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 mode 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 macrocycle mode 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 the macrocycle mode 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 to 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 overridden 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.

Advanced Commands

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).

CSV Report File for macrocycle Mode

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

  • Molecule

    Title of the molecule.

  • SMILES

    SMILES string corresponding to the molecule.

  • Conformers

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

  • LargestRing

    Size of the largest ring system in the molecule.

    Note

    All fused rings are considered to be a part of the macrocycle ring. Within this convention, decalin is assumed to be a 10-membered ring system.

  • Iterations

    This number is equal to the parameter macrocycle -max_iterations.

  • Elapsed Time

    Time used to generate conformers (in seconds).

  • Status

    Failure reason in case conformers are not generated.

    Note

    Message: “No conformer left after post processing” is usually caused by a chirality mismatch between the chirality of the input molecule and the chirality of each generated conformation. It means that the force field refinement was not able to reproduce input chirality. It is recommended therefore to check the correctness of chirality input molecule. This situation is common when the input is taken from the 3D PDB file. A good example is the PDB structure of the rifampicin antibiotic extracted from the 1SKX entry. This molecule has nine atomic chiral centers and two chiral bonds. Its chirality assignment based on the 3D PDB structure differs from the actual chirality of this antibiotic.