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obfit(1)            DragonFly General Commands Manual (urm)           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
     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.

Open Babel 2.2                   July 4, 2008                   Open Babel 2.2

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