NAME

obgen — generate 3D coordinates for a molecule

SYNOPSIS

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 using 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 available 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:

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

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

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 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.