---
name: "indigo-depict"
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-depict"
---

# indigo-depict(1)

molecule and reaction rendering utility

## NAME

indigo-depict - molecule and reaction rendering utility

## SYNOPSIS

**indigo-depict** *infile.{mol,rxn,cml,smi}* *outfile.{png,svg,pdf}* \[**parameters**\]

**indigo-depict** *infile.{cml,rdf,rdf.gz,sdf,sdf.gz,smi}* *outfile\_%s.{png,svg,pdf}* \[**parameters**\]

**indigo-depict** *infile.smi* *outfile.{cml,mol,rdf,rxn,sdf}* \[**parameters**\]

**indigo-depict -** *SMILES* *outfile.{cml,mol,pdf,png,rxn,svg}* \[**parameters**\]

**indigo-depict -help**

## DESCRIPTION

**indigo-depict** is used for depicting molecules.

## OPTIONS

**indigo-depict** can read input files or SMILES code from the standard input. These can be followed by one or more of the following parameters.

- **-w** *\<number\>*

  Picture width in pixels

- **-h** *\<number\>*

  Picture height in pixels

- **-bond** *\<number\>*

  Average bond length in pixels

- **-margins** *\<number\>* *\<number\>*

  Horizontal and vertical margins, in pixels. No margins by default

- **-thickness** *\<number\>*

  Set relative thickness factor. Default is *1.0*

- **-linewidth** *\<number\>*

  Set bond line width factor. Default is *1.0*

- **-label** *\<none\|hetero\|terminal-hetero\|all\>*

  Set atom label display mode. Default is *terminal-hetero*

- **-hydro** *\<on\|off\>*

  Show implicit hydrogens. Default is *on*

- **-\[de\]arom**

  Force \[de\]aromatization

- **-stereo** *\<old\|ext\|none\>*

  Stereogroups display mode. Default is *old*

- **-cdbwsa**

  Center double bonds which have an adjacent stereo bond (disabled by default)

- **-query**

  Treat the input as a query molecule or reaction (disabled by default)

- **-smarts**

  Treat the input as a SMARTS query molecule or reaction (disabled by default)

- **-idfield** *\<string\>*

  SDF/RDF field to be put in place of '%s' in the names of saved files (default is molecule/reaction number)

- **-catalysts** *\<above\|above-and-below\>*

  Reaction catalysts placement w.r.t. the arrow. Default is *above-and-below*

- **-comment** *\<string\>*

  Text comment to be put above the molecule or reaction. No default value

- **-commentoffset** *\<number\>*

  Vertical space (in pixels) between the comment and the structure

- **-commentfield** *\<string\>*

  Use specified SDF/RDF field as a comment

- **-commentname**

  Use molecule/reaction name as a comment

- **-commentsize** *\<number\>*

  Text comment font size factor relative to bond thickness. Default is *6*

- **-commentpos** *\<top\|bottom\>*

  Text comment position (bottom by default)

- **-commentalign \<0..1\>**

  Text comment alignment, a float value: *0* = left, *0.5* = center, *1* = right

- **-coloring \<on\|off\>**

  Enable/disable coloring. Default is *on*

- **-hlthick**

  Enable highlighting with thick lines and bold characters

- **-hlcolor** *\<red\>* *\<green\>* *\<blue\>*

  Enable highlighting with color. Component values must be in range \[*0..255*\]

- **-bgcolor** *\<red\>* *\<green\>* *\<blue\>*

  Set the background color. Component values must be in range \[*0..255*\]

- **-basecolor** *\<red\>* *\<green\>* *\<blue\>*

  Set the default foreground color. Component values must be in range \[*0..255*\]

- **-aamcolor** *\<red\>* *\<green\>* *\<blue\>*

  Set the color of AAM indices. Component values must be in range \[*0..255*\]

- **-dsgcolor** *\<red\>* *\<green\>* *\<blue\>*

  Set the color of data SGroups. Component values must be in range \[*0..255*\]

- **-commentcolor** *\<red\>* *\<green\>* *\<blue\>*

  Set the color of the comment. Component values must be in range \[*0..255*\]

- **-atomnumbers**

  Show atom numbers (for debugging purposes only)

- **-bondnumbers**

  Show bond numbers (for debugging purposes only)

- **-onebased**

  Start atom and bond indices from one. Default is from zero

- **-help**

  Print this help message

## EXAMPLES

```
indigo-depict infile.mol outfile.png -coloring off -arom
indigo-depict database.sdf molecule_%s.png -idfield cdbregno -thickness 1.1
indigo-depict database.smi database.sdf
indigo-depict - CC.[O-][*-]([O-])=O query.png -query
indigo-depict - OCO>>CC(C)N reaction.rxn
```

## AUTHOR

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