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 12 TB of 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
Step 2: Find a location for the sw.jar file
Copy the sw.jar file to a reasonable location such as
/opt/nextmove/sw.jar
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
This is a long command, so we can break down the different parts.
map The SMILES file you want to map follows the word "map"
-T This is the temp directory you want to write temp files to, rather than writing to /tmp
-o The final name of your output map file
-u Argument to keep track of the unmapped compounds.
Important: The unmapped compounds file may be used to generate extensions and is the same as the .anon.ext.map file mentioned in the SmallWorld documentation
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
Step 2.5 Incremental Updates
Suppose you already have a file called <your-file-name>.anon.map, and you want to add some new smiles without remaking the entire map. A worked example is located in the SmallWorld version 4 documentation on pages 17-18 in the Incremental Updates Section
(This part of the wiki page is incomplete. I'll update it when I'm done with my script to automatically generate the cfg file) The creat_cfg.py program is located in
/mnt/nfs/ex9/work/smallworld/create_cfg.py
The create_cfg.py script will automatically generate a cfg file for a map that is composed of two existing SmallWorld Maps. Run as follows:
python create_cfg.py first second combined
Note: first is first.anon.map second is second.anon.map combined is combined.anon.map
The program will look for the .anon.map files and the .anon.map.cfg for the first and second before proceeding
If you have a new SMILES file <newsmiles>.smi that you want to combine with an existing map file, first run the map command in Step 2 for the new file
Make a copy and modify the bash script below with the name of your new map file
You can run this script on any machine
/nfs/ex9/work/smallworld/bash_merge_maps
Replace the OLD_MAPFILE environment variable with the old map
Replace the ADD_MAPFILE environment variable with the map you wish to incrementally add
Replace the NEW_MAPFILE environment variable with the name you want for the new combined map
Step 3: How to Make the New Database Available. Stop the server first!
First, stop the server. You do not need to restart Tomcat every time you want to restart SmallWorld. The TomCat GUI is available at
http://10.20.9.22:8080/
You need the tunnel to access the private network or this link will not work! Also, the admin username and password is required.
In the Manager App, in the Applications section, use the Stop and Start buttons for the sw-ws app to restart the SmallWorld server
Step 4: Move the Map File into the /maps directory
If you followed the example above, your .anon.map file should be located in
/mnt/nfs/ex9/work/smallworld
Now, simply move the map file into the "/sw/maps" directory so it can be recognized by SmallWorld.
mv <your-file-name>.anon.map /mnt/nfs/ex9/work/smallworld/maps
Or, simply
mv <your-file-name>.anon.map maps
Step 5: Restart the Server
Again, go to the TomCat manager under applications and click Start once you are finished moving around the map files.