indigo-deco1

Usage

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

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.