Provided by: indigo-utils_1.1.12-2_amd64 bug


       indigo-deco - molecule scaffold detection and R-group deconvolution


       indigo-deco files [parameters]

       indigo-deco -h


       indigo-deco  perfoms  molecule  scaffold  detection  and  R-group  deconvolution. Accepted
       formats are: Molfile, SDFile, RDFile, SMILES and CML.


       indigo-deco accepts the following parameters.

       -h     Print help message

       -a     Calculate approximate scaffold (default is exact)

       -s <file>
              Write maximum found scaffold to molfile

       -S <file>
              Write all found scaffolds to SD-file

       -l <file>
              Do not calculate scaffold, but load it from file

       -sr <file>
              Write scaffold with R-sites to a file

       -o <file>
              Write resulting highlighted molecules to file

       -r <file>
              Write resulting molecules with separated r-groups to file

       -na    No aromatic consideration

       --     Marks the 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 and 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 and 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 and save highlighted molecules to hl.sdf.


       This  manual  page  was  written  by  Daniel Leidert <>, for the Debian
       GNU/Linux system (but may be used by others).