1obfit(1) User's Reference Manual obfit(1)
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4 obfit — superimpose two molecules based on a pattern
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7 obfit SMARTS-pattern fixed-file outfile
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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.
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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.
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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):
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26 obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf
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29 babel(1), obchiral(1), obfit(1), obgrep(1), obrotate(1).
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31 The web pages for Open Babel can be found at: <http://openbabel.org/>
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33 A guide for constructing SMARTS patterns can be found at:
34 <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>
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37 The obfit program was contributed by Fabien Fontaine
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39 Open Babel is developed by a cast of many, including currrent maintainers
40 Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who
41 have contributed fixes and additions. For more contributors to Open
42 Babel, see <http://openbabel.org/wiki/THANKS>
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45 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
46 Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other
47 contributors.
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49 This program is free software; you can redistribute it and/or modify it
50 under the terms of the GNU General Public License as published by the
51 Free Software Foundation version 2 of the License.
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53 This program is distributed in the hope that it will be useful, but
54 WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABIL‐
55 ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
56 License for more details.
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58Open Babel 2.2 July 4, 2008 Open Babel 2.2