OBDISTGEN(1)

📦
version 3.2.1 · 3 versions
, in arch rolling, opensuse-leap 16.0

🌸 NAME 🌸

okay so bestie, let me introduce you to obdistgen — she's the one who generates rough 3D coordinates for SMILES (or other 0D files). like, she takes your flat little list of atoms and gives it a whole third dimension. main character energy fr 💅

✨ SYNOPSIS ✨

obdistgen filename

one job. one argument. it's giving minimalism and honestly? iconic. 🎀

🦋 DESCRIPTION 🦋

she generates SDFs with distance geometry. that's the whole vibe. distance geometry is the little math party trick that turns your 0D/2D situation into rough 3D coords, and she serves it up as SDF. no cap, she's not here to overexplain — she just does the thing and hands you the file. 🫶

💜 ENVIRONMENT 💜

  • OB_RANDOM_SEED — bestie this is the seed for the pseudo random generator. if it's unset or null, a random seed is used instead, so every run gets its own lil surprise. 🌈

ok but here's the fine print ⭐: this feature is only effective if Open Babel is built with the -DOB_USE_OBRANDOMMT cpreprocessor flag — and it will be automatically enabled when version 4 is released. so rn it's giving "coming soon to a build near you". iykyk. 💀

ngl, don't set OB_RANDOM_SEED expecting it to do something on a build without that flag. she's not listening yet. 🙈

🌟 EXAMPLES 🌟

obdistgen molecule.smi > molecule.sdf

Generate rough 3D coordinates for molecule.smi and write it to molecule.sdf. that's it, that's the whole recipe — pipe the output into your sdf file and you're slaying. ✨

🔥 SEE ALSO 🔥

  • obgen(1) — her sibling, go say hi 👋

the web pages for Open Babel can be found at: https://openbabel.org/ 🌐

👑 AUTHORS 👑

Open Babel is developed by a cast of many, including current maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. for more contributors to Open Babel, see https://openbabel.org/docs/Introduction/thanks.html 💖

like honestly? a whole ensemble cast. everyone ate. 🍓

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.

Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other contributors.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. see the GNU General Public License for more details. ⚠️

fr fr please read that warranty part — no promises, no guarantees, she's free software not a safety net 😭

🎀 and that's the page, bestie! this absolute gem is from Open Babel 3.2, dated May 26, 2026 — yes she's stamped and everything. periodt. 💅✨🦋

📦 where this page comes from