SmallWorld Documentation for Future Developer

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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>
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