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

     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>

AUTHORS

     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>

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.