Without specifically specifying the lone pairs, we do not correctly make this sample molecule because we do not have hypervalent sulfur yet.

-Changed some R to R!H because they were u2 or u3 and therefore impossible to be H
-Added explicit charges to CO so that makeSampleMolecule cretes it correctly

reordering of trees to pass accessibility tests

-reordering of trees to pass accessibility,
-Remove groups Cd_rad_out and Cdpri_rad_out and all their children because their valence is overspecified when taking into account the bond to the backbone

rearrangement of tree order to meet test,

-general rearrangements to meet accessibility tests
-combined two group branches of rough form R2=R1(R3)H that had separate branches for R2 and R3
-moved Cs_H_out_OOH/H to be under the Cs_H_out_OOH group rather than the Cs_H_out_H/NonDeO
-Added T bonds to R2H, which is the sampleBackbone. Previously when merged with a *2 Ct.

-rearranged groups to pass accessibility tests,
-Switched a few `Cd,Cs` to `Cs,Cd`, which functionally will not change RMG performance, but now passes our unit test, unfortunately our makeSampleAtom is not as robust as we would like
-Remove atom from Cd_rad_out to prevent it from possibly being over-specified
-Remove the Cd atom and change name of Cd_rad_out_C_H, Cd_rad_out_C_ND, Cd_rad_out_C_De to Cd_rad_out_H, Cd_rad_out_ND, and Cd_rad_out_De because they were overspecified
-Replaced Cd_rad_out_C with Cd_rad_out_double because it was overspecified
1b2e040

-rearrangement of entries to meet accessibility tests,
-eliminated radadd_cdsingle subtree
-made radadd_intra_Ct viable by removing the extra Ct to allow connection to backbone

-rearrangement of entries to pass accessibility tests
-combination of the radadd_intra_cdsingle and radadd_intra_cddouble branches into one branch
-fixed radadd_intra and it’s sub-entries by adding in the *4 hydrogens
-also removed a Ct from radadd_intra_Ct to allow connection to backbone

-rearrangement of entries to meet accessibility tests
-combination of radadd_intra_cddouble and radadd_intra_cdsingle branches into one branch
-fixed radadd_intra and it’s sub-entries
-added *4 labels/appropriate hydrogens to match backbone properly
-removed a Ct from radadd_intra_Ct to allow connection to backbone

-rearrangement of entries to pass accessibility tests
-Changed R to R!H for *1 and *2 since they have double bonds on the root backbone.

-removal of depreciated group CdsJ-2 from the CJ OR statement
-rearrangement of entries in tree to pass accessibility tests
-Change all *1 C to Cs in intra_substituionCS_cycilzation. Based on original backbones (from several PRs prior), this seems to be the original intent of the family.Also simplified the *1`C` subtree to `Cs` and eliminated entries for Cds and Ct in that subtree.
-Cs-RRR is overspecified because the way the subtree is set up, *1 C should only have 2 more bonds: It and all children were changed to have one less atom. Most groups just reduced, but a few completely deleted: Cs-(TwoDe)S, Cs-(TwoDe)C, Cs-HHS, and Cs-HHC, and one group added Cs-HH
-In a similar vein, the *3 tree was also overspecified for many entries. Used a similar approach to delete or simplify entries

-rearrangement of entries to pass accessibility tests
-*3 subtree was overspecified for many groups. I have removed many of these groups and reduced the rest. This applies to all groups below CdsJ in that subtree.
-Add two groups XSR4J_SS_Cs, XSR4J_SS_Ss which further specify atomtypes on backbones to accomodate rules
-change rule number 2 to use groups XSR3J_S;C-HHH;CsJ-HH. I had to go back to commit 5f2c3c1 to see what the original intent was, but I'm fairly sure it is now correct

-rearrangement of entries to meet accessibility tests
-removal of the redundant CJ group in favor of the CdsJ group
-*3 subtree was overspecified for many groups. I have removed many of these groups and reduced the rest. This applies to all groups below CdsJ in that subtree

-S-RR *1 and *2 subtree is also overpecified for many groups, removed many of these groups the same way we treated the *3 subtree.

-Changed the following rules with indicated indices. They should all point to the original intent, but require less groups to do so:
2. XSR3J_S;SsJ-3-Cs;S-HC --> XSR3J_S_Cs;SsJ;S-H
3. XSR3J_S;CsJ-3-CsHH;S-HC --> XSR3J_S_Cs;CsJ-HH;S-H
4. XSR3J_S;CsJ-3-SsHH;S-HSs --> XSR3J_S_Ss;CsJ-HH;S-H
5. XSR3J_S;SsJ-3-Cs;S-Cs(HHH)C --> XSR3J_S_Ss;SsJ;S-H
6. XSR3J_S;CsJ-3-SsHH;S-Cs(HHH)Ss --> XSR3J_S_Ss;CsJ-HH;S-Cs(HHH)
7. XSR3J_S;CsJ-3-SsHH;S-Ss(H)Ss --> XSR3J_S_Ss;CsJ-HH;S-Ss(H)
8. XSR5J_SSS;CsJ-CsCsH;S-Cs(NonDe)C --> XSR5J_S_CsRCs;CsJ-CsH;S-Cs(NonDe)
9. XSR6J_SSSS;CsJ-CsCsH;S-Cs(NonDe)C --> XSR6J_S_CsRRCs;CsJ-CsH;S-Cs(NonDe)

-Added a few backbone groups to accomodate rule changes: XSR3J_S_Cs, XSR3J_S_Ss, XSR5J_SSS_CsRCs, XSR6J_SSSS_CsRRCs

rearrangement of entries to meet accessibility tests
-Remove an R atom on all backbones which should be part of an end groups
-Also remove same unlabeled R atom on most general end group S-RR as it is not a reacting group and not necessary. This maintains the requirement that the subgraph of backbones must be the same as the most general end node.
-*3 subtree was overspecified for many groups. I have removed many of these groups and reduced the rest. This applies to all groups below CdsJ in that subtree.
-Changed names in rules accordingly
-To accommodate rule number 3, I have created a new group which further specifies atomtype along the backbone, as is the only reasonable interpreation of the author's intent.