MakeRocsDB

Overview

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 scalability, this version of ROCS comes with a utility to convert existing OMEGA dbase files into a .rocsdb file. This is not required for normal ROCS usage, only for scaling to 64 CPUs and beyond under MPI.

Example Commands

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.

Command Line Help

A description of the command line interface can be obtained by executing MakeRocsDB with the --help option.

> makerocsdb --help

will generate the following output:

Help functions:
  makerocsdb --help simple      : Get a list of simple parameters
  makerocsdb --help all         : Get a complete list of parameters
  makerocsdb --help defaults    : List the defaults for all parameters
  makerocsdb --help <parameter> : Get detailed help on a parameter
  makerocsdb --help html        : Create an html help file for this program
  makerocsdb --help versions    : List the toolkits and versions used in the application

Required Parameters

makerocsdb has only 2 required command-line parameters:

-in <filename>

Input dbase file to be converted. Can be any one of the molecule file formats described in Section The Database File.

-out <prefix>

Prefix for output .rocsdb file.