This is the command indigo-deco that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
indigo-deco - molecule scaffold detection and R-group deconvolution
SYNOPSIS
indigo-deco files [parameters]
indigo-deco -h
DESCRIPTION
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
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.
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