Creating Maps on SmallWorld

Written by Jennifer Young on April 10, 2019

Install

Step 1: Create the /sw directory

SmallWorld requires a /sw directory which contains /anon and /maps The /sw directory is located on n-9-22 in /srv/db4

This directory contains: The /anon directory contains pre-computed subgraphs The /maps directory contains text files computed by SmallWorld that map your molecules of choice to the corresponding nodes in the anonymous graph index

Run

Important! Currently, we only run SmallWorld map generation on n-9-22

Step 1: Set SWDIR environment variable

Determine where the /sw directory with the /anon and /maps directory and if using csh, set the SWDIR variable using

   setenv SWDIR /srv/db4

If using bash, set the SWDIR variable using

   export SWDIR=/srv/db4

Step 2: Generate the map files

Run sw.jar to convert your smiles file into a map file.

(Optional: use the time command to see how long this takes)

(Optional: tee your results into a log file to check progress)

Here is an example where wait-ok.smi is your .smi file to map:

   (time java -jar /opt/nextmove/sw.jar map /mnt/nfs/ex9/work/smallworld/wait-ok.smi 
   -T /mnt/nfs/ex9/work/smallworld/scratch_sw 
   -o /mnt/nfs/ex9/work/smallworld/wait-ok.anon.map 
   -u /mnt/nfs/ex9/work/smallworld/wait-ok.anon.unmapped)
    |& tee /mnt/nfs/ex9/work/smallworld/wait-ok_log

For now, generate the map files in the /mnt/nfs/ex9/work/smallworld directory so they can be easily moved to the maps directory when the server is restarted