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>

How to Build Smallworld Maps/Databases

Consolidate smiles into /export/db3/temp_mapping.

Use the script located in that directory called smallworld_map_script.

Here is the content of the script:

#!/bin/csh -f
setenv SWDIR /export/db3/public_smallworld_4th_gen/

alias sw 'time java -jar /opt/nextmove/smallworld-5.1/sw.jar'

set target = '*.smi'

foreach i ($target)
	echo '(sw map' $i '-T tmp/ -o '${i}'.anon.map -u '${i}'.anon.unmapped) |& tee '${i}'_log'
	(sw map $i -T tmp/ -o ${i}.anon.map -u ${i}.anon.unmapped) |& tee ${i}_log
	echo 'sw blm -p 0.01 '${i}'.anon.map'
	sw blm -p 0.01 ${i}.anon.map
end

Command Details

setenv sets the environment where the anon master map is

java -jar /opt/nextmove/smallworld-5.1/sw.jar shortened to sw via alias

map will map the smiles based on the current anon master map.

• -T stores temp files so /tmp does not get overloaded
• -o output with custom name you like
• -u will collect the unmapped molecules to send to Nextmove or to use swextend

tee will log the progress of the process

Splitting Databases

[Follow this page if John has asked you to split the database into smaller slices.]

Active Smallworld Instances

Caption text

Type	URL	Machine:Port	Directory
Public	http://sw.docking.org/	10.20.0.5:5020	/nfs/db3/public_smallworld_4th_gen
Private	http://swp.docking.org/	10.20.0.5:8080	/nfs/db3/private_smallworld_4th_gen
Super Private	http://swc.docking.org/	10.20.0.5:5099	/nfs/db3/super_private_smallworld_4th_gen

Customize Smallworld FrontEnd To Our Needs (Smallworld 5.5)

These instructions only worked and compiled for me in the machine called epyc which is running Rocky 8 Linux operating system.

Summary of changes in swsearch.js:

• Conditional hyperlinks attached to smallworld hits. Leads to zinc20, cartblanche22, or nothing.

Summary of changes in search.html:

• Add 'Ask Questions' and contact info

Install Prerequisite Packages

1. Install Apache Maven

   • dnf install maven -y

2. In your home directory, create a new directory to hold the files for the upcoming procedures

   • mkdir /mnt/nfs/home/jjg/arthor_build_from_source

3. Download these latest Arthors and store them in 'arthor_build_from_source/'. Here's how to download Arthor.
   • arthor-3.4.7-source.tar.gz
   • arthor-3.4.7-centos7.tar.gz
4. Extract contents from the tar.gz files

   • tar -xvf arthor-3.4.7-source.tar.gz
     tar -xvf arthor-3.4.7-centos7.tar.gz

5. Install Apache Maven Arthor dependencies through this script

Hyperlink Results to ZINC20

1. Open swsearch.js

   vim /export/db3/smallworld_extract/.extract/webapps/ROOT/WEB-INF/static/js/swsearch.js

2. Search this:

   ?div.append("<b><a target='_blank' href='" + href + "'>" + id + "</a></b>");

3. On the else statement replace the line with this

   div.append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>");

Add 'Ask Questions' On Smallworld

1. Open search.html

   vim /export/db3/smallworld_extract/.extract/webapps/ROOT/WEB-INF/static/search.html

2. Search 'Scoring Methods'

   ?Scoring Methods

3. At the end of that big block of 'div', add this:

   <div class="section-head">
           Ask Questions
           <table class="swopt searchasyoudraw" style="width: 100%">
                   <th style="text-align: left">Email us: jjiteam@googlegroups.com</th>
           </table>
   </div>

Restarting Smallworld Instance(s)

1. Ssh to abacus and become root
2. execute run_sw_on_reboot.sh to show restart all instances on the machine

   bash /root/run_arthors_on_reboot.sh

3. execute start_smallworld to restart specific Smallworld instance. It will show you options to choose from.

   start_smallworld