4.1 makerocsdb

Important Note: The format for .rocsdb is specific for ROCS. The format may change in the future, following more work in optimizing for large clusters. Or, the format may ultimately be retired if no longer needed.

In order to provide maximum throughput for PVM scalability, this version of ROCS comes with a new utility to convert existing dbase files into a new .rocsdb file. This is not required for normal ROCS usage, only for scaling to 64 CPUs and beyond under PVM.

makerocsdb has only 2 required command-line parameters:

-in: Input dbase file to be converted. Can be any one of the molecule file formats described in Section 2.2.1.
-out: Prefix for output .rocsdb file.

So to convert an Omega database file, omega_confs.oeb.gz into ROCS DB format:

prompt> makerocsdb -in omega_confs.oeb.gz -out rocsinput

will create a new file, rocsinput.rocsdb

By default, makerocsdb will apply the same contiguous conformer test that ROCS does and will attempt to merge contiguous conformers into a single multi-conformer molecule on output. If this behavior is not desired, then the -scdbase flag can be set to true and each input molecule will be written into the rocsdb file as a separate molecule.