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

       obabel(1), obchiral(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 3.1                                    Oct 10, 2019                                          obfit(1)