OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.

4.1 Command Line Interface
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OMEGA APPLICATION USAGE
A description of the command line interface can be obtained by executing OMEGA with the --help option.
prompt> omega2 --help
will generate the following output:
Help functions:
omega2 --help simple : Get a list of simple parameters
omega2 --help all : Get a complete list of parameters
omega2 --help : Get detailed help on a parameter
omega2 --help html : Create an html help file for this program
4.1.1 Required Parameters
-in
File containing one or more molecular connection tables to be processed by OMEGA. Multiple input files of the
same format can be merged together into a single input file using the cat command. A pipe can be used to avoid
writing the merged input file to disk.
cat filename1.ism filename2.ism | omega2 -in .ism -out output.oeb.gz
-out
File to write conformers generated by OMEGA. Gzipped OEBinary is the recommended output format.
4.1.2 Optional Parameters
Execute Options
-param
The argument for this flag is the name of a file containing control parameters. The control parameter file acts
to either replace or augment the command line interface. All parameters necessary for program execution may
be provided in the control parameter file, although any command given explicitly on the command line will
supersede options found in the parameter file. The application generates a new parameter file containing the full
set of execution parameters upon every execution. The name of the parameter file is created by combining the
prefix base name with the ‘.parm’ extension.
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