From Open Babel
Jump to: navigation, search


obgen -- generate 3D coordinates for a molecule


obgen filename


The obgen tool will generate 3D coordinates for molecules in a file (e.g. multi-molecule SMILES files). The resulting structure will be optimized using the given forcefield and checked for the lowest-energy conformer using a Monte Carlo search.

Output will be sent to standard output in the SDF file format.

NOTE: Currently, obgen does not ensure that the new 3D coordinates will retain proper stereochemistry from the input.


If no filename is given, obenergy will give all options including the available forcefields.

-ff forcefield
Select the forcefield


View the possible options, including available forcefields:


Generate 3D coordinates for the molecule(s) in file test.smi:

  obgen test.smi

Generate 3D coordinates for the molecule(s) in file test.smi using the UFF forcefield:

  obgen -ff UFF test.smi

See Also

babel, obenergy, obminimize, obconformer.

The web pages for Open Babel can be found at: <http://openbabel.org/>


The obgen program was contributed by Tim Vandermeersch.

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 (C) 2007-2008 by Tim Vandermeersch. Some portions Copyright (C) 2001-2008 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.