoDe"
A few children of "C/H2/TwoDe" needed changing
-4C and 5C to Cd in "C/H2/CdCd" (50 rules)
-5Cd to CS in "C/H2/CtCS" (0 rules)
-5C to CS in "C/H2/CbCS" (0 rules)
-5C to CS in "C/H2/COCS" (0 rules)
-4C to Cd and 5C to CS in "C/H2/CdCS" (0 rules)
-4C and 5C to CS in "C/H2/CSCS" (0 rules)
-4C to Cd in "C/H2/CdCb" (0 rules)
-4C to Cd in "C/H2/CdCO" (0 rules)

Changed 3C to Cd in "C_rad/H/CdCt" (0 rules affected)

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

Change 3C to Cd in "C_rad/H/CdCs" (57 rules affected)

Change 3C and 4C to Cd in "C_rad/H/CdCd" (57 rules affected)

Add CS to 4 and 5 of "C_rad/H/TwoDe"
Change C to Cd or C to CS accordingly for the following children:
-"C_rad/H/CdCb"
-"C_rad/H/CtCS"
-"C_rad/H/CdCb"
-"C_rad/H/CbCS"
-"C_rad/H/CdCO"
-"C_rad/H/CdCS"
-"C_rad/H/CSCS"

*Still more to come
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)