OBRMS(1)

💅 OBRMS(1) 💅

okay bestie so this is a page from the User's Reference Manual — yeah, the official one — and it's about obrms, which is genuinely one of the most useful little tools in the Open Babel lineup. it does one thing and it does it iconically. let's get into it 🫶

✨ NAME ✨

obrms — calculates the heavy-atom RMSD between two chemically identical structures. that's it. that's the whole personality. ngl it's giving "one job, done slayfully" 💅

🌸 SYNOPSIS 🌸

obrms [-fmxso] filename1 filename2

🦋 DESCRIPTION 🦋

so basically obrms computes the heavy-atom RMSD of identical compound structures. RMSD = how far apart the atoms sit after you've lined the two molecules up, and "heavy-atom" means we're not counting hydrogens here — main character atoms only, periodt.

if your files have multiple structures in them, the structures get compared one-by-one: structure 1 vs structure 1, structure 2 vs structure 2, and so on down the line. adorable, orderly, no chaos. BUT — if you pass --firstonly, it switches it up: only the first structure in the reference file gets used, and everything in the test file gets compared against that one. 💖

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🎀 OPTIONS 🎀

• -f, --firstonly — use only the first structure in the reference file. without this, the n-th molecule in the reference file gets compared to the n-th molecule in the test file (matched pairs, so cute). with it, it's first-vs-everyone. 👑
• -m, --minimize — compute the minimum RMSD achievable by applying a rigid-body transformation to the test molecule. lowkey the flexiest option here: it finds the best possible alignment, no cap. ✨
• -x, --cross — compute all n^2 RMSDs between the molecules of the reference file. heads up though: the test file is ignored entirely when you do this. like, fully ignored. don't come for her. 💀
• -s, --separate — separate the reference file into its constituent molecules (i.e. the disconnected fragments) and report the best RMSD. 🧚
• -t t, --timeout t — give up on matching after the specified number of seconds. sometimes you just gotta know when to walk away, bestie. 🙈
• -o file, --out file — re-oriented test structure output. this one's used with -m, so don't be out here using it alone. 🍓

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🌈 EXAMPLES 🌈

obrms ref.sdf test.sdf

calculates the RMSD between ref.sdf and test.sdf. both files should have the same number of molecules — that's the vibe check, and if you fail it, that's on you bestie. 🫶

obrms -f ref.sdf test.sdf

calculates the RMSD between the first molecule in ref.sdf and each molecule in test.sdf. one reference, all the contenders. main character energy fr fr. 🔥

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👀 SEE ALSO 👀

obfit(1) — her sibling, go say hi.

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

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💜 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> — genuinely a whole ensemble cast, we love to see it 🌸

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📜 COPYRIGHT 📜

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. 🎀

yeah the all-caps warranty bit is real and it means what it says — no promises, no takebacks, read the GPL for the full tea. 💀

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and that's the whole page, bestie! this one's from Open Babel 3.2, dated May 26, 2026 — so go forth, compute those RMSDs, and remember: chemically identical structures only, that's the rule 💖✨🎀