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obrotate(1)		    User's Reference Manual		   obrotate(1)

     obrotate -- batch-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 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.

     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

     babel(1), obchiral(1), obfit(1), obgrep(1), obprop(1), obrotate(1).

     The web pages for Open Babel can be found at: <>

     A guide for constructing SMARTS patterns can be found at:

     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 Ba-
     bel, see <>

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

      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 Li-
     cense for more details.

Open Babel 2.2			 July 4, 2008			Open Babel 2.2


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