obrotate(1) | General Commands Manual (urm) | obrotate(1) |
NAME¶
obrotate
—
batch-rotate dihedral angles matching SMARTS
patterns
SYNOPSIS¶
obrotate |
'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle |
DESCRIPTION¶
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). 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. 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.EXAMPLES¶
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. To set the value of the first dihedral angle to 90 degrees:obrotate 'c1ccncc1CCC' pyridines.sdf
5 6 7 8 90
obrotate 'c1ccncc1CCC' pyridines.sdf
4 6 7 8 90
obrotate 'c1ccncc1CCC' pyridines.sdf
5 6 7 8 90
obrotate 'c1ccncc1CCC' pyridines.sdf
8 7 6 5 90
SEE ALSO¶
babel(1), obchiral(1), obfit(1), obgrep(1), obprop(1), obrotate(1). The web pages for Open Babel can be found at: < http://openbabel.org/> A guide for constructing SMARTS patterns can be found at: < http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>AUTHORS¶
The obgrep program was contributed by Fabien Fontaine 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 < http://openbabel.org/wiki/THANKS>COPYRIGHT¶
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.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.
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.
July 4, 2008 | Open Babel 2.2 |