Obrotate

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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 1. 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 pattern, 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, obchiral, obfit, obgrep, obprop.

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 obrotate 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 the Contributor list.

Copyright

Copyright © 1998-2001 by OpenEye Scientific Software, Inc. Some portions Copyright © 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, version 2, as published by the Free Software Foundation.

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.