> My question is, is there a code that I could use to generate these strings, 
> or at least a source that would help me understand the rationale for 
> generating the substituted cyclohexane with a SMILES string?


There’s lots of documentation (and examples) on SMILES, e.g. 
http://opensmiles.org/opensmiles.html

Moreover, you can take a SMILES string and insert it in Avogadro:
http://manual.avogadro.cc/content/2-building-molecules/7-building-with-smiles.html

Hope that helps,
-Geoff
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