<!-- manual page source format generated by PolyglotMan v3.2, --> <!-- available at http://polyglotman.sourceforge.net/ --> <html> <head> <title>obfit</title> </head> <body bgcolor='white'> <a href='#toc'>Table of Contents</a><p> <h2><a name='sect0' href='#toc0'>Name</a></h2> <p> <b>obfit</b> -- superimpose two molecules based on a pattern <p> <h2><a name='sect1' href='#toc1'><b>Synopsis</b></a></h2> <p> <b>obfit</b> <i>SMARTS-pattern</i> <i>fixed-file</i> <i>outfile</i> <p> <h2><a name='sect2' href='#toc2'><b>Description</b></a></h2> <p> 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. <p><p> 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. <p> <h2><a name='sect3' href='#toc3'><b>Examples</b></a></h2> <p> 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): <pre> obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf </pre> <p> <h2><a name='sect4' href='#toc4'><b>See</b> <b>Also</b></a></h2> <p> <a href='babel.html'>babel(1)</a> , <a href='obchiral.html'>obchiral(1)</a> , <a href='obfit.html'>obfit(1)</a> , <a href='obgrep.html'>obgrep(1)</a> , <a href='obrotate.html'>obrotate(1)</a> . <p><p> The web pages for Open Babel can be found at: <<b><a href="http://openbabel.org/">http://openbabel.org/</a></b>> <p><p> A guide for constructing SMARTS patterns can be found at: <<b><a href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html</a></b>> <p> <h2><a name='sect5' href='#toc5'><b>Authors</b></a></h2> <p> The obfit program was contributed by Fabien Fontaine <p><p> 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 <<b><a href="http://openbabel.org/wiki/THANKS">http://openbabel.org/wiki/THANKS</a></b>> <p> <h2><a name='sect6' href='#toc6'><b>Copyright</b></a></h2> <p> Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.<br> Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other contributors. <p><p> 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. <p><p> 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. <p> <hr><p> <a name='toc'><b>Table of Contents</b></a><p> <ul> <li><a name='toc0' href='#sect0'>Name</a></li> <li><a name='toc1' href='#sect1'>Synopsis</a></li> <li><a name='toc2' href='#sect2'>Description</a></li> <li><a name='toc3' href='#sect3'>Examples</a></li> <li><a name='toc4' href='#sect4'>See Also</a></li> <li><a name='toc5' href='#sect5'>Authors</a></li> <li><a name='toc6' href='#sect6'>Copyright</a></li> </ul> </body> </html>
