OBFIT(1)

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

✨ OBFIT 💅 (section 1 of the User's Reference Manual, bestie)

okay so real talk: obfit is the little Open Babel icon that superimposes two molecules based on a pattern. That's the whole vibe. She's a one-trick pony and she ATE. 🫶

🌸 SYNOPSIS 🌸

obfit SMARTS-pattern fixed-file outfile

Three args, no options, no notes. She's low maintenance like that. 💅

🦋 DESCRIPTION 🦋

So here's the tea ☕ — obfit superimposes two molecules using a quaternion fit. Iconic. The atoms it uses to line the two molecules up are defined by the SMARTS-pattern you hand it, so you pick the scaffold, she does the math.

What is this even for, you ask? Bestie, it's literally made for aligning congeneric series of molecules on a common structural scaffold for 3D-QSAR studies. Also highkey useful for displaying the results of conformational generation. iykyk. ✨

Any molecules that match the SMARTS-pattern you supplied get rotated and translated to give you the smallest possible RMSD between those matching regions. The way she minimizes that RMSD... obsessed. 🎀

And if a molecule doesn't match the SMARTS-pattern? No drama, no transformation — it just gets output as-is, untouched, unbothered, main character energy. 🦋

💖 EXAMPLES 💖

Say you want to align all the molecules in 'testmv.sdf' onto a single molecule of 'testref.sdf' by superimposing them on its N-methylpiperidyl portion — and output a brand new SD file to standard output. Slay, here's the line:

obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf

That SMARTS pattern? That's the N-methylpiperidyl bit. She's serving. 🔥

👑 SEE ALSO 👑

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

A guide for constructing SMARTS patterns can be found at: <https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>

(go read the SMARTS guide ngl, it's giving essential lore 📚)

🌈 AUTHORS 🌈

The obfit program was contributed by Fabien Fontaine — ty king 👑.

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>

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.

no cap on that warranty disclaimer — she comes with absolutely zero warranty, so read it fr fr 🙈

and that's the whole page, bestie 🧚 — obfit, from Open Babel 3.2, dated May 26, 2026, section 1 of the User's Reference Manual. periodt. 💜

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