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 <parameter> : Get detailed help on a parameter omega2 --help html : Create an html help file for this program
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
This section has a series of example OMEGA command-line executions. Each example is followed by a brief description of its behavior. Sample data files can be found in the data directory.
prompt> omega2 drugs.smi drugs.oeb.gz prompt> omega2 -in drugs.smi -out drugs.oeb.gz
These two commands will yield identical results. These execute OMEGA with the default parameters. The file drugs.smi is opened in SMILES format for input, and the output is written to the file drugs.oeb.gz in gzipped OEBinary format.
prompt> omega2 -in drugs.smi -out drugs.oeb.gz -maxconfs 1
The parameter -maxconfs can be used to specify the maximum number of conformers for each output molecule. This command will generate a single low energy conformer for every molecule in drugs.smi.
prompt> omega2 -in drugs.smi -out drugs.oeb.gz -param myparameters
This command is the same as the Basic Commands above except for the -param flag. It executes OMEGA with the parameters found in the myparameters file. The file drugs.smi is opened in SMILES format for input, and the output is written to the file drugs.oeb.gz in gzipped OEBinary format.
prompt> omega2 -param myparameters drugs.smi drugs.oeb.gz prompt> omega2 drugs.smi drugs.oeb.gz -param myparameters
The first of these two commands will yield exactly the same results as the example above. drugs.smi will be mapped to the -in flag and drugs.oeb.gz will be mapped to the -out flag begin the second to last and last command-line arguments respectively. Unfortunately, the second of these two commands, will fail to parse because the implicit input and output arguments are not the final two arguments in the list.
prompt> omega2 -in drugs.smi -out drugs_maxconfs600.oeb.gz -param myparameters -maxconfs 600
Again, this is a very similar command. It executes OMEGA using the parameters in the myparameters file, except the -maxconfs parameter is over-ridden with the 600 from the command line. The command-line -maxconfs parameter would take precedence over the value in the parameter file independent of the order of flags on the command line.
prompt> DBQuery "barbiturate" | omega2 -in .sdf -out .oeb.gz | vida2 .oeb.gz
This execution assumes that a process called “DBQuery” can be called with the parameter “barbiturate” and return a stream of molecules in MDL’s .sdf format. This output is piped into OMEGA, which interprets the format correctly and generates multiconformer molecules using the default parameters. OMEGA writes the output to std::cout in gzipped OEBinary format, which is read by OpenEye’s VIDA molecular viewer.
prompt> omega2 -in drugs.mol2 -out drugs.oeb.gz -fromCT true
The -fromCT true flag will cause OMEGA to ignore the input conformations in the drugs.mol2 file. An initial conformation will be generated by a distance-bounds algorithm from the connection-table of the molecules in the input file. Be aware that the default value of -fromCT is true, however it is listed explicitly here for emphasis.
prompt> omega2 -in drugs.smi -out drugs.oeb.gz -log null
The -log flag normally allows specification of the log file’s name. However, nul and null are reserved names which indicate that no log file will be written (this includes failure modes).
OMEGA provides the facility for users to select one of a number of pre-defined force fields. The force field selected may be different for model construction and torsion search. The ability to select a force field provides a mechanism for task specificity. Some force fields may be more appropriate for solution phase ensemble generation, whilst others may excel for bioactive conformer reproduction. The following pre-defined force fields may be used as arguments to the -buildff and -searchff flags.
A file of alternate torsion rules may be specified with the -settorlib command. OMEGA will match only the first rule found for a torsion angle, and discontinue matching alternate possible rules. Thus, a correctly ordered torsion file will be arranged with the most specific patterns appearing at the top of the file, and more general patterns appearing toward the end. Simple torsion rules are composed of a single SMARTS pattern containing at least four atom expressions, followed by a listing of the torsion angles that OMEGA will sample. Each reference atom in the SMARTS pattern that is used to define the torsion angle being sampled must have a map index (numbered 1 through 4) specified that indicates the ordering of the atoms in the torsion angle. The pattern must appear all on a single line, with a carriage return separating one rule from the next. Comments in the file must be preceded with a # character. The following is an example of a simple torsion rule.
#methyl ester pattern [O:1]=[C:2]-[O:3][CH3:4] 0
More advanced rules may be included that alter the energy calculation for particular torsion angles. In these types of torsion rules, a SMARTS pattern with associated map indices is still used to define the molecular environment in which the rule is to be applied, but the sampled values appear on subsequent lines with one torsion angle per line. The first number per line indicates the torsion angle, in degrees, that OMEGA must sample. If a second number follows a torsion angle on the same line, the value is added to the total energy computed for that conformer. The following is an example of an advanced torsion rule.
#experimental structure test O=[C:1][NX3H:2][c:3]([cH,nH0])[nH:4] 0 180 10.0 <end>