obfit - Man Page

superimpose two molecules based on a pattern


obfitSMARTS-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(1), obchiral(1), obfit(1), obgrep(1), obrotate(1).

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 <http://openbabel.org/wiki/THANKS>

Referenced By

babel(1), obchiral(1), obconformer(1), obgrep(1), obprop(1), obrotamer(1), obrotate(1).

July 4, 2008