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


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

     babel(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
     MERCHANTABILITY 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

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