<!-- manual page source format generated by PolyglotMan v3.2, --> <!-- available at http://polyglotman.sourceforge.net/ --> <html> <head> <title>obgrep</title> </head> <body bgcolor='white'> <a href='#toc'>Table of Contents</a><p> <h2><a name='sect0' href='#toc0'>Name</a></h2> <p> <b>obgrep</b> -- an advanced molecular search program using SMARTS <p> <h2><a name='sect1' href='#toc1'><b>Synopsis</b></a></h2> <p> <b>obgrep</b> [<i>OPTIONS</i>] <i>‘SMARTS-pattern’</i> <i>filename</i> <p> <h2><a name='sect2' href='#toc2'><b>Description</b></a></h2> <p> The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files. <p> <h2><a name='sect3' href='#toc3'><b>Options</b></a></h2> <p> If only a filename is given, obgrep will attempt to guess the file type from the filename extension. <p> <dl> <dt><b>-c</b> </dt></dt> <dd> Print the number of matches <p></dd> <dt><b>-f</b> </dt></dt> <dd> Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern <p></dd> <dt><b>-i</b> <i>format</i></dt></dt> <dd> Specifies input and output format, see <a href='babel.html'>babel(1)</a> for available formats <p></dd> <dt><b>-n</b> </dt></dt> <dd> Only print the name of the molecules <p></dd> <dt><b>-t</b> <i>#</i> </dt></dt> <dd>Print a molecule only if the pattern occurs # times inside the molecule <p></dd> <dt><b>-v</b> </dt></dt> <dd> Invert the matching, print non-matching molecules <p></dd> </dl> <h2><a name='sect4' href='#toc4'><b>Examples</b></a></h2> <p> Note that in all examples, the SMARTS pattern is enclosed in single quotes '...' to ensure it is not changed by the shell. <p><p> Print all the molecules with a methylamine group:<br> <pre>obgrep 'CN' database.smi</pre> <p><p> Print all the molecules without a methylamine group:<br> <pre>obgrep -v 'CN' database.smi</pre> <p><p> Print the number of molecules without a methylamine group:<br> <pre>obgrep -v -c 'CN' database.smi</pre> <p><p> Print methylamine (if it exists in the file):<br> <pre>obgrep -f 'CN' database.smi</pre> <p><p> Print methylamine and/or methanol (if they exist):<br> <pre>obgrep -f 'C[N,O]' database.smi</pre> <p><p> Print all molecules with aromatic carbon in all SMILES files in the directory (i.e., *.smi):<br> <pre>obgrep 'c' *.smi</pre> <p> <h2><a name='sect5' href='#toc5'><b>See</b> <b>Also</b></a></h2> <p> <a href='babel.html'>babel(1)</a> , <a href='obfit.html'>obfit(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='sect6' href='#toc6'><b>Authors</b></a></h2> <p> The obgrep 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='sect7' href='#toc7'><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'>Options</a></li> <li><a name='toc4' href='#sect4'>Examples</a></li> <li><a name='toc5' href='#sect5'>See Also</a></li> <li><a name='toc6' href='#sect6'>Authors</a></li> <li><a name='toc7' href='#sect7'>Copyright</a></li> </ul> </body> </html>
