---
name: "indigo-deco"
section: "1"
platform: "linux"
package: "indigo-utils"
version: "1.2.3-3.1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/indigo-deco"
---

# indigo-deco(1)

molecule scaffold detection and R-group deconvolution

## 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.

## AUTHOR

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