From Open Babel
Revision as of 08:09, 3 July 2008 by Ghutchis (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


obfit -- superimpose two molecules based on a SMARTS pattern


obfit SMARTS-pattern fixed-file outfile


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.


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

babel, obchiral, obgrep, obrotate.

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

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


The obfit program was contributed by Fabien Fontaine.

Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see the Contributor list.


Copyright © 1998-2001 by OpenEye Scientific Software, Inc. Some portions Copyright © 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, version 2, as published by the Free Software Foundation.

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.