obgen (1) Linux Manual Page

obgen – generate 3D coordinates for a molecule

Synopsis

[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 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

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

babel(1), obminimize(1), obconformer(1).

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

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

Authors

The obgen program was contributed by An Tim Vandermeersch.

An -nosplit Open Babel is developed by a cast of many, including currrent maintainers An Geoff Hutchison , An Chris Morley , An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>

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.