indigo-deco1
Molecule scaffold detection and r-group deconvolution
Usage
indigo-deco files
[parameters]
indigo-deco -h
Overview
indigo-deco perfoms molecule scaffold detection and R-group deconvolution. Accepted formats are: Molfile, SDFile, RDFile, SMILES and CML.
Options
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
Examples
- 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
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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.