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
SWBB	http://swbb.docking.org/	10.20.0.5:8081	/nfs/db3/swbb_5th_gen
SWCC	http://swcc.docking.org/	10.20.0.5:8082	/nfs/db3/swcc_5th_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.
• Adding clipboard icon to copy SMILES of hits.

Summary of changes in search.html:

• Add 'Ask Questions' and contact info
• Add 'Database Information' hyperlink
• Pre-toggle Advanced Option

Summary of changes in smallworld-swagger.yaml:

• Change API route to be just "/"

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/smallworld_build_from_source

3. Download these latest Smallworlds and store them in 'smallworld_build_from_source/'. Here's how to download Smallworld.
   • smallworld-java-5.5.tar.gz
   • smallworld-java-src-5.5.tar.gz
4. Extract contents from the tar.gz files

   • tar -xvf smallworld-java-5.5.tar.gz
     tar -xvf smallworld-java-src-5.5.tar.gz

5. Install Apache Maven Smallworld Dependencies

   • cd /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java/lib/
     bash mvn-install.sh

Customizing swsearch.js

Location: /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/js/swsearch.js

Conditional Hyperlinks

1. vim /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/js/swsearch.js
2. Search for this

   • ?div.append("<b>" + id + "</b>");

3. Replace the inside of the else statement with these lines of code

   •                 if (id.substring(0,6) == "ZINC00") {
                             div.append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>");
                     } else if(id.substring(0,4) == "ZINC" && id.substring(4,6) != "00") {
                             div.append("<b><a target='_blank' href='https://cartblanche22.docking.org/substance/"+id+"'>" + id + "</a></b>");
                     } else {
                             div.append("<b>" + id + "</b>");
                     }

Copy SMILES of Hits

1. Search for this

   ?var $props

2. Add this line at the end of the appends

                                  .append('<br/><b>Copy SMILES: </b><a href="#" onclick="copySmiles(\'' + get_smiles_parts(data.hitSmiles)[0] + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>');

3. It should look like this

           var $props = $('<div>').append('<b>SWIDX:</b> ' + data.anonIdx)
                                  .append('<br/><b>MW:</b> ' + data.mw)
                                  .append('<br/><b>MF:</b> ' + data.mf)
                                  .append('<br/><b>Copy SMILES: </b><a href="#" onclick="copySmiles(\'' + get_smiles_parts(data.hitSmiles)[0] + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>');

4. Then add this function anywhere except inside another function's scope

   function copySmiles(smiles) {
           navigator.clipboard.writeText(smiles);
   }

Customizing search.html

Location: /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/search.html

Add 'Ask Questions' and 'Database Information'

1. vim /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/search.html
2. Search 'Scoring Methods'

   ?Scoring Methods

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

   <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>
   <div class="section-head">
           Database Descriptions
           <table class="swopt searchasyoudraw" style="width: 100%">
                   <th style="text-align: left">
                          <a href="https://wiki.docking.org/index.php/Smallworld_and_Arthor_Databases#Smallworld_Databases" target="_blank">Database Information Link</a>
                   </th>
           </table>
   </div>

4. It should look like this

               <div class="section-head">
                   Scoring Methods
               </div>
               <table id="swscore">
   
               </table>
           </div>
           <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>
           <div class="section-head">
                   Database Descriptions
                   <table class="swopt searchasyoudraw" style="width: 100%">
                           <th style="text-align: left">
                                   <a href="https://wiki.docking.org/index.php/Smallworld_and_Arthor_Databases#Smallworld_Databases" target="_blank">Database Information Link</a>
                           </th>
                   </table>
           </div>

Pre-toggle Advanced Option

1. Inside the script element, add this function

   window.onload = function() {
           $('#advPanel').css('display', $(this).prop('checked', true) && 'block'); update_visible_columns();
   }

2. Then search for "update_visible_columns" and scroll till you find the input checkbox element

   ?update_visible_columns

3. In the input box element, add the checked option. Should look like this

   <input name="optAdv" type="checkbox"
                              onchange="$('#advPanel').css('display', $(this).prop('checked') ? 'block' : 'none'); update_visible_columns();" checked>

Change API Route to "/"

1. path smallworld-java-src/web/target/sw-ws-5.6.1/WEB-INF/static/swagger/smallworld-swagger.yaml

Compile Code To Make WAR File

1. Build WAR File

   cd /nfs/home/jjg/smallworld_build_from_source/smallworld-java-src
   mvn install -Pbootable

2. If it works, then the new WAR File is located at /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/target/sw-ws-5.5.war

Restarting Smallworld Instance(s)

Old Way

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

New Way

1. Ssh to abacus and become root. Then run

   systemctl <start|stop|restart> <sw|swp|swc|swbb|swcc>