Tutorial 0: Basic usage of FastROCS TKΒΆ

FastROCS TK is primarily designed to be used as a server/client interface. Example scripts are provided with FastROCS TK to help you get up and running. This tutorial demonstrates the use of the ShapeDatabaseServer and ShapeDatabaseClient. example scripts, which are provided below.

After FastROCS TK has been installed follow these simple steps for the most basic usage of FastROCS TK:

  1. Start the server on an OMEGA conformer database in your terminal in the virtual environment you used to install the OpenEye Toolkits

    (fastrocs) $ ShapeDatabaseServer.py your_database.oeb
    
  2. Query the server from another terminal using the same virtual environment

    (fastrocs) $ ShapeDatabaseClient.py localhost:8080 your_query.sdf output_overlays.sdf
    

Note

The server can be queried from the same terminal by putting the ShapeDatabaseServer process in the background by doing ctrl z && bg.

Warning

For best performance, do not use GNU Zipped (.gz) molecule databases with FastROCS. Uncompress the .oeb.gz to .oeb first.

For more advanced options see the --help menu

(fastrocs) $ ShapeDatabaseClient.py --help
usage: ShapeDatabaseClient.py [-h] [--tversky] [--shapeOnly]
                              [--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]
                              server:port query results [nHits]

positional arguments:
  server:port           Server name and port number of database to search i.e.
                        localhost:8080.
  query                 File containing the query molecule to search (format
                        not restricted to *.oeb).
  results               Output file to store results (format not restricted to
                        *.oeb).
  nHits                 Number of hits to return (default=100).

optional arguments:
  -h, --help            show this help message and exit
  --tversky             Switch to Tversky similarity scoring
                                     (default=Tanimoto).
  --shapeOnly           Switch to shape-only scores (default=Combo).
  --alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}
                        Optimize using alternative starts (default=inertial).
                        To perform N random starts do "--alternativeStarts
                        random N" (default N=10)