trimBuiltSmiles() deduplicates a set of SMILES by comparing their molecular formulae via the helper function MolFormFromSmiles.rcdk.

However, some structural isomers get 'trimmed' in this way...and they shouldn't be.

Minimal example:

las_gensmiles <- "OS(=O)(=O)c1ccc(cc1)C([R1])[R2]"
r1ton <- "{C,C}"
nr1ton <- "{9-13}"
split <- splitRrange(las_gensmiles,nR1toN = nr1ton)  #"(5-7,4-6)"
las_series <- buildSmiles(las_gensmiles,R1toN = r1ton, nR1toN = split)

gives

las_series
[1] "OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCC"     "OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCCC"   
[3] "OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCCCC"   "OS(=O)(=O)c1ccc(cc1)C(CCCCCC)CCCC"   
[5] "OS(=O)(=O)c1ccc(cc1)C(CCCCCC)CCCCC"   "OS(=O)(=O)c1ccc(cc1)C(CCCCCC)CCCCCC" 
[7] "OS(=O)(=O)c1ccc(cc1)C(CCCCCCC)CCCC"   "OS(=O)(=O)c1ccc(cc1)C(CCCCCCC)CCCCC" 
[9] "OS(=O)(=O)c1ccc(cc1)C(CCCCCCC)CCCCCC"

corresponding to

sapply(las_series,MolFormFromSmiles.rcdk)
    OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCC    OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCCC 
                         "C16H26O3S"                          "C17H28O3S" 
  OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCCCC    OS(=O)(=O)c1ccc(cc1)C(CCCCCC)CCCC 
                         "C18H30O3S"                          "C17H28O3S" 
  OS(=O)(=O)c1ccc(cc1)C(CCCCCC)CCCCC  OS(=O)(=O)c1ccc(cc1)C(CCCCCC)CCCCCC 
                         "C18H30O3S"                          "C19H32O3S" 
  OS(=O)(=O)c1ccc(cc1)C(CCCCCCC)CCCC  OS(=O)(=O)c1ccc(cc1)C(CCCCCCC)CCCCC 
                         "C18H30O3S"                          "C19H32O3S" 
OS(=O)(=O)c1ccc(cc1)C(CCCCCCC)CCCCCC 
                         "C20H34O3S" 

trimBuiltSmiles(las_series)
[1] "OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCC"     "OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCCC"   
[3] "OS(=O)(=O)c1ccc(cc1)C(CCCCC)CCCCCC"   "OS(=O)(=O)c1ccc(cc1)C(CCCCCC)CCCCCC" 
[5] "OS(=O)(=O)c1ccc(cc1)C(CCCCCCC)CCCCCC"

where SMILES with R1,R2 as 6,5; 6,4; 7,4; and 7,5 are trimmed off. The latter 3 should not be trimmed as they are structurally different from 5,5; 5,6; and 6,6 resp. although having the same MF.

Ideally, should eliminate potential duplicates at earlier stage even before they are generated, somewhere within buildSmiles or splitRrange (?)

Alternatively, could deduplicate by comparing canonical smiles instead of comparing MFs. Probably faster than doing isomorphism check.