obgen1

Usage

Overview

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:

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