obfit(1) User's Reference Manual obfit(1)NAMEobfit — superimpose two molecules based on a pattern
SYNOPSISobfit 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 out‐
put 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 ALSObabel(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 MERCHANTABIL‐
ITY 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
