obgen man page

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.

-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(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>


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 < http://openbabel.org/wiki/THANKS>


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