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

       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

SEE ALSO

       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>

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 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU  General  Public
       License for more details.

Open Babel 3.1                                    Oct 10, 2019                                       obrotate(1)