obrotate(1) General Commands Manual (urm) obrotate(1)

obrotatebatch-rotate dihedral angles matching SMARTS patterns

obrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle

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.

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

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.

Since the atoms to define the dihedral do not need to be directly connected, the nitrogen in the pyridine can be used:

obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90

Keep the pyridyl ring fixed and moves the aliphatic chain:

obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90

Keep the aliphatic chain fixed and move the pyridyl ring:

obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90

obabel(1), obchiral(1), obfit(1), obgrep(1), obprop(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

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 (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison and other contributors.

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.

October 10, 2019 Open Babel 3.1