# Example Commands¶

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.

## Basic Commands¶

prompt> oeomega classic drugs.smi drugs.oeb.gz
prompt> oeomega classic -in drugs.smi -out drugs.oeb.gz


These two commands will yield identical results. These execute OMEGA classic 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> oeomega macrocycle -in drugs.smi
prompt> oeomega macrocycle -in pdb_10_examples.oeb -prefix pdbexamples -mpi_np 8


The first command executes OMEGA macrocycle with the default parameters. By default, the conformers are written to the file oeomega_macrocycle_conformers.oeb.gz. The macrocycle mode execution will take a longer time than the classic mode and usually result in fewer conformers for the same input molecule. The second command executes OMEGA macrocycle using an input file with macrocyclic molecules. The conformers are written to the file pdbexamples_conformers.oeb.gz and the execution time will be even longer because of the macrocyclic molecules. It is preferable to run OMEGA macrocycle under Open MPI using the maximum number of CPU cores available.

## Using Parameters and Param Files¶

prompt> oeomega classic -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> oeomega classic -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 classic 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> oeomega classic -param myparameters drugs.smi drugs.oeb.gz
prompt> oeomega classic 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> oeomega classic -in drugs.smi -out drugs_maxconfs600.oeb.gz
-param myparameters -maxconfs 600


Again, this is a very similar command. It executes OMEGA classic 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> oeomega classic -in drugs.mol2 -out drugs.oeb.gz -fromCT true


The -fromCT true flag will cause OMEGA classic 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> oeomega classic -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).

## Log file for macrocycle mode¶

For each molecule in the input file, a row of data with the following columns is recorded:

Molecule, Conformers, Converged, Iterations, Energy Filtered, Unique Minima

• Conformers

Number of conformers in the output file. Its maximum number is always smaller or equal to the value of the -maxconfs

• Converged

Fraction describing the level of convergence at the termination $$(n-n_u)/n$$, where $$n$$ is the number of conformations produced in the last iteration cycle within a specified energy window, and $$n_u$$ is the number of unique conformations produced in that iteration cycle.

• Iterations

This number is equal to the parameter -max_iterations

• Energy Filtered

The number of conformations rejected because of their energy exceeding specified energy window

• Unique Minima

Total number of unique conformations produced within a run