obrotate(1) User's Reference Manual obrotate(1)NAMEobrotate — batch-rotate dihedral angles matching SMARTS patterns
SYNOPSISobrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle
DESCRIPTION
The obrotate program rotates the torsional (dihedral) angle of a speci‐
fied 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 pack‐
age, 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 con‐
nected 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
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 con‐
nected, 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
SEE ALSObabel(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.
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 MERCHANTABIL‐
ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
License for more details.
Open Babel 2.2 July 4, 2008 Open Babel 2.2
