1obfit(1)                    User's Reference Manual                   obfit(1)
2

NAME

4     obfit — superimpose two molecules based on a pattern
5

SYNOPSIS

7     obfit SMARTS-pattern fixed-file outfile
8

DESCRIPTION

10     Superimpose two molecules using a quaternion fit. The atoms used to fit
11     the two molecules are defined by the SMARTS pattern given by the user. It
12     is useful to align congeneric series of molecules on a common structural
13     scaffold for 3D-QSAR studies. It can also be useful for displaying the
14     results of conformational generation.
15
16     Any molecules matching the supplied SMARTS pattern will be rotated and
17     translated to provide the smallest possible RMSD between the matching
18     regions. If a molecule does not match the SMARTS pattern, it will be out‐
19     put with no transformation.
20

EXAMPLES

22     Align all the molecules in 'testmv.sdf' on a single molecule of
23     'testref.sdf' by superimposing them on its N-methylpiperidyl portion (and
24     outputting a new SD file to the standard output):
25
26           obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf
27

SEE ALSO

29     babel(1), obchiral(1), obfit(1), obgrep(1), obrotate(1).
30
31     The web pages for Open Babel can be found at: <http://openbabel.source‐
32     forge.net/>
33
34     A guide for constructing SMARTS patterns can be found at:
35     <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>
36

AUTHORS

38     The obfit program was contributed by Fabien Fontaine
39
40     Open Babel is developed by a cast of many, including currrent maintainers
41     Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who
42     have contributed fixes and additions.  For more contributors to Open
43     Babel, see <http://openbabel.sourceforge.net/wiki/THANKS>
44

46     Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
47     Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other
48     contributors.
49
50      This program is free software; you can redistribute it and/or modify it
51     under the terms of the GNU General Public License as published by the
52     Free Software Foundation version 2 of the License.
53
54      This program is distributed in the hope that it will be useful, but
55     WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABIL‐
56     ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
57     License for more details.
58
59Open Babel 2.1                   April 7, 2007                  Open Babel 2.1
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