OBGEN(1)

💖 obgen(1) — the girl's guide to generating 3D coords 💖

okay so bestie, welcome to obgen, from the User's Reference Manual (that's the manual name, slay). this is the tool that takes your molecules and gives them actual 3D coordinates, no cap. let's get into it 🎀

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✨ NAME ✨

obgen — generate 3D coordinates for a molecule. that's the whole vibe. literally her job 🦋

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🌸 SYNOPSIS 🌸

obgen [OPTIONS] filename

like, options first, filename last. classic. 💅

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💜 DESCRIPTION 💜

so the obgen tool will generate 3D coordinates for molecules in a file (think multi-molecule SMILES files, iykyk). the resulting structure gets optimized using the given forcefield, and then it's checked for the lowest-energy conformer using a Monte Carlo search — very main character energy, she's out here doing a whole search for the best conformer 🔥

output goes to standard output in the SDF file format. periodt. ✨

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🎀 OPTIONS 🎀

okay important thing first, bestie: if no filename is given, obgen will give all options including the available forcefields. so running her bare is basically asking for the menu 🍓

• -ff forcefield — selects the forcefield. that's it, that's the option. she's simple like that 💅

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🦋 ENVIRONMENT 🦋

• OB_RANDOM_SEED — the seed for the pseudo random number generator; the random seed is used if it's unset or null. 🎲

listen, this one has a whole lore drop attached: this feature is effective if Open Babel is built with the -DOB_USE_OBRANDOMMT cpreprocessor flag — which will be automatically enabled when version 4 is released. so yeah, future energy 🙈✨

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🌈 EXAMPLES 🌈

view the possible options, including available forcefields — just her, no arguments:

obgen

generate 3D coordinates for the molecule(s) in file test.smi:

obgen test.smi

generate 3D coordinates for the molecule(s) in file test.smi using the UFF forcefield:

obgen -ff UFF test.smi

look at those. flawless. 👑

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💀 SEE ALSO 💀

• obabel(1)
• obconformer(1)
• obminimize(1)

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

the web pages for Open Babel Molecular Mechanics can be found at: <https://openbabel.org/docs/Forcefields/Overview.html>

go read them, bestie, they're giving lore 🧚

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🫶 AUTHORS 🫶

the obgen program was contributed by Tim Vandermeersch. 💖

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> — truly a whole ensemble cast 🌟

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⭐ COPYRIGHT ⭐

Copyright (C) 2007-2008 by Tim Vandermeersch.

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.

that's the legal bit and it is not a vibe you ignore, bestie — no warranty, fr fr 💀

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<rainbow>and that's the whole page! ✨ this was **Open Babel 3.2**, dated **May 26, 2026** — mwah, bye bestie 💋🦋💖</rainbow>