---
name: "obfit"
section: "1"
platform: "linux"
package: "openbabel"
version: "3.2.1-1"
release: "Arch Linux 2026-11-01"
platforms: ["linux"]
url: "https://new.carta.tech/obfit"
---

# obfit(1)

superimpose two molecules based on a pattern

## NAME

**obfit** – superimpose two molecules based on a pattern

## SYNOPSIS

**obfit** *SMARTS-pattern* *fixed-file* *outfile*

## DESCRIPTION

Superimpose two molecules using a quaternion fit. The atoms used to fit the two molecules are defined by the *SMARTS-pattern* given by the user. It is useful to align congeneric series of molecules on a common structural scaffold for 3D-QSAR studies. It can also be useful for displaying the results of conformational generation.

Any molecules matching the supplied *SMARTS-pattern* will be rotated and translated to provide the smallest possible RMSD between the matching regions. If a molecule does not match the *SMARTS-pattern*, it will be output with no transformation.

## EXAMPLES

Align all the molecules in 'testmv.sdf' on a single molecule of 'testref.sdf' by superimposing them on its N-methylpiperidyl portion (and outputting a new SD file to the standard output):

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

## SEE ALSO

[obabel(1)](/obabel/1.md), [obchiral(1)](/obchiral/1.md), [obgrep(1)](/obgrep/1.md), [obrotate(1)](/obrotate/1.md).

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**\>

## AUTHORS

The obfit program was contributed by Fabien Fontaine

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

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.