INDIGO-DEPICT(1)

💅 INDIGO-DEPICT(1) — the manual page, but make it cute

okay so bestie, welcome to indigo-depict, a molecule and reaction rendering utility from the indigo crew. this page lives in section 1 of the User Manual and it is literally your glow-up guide for turning chemistry files into pictures. let's get into it 🎀

✨ 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

like… look at those braces. it's giving flexible. 💅

🌸 DESCRIPTION 🌸

indigo-depict is used for depicting molecules. that's it, that's the job, and it ate. ✨

👑 OPTIONS 👑

okay so indigo-depict can read input files or SMILES code from the standard input. after that you can tack on one or more of the following parameters. and yes, we're listing every single one, no skips, no cap. 🫶

• -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, so it's giving full bleed.
• -thickness <number> — sets the relative thickness factor. default is 1.0.
• -linewidth <number> — sets the bond line width factor. default is 1.0.
• -label <none|hetero|terminal-hetero|all> — sets the atom label display mode. default is terminal-hetero.
• -hydro <on|off> — show implicit hydrogens. default is on.
• -[de]arom — force [de]aromatization. yes that's one option with a little choose-your-own-adventure in the middle, iconic.
• -stereo <old|ext|none> — stereogroups display mode. default is old.
• -cdbwsa — center double bonds which have an adjacent stereo bond. disabled by default, so it's a whole opt-in moment.
• -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> — the SDF/RDF field that gets put in place of '%s' in the names of saved files. default is the molecule/reaction number.
• -catalysts <above|above-and-below> — reaction catalysts placement w.r.t. the arrow. default is above-and-below.
• -comment <string> — a 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 the specified SDF/RDF field as a comment.
• -commentname — use the 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. bold AND thick, the drama of it all.
• -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 bestie, don't ship it like that.
• -bondnumbers — show bond numbers. also for debugging purposes only.
• -onebased — start atom and bond indices from one. default is from zero.
• -help — print this help message.

🧚 EXAMPLES 🧚

here's the tea, real invocations, verbatim, go copy them:

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

note the - in the last two — that's how you tell it "the input is coming from stdin, bestie". and %s in the second one is doing the placeholder thing, iykyk. 💜

💖 AUTHOR 💖

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

and that's the whole page! this was indigo version vibes, dated 29/12/2013 — yeah, a lil vintage, but she still slays. 🌈 stay rendering, bestie 💅✨