<!-- manual page source format generated by PolyglotMan v3.2, --> <!-- available at http://polyglotman.sourceforge.net/ --> <html> <head> <title>obrotate</title> </head> <body bgcolor='white'> <a href='#toc'>Table of Contents</a><p> <h2><a name='sect0' href='#toc0'>Name</a></h2> <p> <b>obrotate</b> -- batch-rotate dihedral angles matching SMARTS patterns <p> <h2><a name='sect1' href='#toc1'><b>Synopsis</b></a></h2> <p> <b>obrotate</b> <i>‘SMARTS-pattern’</i> <i>filename</i> <i>atom1</i> <i>atom2</i> <i>atom3</i> <i>atom4</i> <i>angle</i> <p> <h2><a name='sect2' href='#toc2'><b>Description</b></a></h2> <p> The obrotate program rotates the torsional (dihedral) angle of a specified bond in molecules to that defined by the user. In other words, it does the same as a user setting an angle in a molecular modelling package, but much faster and in batch mode (i.e. across multiple molecules in a file). <p><p> The four atom IDs required are indexes into the SMARTS pattern, which starts at atom 0 (zero). The angle supplied is in degrees. The two atoms used to set the dihedral angle <atom1> and <atom4> do not need to be connected to the atoms of the bond <atom2> and <atom3> in any way. <p><p> The order of the atoms matters -- the portion of the molecule attached to <atom1> and <atom2> remain fixed, but the portion bonded to <atom3> and & <atom4> moves. <p> <h2><a name='sect3' href='#toc3'><b>Examples</b></a></h2> <p> Let’s say that you want to define the conformation of a large number of molecules with a pyridyl scaffold and substituted with an aliphatic chain at the 3-position, for example for docking or 3D-QSAR purposes. <p><p> To set the value of the first dihedral angle to 90 degrees:<br> <pre>obrotate ‘c1ccncc1CCC’ pyridines.sdf 5 6 7 8 90</pre> <p><p> Here 6 and 7 define the bond to rotate in the SMARTS patter, i.e., c1-C and atoms 5 and 8 define the particular dihedral angle to rotate. <p><p> Since the atoms to define the dihedral do not need to be directly connected, the nitrogen in the pyridine can be used:<br> <pre>obrotate ‘c1ccncc1CCC’ pyridines.sdf 4 6 7 8 90</pre> <p><p> Keep the pyridyl ring fixed and moves the aliphatic chain:<br> <pre>obrotate ‘c1ccncc1CCC’ pyridines.sdf 5 6 7 8 90</pre> <p><p> Keep the aliphatic chain fixed and move the pyridyl ring:<br> <pre>obrotate ‘c1ccncc1CCC’ pyridines.sdf 8 7 6 5 90</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='obprop.html'>obprop(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 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='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>
