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OBFIT(1) User's Reference Manual OBFIT(1) 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 re- sults of conformational generation. Any molecules matching the supplied SMARTS-pattern will be rotated and translated to provide the smallest possible RMSD between the matching re- gions. 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), 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> 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 un- der 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 FIT- NESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 3.2 May 26, 2026 OBFIT(1)
NAME | SYNOPSIS | DESCRIPTION | EXAMPLES | SEE ALSO | AUTHORS | COPYRIGHT
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