obfit - Man Page

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

obabel(1), obchiral(1), obgrep(1), obrotate(1).

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>

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 (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.

obabel(1), obchiral(1), obconformer(1), obgrep(1), obprop(1), obrms(1), obrotamer(1), obrotate(1).