indigo-depict1

Molecule and reaction rendering utility

Usage

indigo-depict -help

Overview

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

Releases

Unchanged in 6 releases since Debian 8 (Jessie).

8–13