More fixes to R_Addition Multiple Bond

These were found using the checkWellFormed function.

-changed CtJ's had an atom C, that I've changed to  so that it's children
can include nitrogen (1 occurrence in rules.py, The original paper looks
like it only consider C, so I changed the rule from Ct-H_Ct-H;CtJ to
Ct-H_Ct-H;CtJ_Ct
-changed OdR had an atom {C,S} changed to Od-R!H, to include nitrogen in
children (no rules affected)
-reordered atoms in CsJ-OneDeNsCs. Doesn't change graph, but makes Adjlist
more obviously a subgroup of parent
-added nitrogen atoms N3s and N5s into set of possible atoms for CsJ-OneDe
-changed O to Os in OJ-Os. Adj list restricts the atom to Os (and it's in
the name) (also changed in 13 rules)
-changed some C atoms to Cd or Cs according to definition in
Cds-HH_Cds-Cs\H3/H. Also reordered pretty much the entire adj list so it
matched up with it's parent's ordering. (also changed in 3 rules)
-O_atom_triplet allows 2S and 2T. Changed it to only 2T.
-CH_quartet changed to from C 3Q --> Cs 3Q. There were two groups named
CH_quartet, I clarified one of them and deleted the other.
-Two definitions of Y_1centerbirad. Deleted one of them (kept one that
allows nitrogen)
-Removed group N3_atom_quartet which was a duplicate from merge (same as
N_atom_quartet)
-Deleted one instance of OJ-OneDe (they were identical)
-O_rad/OneDe was previously both renamed to OJ-OneDe and the adjlist was
changed to include nitrogen. However, the rule that uses it was created
using AGvandeputte's GAV value without nitrogen. As such, I've re-created
a group O_rad/OneDe with no nitrogen and made it a child of the more
general OJ-OneDe. Name is kinda non-descriptive though...Also gave it a
random index, which are all screwed up anyway.
- Same history and solution as above for O_rad/NonDe to OJ-NonDe. Also had
  to move some of children around to preserve correct relationships.

  Changes to tree:
-L6: Cds-NonDe2_N3d changed to L5. Clearly a typo based on positioning,
  name, and comparing adj list with relatives.
  -Added O_atom_singlet, NH_singlet, and CH2_singlet under Y_1centerbirad.
  They had definitions but did not appear in the tree
  -Changed level of CtJ_Ct and CtJ_N3t from L3: to L4. They actually are
  the child of one of their siblings CtJ! That sounds like the plot of a
  crappy novel.