OBGEN(1) General Commands Manual (urm) OBGEN(1)

obgen — generate 3D coordinates for a molecule

obgen [OPTIONS] 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.

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

forcefield
Select the forcefield

Seed for pseudo random number generator; random seed is used if unset or null. This feature is effective if Open Babel is built with -DOB_USE_OBRANDOMMT cpreprocessor flag (will be automatically enabled when version 4 is released).

View the possible options, including available forcefields:

obgen

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

obabel(1), obconformer(1), obminimize(1).

The web pages for Open Babel can be found at: https://openbabel.org/

The web pages for Open Babel Molecular Mechanics can be found at: https://openbabel.org/docs/Forcefields/Overview.html

The obgen program was contributed by Tim Vandermeersch.

Open Babel is developed by a cast of many, including current maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see https://openbabel.org/docs/Introduction/thanks.html

Copyright (C) 2007-2008 by Tim Vandermeersch.

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.

May 26, 2026 Open Babel 3.2