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OBGEN(1) User's Reference Manual OBGEN(1) NAME obgen -- generate 3D coordinates for a molecule SYNOPSIS obgen [OPTIONS] filename DESCRIPTION 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 us- ing a Monte Carlo search. Output will be sent to standard output in the SDF file format. OPTIONS If no filename is given, obgen will give all options including the avail- able forcefields. -ff forcefield Select the forcefield ENVIRONMENT OB_RANDOM_SEED 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). EXAMPLES 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 SEE ALSO 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> AUTHORS 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 Copyright (C) 2007-2008 by Tim Vandermeersch. This program is free software; you can redistribute it and/or modify it un- der 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 FIT- NESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 3.2 May 26, 2026 OBGEN(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | ENVIRONMENT | EXAMPLES | SEE ALSO | AUTHORS | COPYRIGHT
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