indigo-deco files [options]
Performs molecule scaffold detection and R-group deconvolution
Accepted formats are: Molfile, SDFile, RDFile, SMILES
-h         print this help message
-a         calculate approximate scaffold (default is exact)
-s   write maximum found scaffold to molfile
-S   write all found scaffolds to SD-file
-d   do not calculate scaffold, but load it from file
-o   write resulting highlighted molecules to file
-r   write resulting molecules with separated r-groups to file
-na        no aromatic consideration
--         marks end of options


indigo-deco *.mol -o hl.sdf -s scaf.sdf
  read molecules from molfiles in the current directory
  save maximum found scaffold to scaf.mol
  save highlighted molecules to hl.sdf
indigo-deco structure.mol many.sdf -s scaf.mol -S allscafs.sdf -r rg.sdf
  read one molecule from structure.mol and multiple molecules from many.sdf
  save molecules with r-rgoups to rg.sdf
  save all found scaffolds to allscafs.sdf
indigo-deco *.smi -d readyscaf.mol -o hl.sdf
  read multiple molecules from every SMILES file in the current directory
  read scaffold from readyscaf.mol
  save highlighted molecules to hl.sdf