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.Dd November 25, 2005
.Os "Open Babel" 2.0
.Dt obrotate 1 URM
.Sh NAME
.Nm obrotate
.Nd "batch-rotate dihedral angles matching SMARTS patterns"
.Sh SYNOPSIS
.Nm
.Ar 'SMARTS-pattern'
.Ar filename
.Ar atom1
.Ar atom2
.Ar atom3
.Ar atom4
.Ar angle
.Sh 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).
.Pp
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. 
.Pp
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.
.Sh 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.
.Pp
To set the value of the first dihedral angle to 90 degrees:
.Dl "obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90"
.Pp
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.
.Pp
Since the atoms to define the dihedral do not need to be directly
connected, the nitrogen in the pyridine can be used:
.Dl "obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90"
.Pp
Keep the pyridyl ring fixed and moves the aliphatic chain:
.Dl "obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90"
.Pp
Keep the aliphatic chain fixed and move the pyridyl ring:
.Dl "obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90"
.Sh SEE ALSO
.Xr babel 1 ,
.Xr obchiral 1 ,
.Xr obfit 1 ,
.Xr obgrep 1 ,
.Xr obprop 1 .
.Pp
.Pp
The web pages for Open Babel can be found at:
<\fBhttp://openbabel.sourceforge.net/\fR>
.Pp
A guide for constructing SMARTS patterns can be found at:
<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR>
.Sh AUTHORS
The obgrep program was contributed by
.An Fabien Fontaine
.Pp
.An -nosplit
Open Babel is developed by a cast of many, including currrent maintainers
.An Geoff Hutchison ,
.An Chris Morley ,
.An Michael Banck , 
and innumerable others who have contributed fixes and additions. 
For more contributors to Open Babel, see 
<\fBhttp://openbabel.sourceforge.net/THANKS.shtml\fR>
.Sh COPYRIGHT
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison and
other contributors.
.Pp
 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.
.Pp
 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.