indigo-deco(1) 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.
Print help message
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
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 <[email protected]>, for the Debian GNU/Linux system (but may be used by others).