SmallWorld Documentation for Future Developer

Introduction

Here is the link to Smallworld's manual

• Username: ucsf@nextmovesoftware.com
• Password: <Ask jjiteam@googlegroups.com>

All smallworld databases live in abacus' db3.

Smallworld frontend files are consolidated and located at /export/db3/smallworld_extract/.extract.

Execute command start_smallworld to see options on which smallworld instance to start/restart.

How to Download Smallworld

1. Ssh to abacus and become root. Prepare directory

    mkdir /opt/nextmove/smallworld-<version> && cd /opt/nextmove/smallworld-<version>

2. Download Software with this link
   • Username: ucsf@nextmovesoftware.com
   • Password: <Ask jjiteam@googlegroups.com>
3. Go to releases. Look for smallworld-java-<version>.tar.gz and copy the link address.
4. Download using wget

    wget --user ucsf@nextmovesoftware.com --password <Ask jjiteam@googlegroups.com> <link address>

5. Decompress the file

   •  tar -xvf <file_name>

How to Launch Smallworld For The First Time

Prepare Files and Directories

1. Ssh to abacus and become root
2. Open a port in the firewall

   firewall-cmd --permanent --add-port=<port_number>/tcp 
   firewall-cmd --reload

3. Go to smallworld databases directory

   cd /export/db3/

4. Create a Smallworld directory and go to it

   mkdir <smallworld_dir> && cd <smallworld_dir>

5. Inside that directory, create these
   • a symbolic link to the smallworld anon map

   ln -s /export/db2/smallworld_anon_21Q4 anon

   • a sub-directory called maps to store databases

   mkdir maps

   • a smallworld config file

   vim smallworld.cfg

   • Add this block of code inside the config file

   [WebApp]
   DepictionUrl=./depict/svg?w=%w&h=%h&smi=%s&qry=%q&cols=%c&cmap=%m
   ResolverUrl=./util/smi2mol?smi=%s
   SearchTimeOut=5000
   SearchAsYouDraw=true
   [Score]
   Name=Atom Alignment
   Description=Aligns and scores each hit relative to the query atom types, differences are categorised as MAJ, MIN, HYB, SUB 
   Class=com.nmsoftware.smallworld.score.SimpleAtomAlignment 
   EnabledByDefault=false
   MappingMode=EditMap
   [Score]
   Name=SMARTS Alignment
   Description=Treat input as SMARTS and align and score each hit relative to the query atom expressions in the input 
   Class=com.nmsoftware.smallworld.score.SmartsAtomAlignment 
   EnabledByDefault=false
   [Score]
   Name=ECFP4
   Description=Extended Connectivity Circular Fingerprint
   Class=com.nmsoftware.smallworld.score.EcfpTanimoto
   Radius=2
   EnabledByDefault=true
   [Score]
   Name=Daylight
   Description=Path based fingerprint
   Class=com.nmsoftware.smallworld.score.DaylightTanimoto
   EnabledByDefault=true

   • SearchTimeOut should be the only option you'll change in the future. It caps search time to lessen strain on machine.
6. Place any *.anon.maps you've already compiled for testing into the maps sub-directory.

Start Smallworld Instance

1. Go to smallworld extract directory

   cd /export/db3/smallworld_extract

2. Create a screen

   screen -S <screen_name>

3. Export the smallworld directory you've made

   export SWDIR=/export/db3/<smallworld_dir>

4. Launch java

   java -jar /opt/nextmove/smallworld-<version>/sw-ws-<version>.jar --httpPort=<port_number>

Creating Maps on SmallWorld

See the corresponding wiki page: http://wiki.docking.org/index.php/Creating_Maps_on_SmallWorld

Running SmallWorld from the Command Line

We have been running SmallWorld on n-9-22 as www which uses csh as the default shell. There is a file in /mnt/nfs/soft/www/home/smallworld called run_sw which contains the following commands to set up the SmallWorld Command Line Interface (CLI)

Set the SWDIR environment variable so SmallWorld scripts can access the 12 TB index

   setenv SWDIR /srv/db4

Set the path to the SmallWorld C++ Executables

   set path = ($path /opt/nextmove/bin)

Alias the keyword "sw" to access the Java CLI

   alias sw 'java -jar /opt/nextmove/sw.jar'

Tips for Running SmallWorld on the Command Line

Use sw help to get information about available commands

    sw help