Arthor Documentation for Future Developer

Introduction

Here is the link to Arthor's manual

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

Arthor configurations and the frontend files are consolidated in /nfs/soft2/arthor_configs/.

/nfs/soft2/arthor_configs/start_arthor_script.sh can start/restart Arthor instances on respective machines.

Launch the script to see the options available.

How To Download Arthor

1. Ssh to nfs-soft2 and become root. Prepare directory

    mkdir /export/soft2/arthor_configs/arthor-<version> && cd /export/soft2/arthor_configs/arthor-<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 Arthor For The First Time

Prepare Files and Directories

1. Ssh to nfs-exc and become root
2. Open a port in the firewall

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

3. Go to Arthor Config directory

   cd /export/soft2/arthor_configs/arthor-<latest_version>

4. Create an Arthor config file

   vim <name_of_file>.cfg

   • Add these lines in the file. Check the manual for more options.

   DataDir=/local2/public_arthor
   MaxConcurrentSearches=6
   MaxThreadsPerSearch=8
   AutomaticIndex=false
   AsyncHitCountMax=20000
   Depiction=./depict/bot/svg?w=%w&h=%h&svgunits=px&smi=%s&zoom=0.8&sma=%m&smalim=1
   Resolver=https://sw.docking.org/util/smi2mol?smi=%s

Start Arthor Instance

1. Now ssh into a machine you wish to run an Arthor instance on and become root
2. Change your shell to bash if you havn't already

   bash

3. Create a screen

   screen -S <screen_name>

4. Prepare Arthor Config Path

   export ARTHOR_CONFIG="/nfs/soft2/arthor_configs/arthor-<version>/<name_of_config_file>.cfg"

5. Launch java

   java -jar -Dserver.port=<port_number> /nfs/soft2/arthor_configs/arthor-<version>/arthor-server-<version>.war

Configuration Details

• DataDir: This is the directory where the Arthor data files live. Location where the index files will be created and loaded from.

• MaxConcurrentSearches: Controls the maximum number of searches that can be run concurrently by setting the database pool size. When switching between a large number of databases it can be useful to have a larger pool size, the only trade off is keeping file pointers open.

• MaxThreadsPerSearch: The number of threads to use for both ATDB and ATFP searches

• Set AutomaticIndex to false if you don't want new smiles files added to the data directory to be indexed automatically

• AsyncHitCountMax: The upper-bound for the number of hits to retrieve in background searches.

• Resolver: Using Smallworld API, allows input box to take in a SMILE format and automatically draw on the board.

Check Arthor manual for more configuration options

How to Build Arthor Databases

We can build Arthor Databases anywhere. Consolidate smiles into one directory so you can index them all one by one.

Just use the script located at /nfs/home/jjg/scripts/arthor_index_script.sh at the directory where you stored the smiles.

Here is the content of the script:

#!/bin/bash

target="*.smi"
threads='48'
version="3.6.1"


export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-$version/arthor-$version-centos8/
export PATH=$ARTHOR_DIR/bin/:$PATH

for j in $target
do
        echo 'smi2atdb -v -r -j '$threads' -p '$j' '${j}'.atdb |& tee -a '${j}'_log'
        time smi2atdb -v -r -j $threads -p $j ${j}.atdb |& tee -a ${j}_log
	echo 'smi2atfp -j '$threads' -p '$j' '${j}.atfp' |& tee -a '${j}'_log'
        time smi2atfp -j $threads -p $j ${j}.atfp |& tee -a ${j}_log
done

for i in $target*atdb
do
	echo 'atdb2fp -j '$threads' '$i
        time atdb2fp -j $threads $i
	chmod 744 $i.fp
done

Command Details

smi2atdb creates the atdb files needed for Substructure searching.

• -v verbose
• -r Compute and store ring size information in the index allowing ring size (3-10) expressions ([r6] and [Z5])
• -j is the amount of threads to use to index the smiles file
• -p stores the position of the original file

atdb2fp makes substructure searching faster

smi2atfp creates atfp files for similarity searching

Setting up Round Table

"Round Table allows you to serve and split chemical searches across multiple host machines. The implementation provides a lightweight proxy that forwards requests to other Arthor host servers that do the actual search. Communication is done using the existing Web APIs.

Setting up Host Server

1. Ssh to nfs-soft2 and become root
2. Open a port in the firewall

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

3. Go to Arthor Config Directory

   cd /export/soft2/arthor_configs/arthor-<version>

4. Create Round Table Head configuration file. Here is an example:

5. [RoundTable]
   RemoteClient=http://10.20.0.41:8008
   RemoteClient=http://10.20.5.19:8008
   Resolver=https://sw.docking.org/util/smi2mol?smi=%s

6. Now ssh into a machine you wish to run the round table head on and become root
7. Change your shell to bash if you havn't already

   bash

8. Create a screen

   screen -S <screen_name>

9. Prepare Arthor Config Path

   export ARTHOR_CONFIG="/nfs/soft2/arthor_configs/arthor-<version>/<round_table_head>.cfg"

10. Launch java

    java -jar /nfs/soft2/arthor_configs/arthor-<version>/arthor-<version>-centos7/java/arthor.jar --httpPort=<port_number>

Active Arthor Instances

Public Arthor

Rocky Linux Machine	Port	Round Table Data Directory	Which Arthor
arthor	10.20.200.100:8080	/local3/public_arthor/	Public Arthor

Private Arthor

Rocky Linux Machine	Port	Round Table Data Directory	Which Arthor
arthor	10.20.200.100:8081	/local3/private_arthor/	Private Arthor

Super Private Arthor

Rocky Linux Machine	Port	Round Table Data Directory	Which Arthor
arthor	10.20.200.100:8082	/local3/super_private_arthor/	Private Arthor

Arthor BB, CC, and Covalent

CentOS 7 Machine	Port	Data Directory	Which Arthor
epyc-A40	10.20.200.92:8081	/local2/arthorbb	ArthorBB
epyc-A40	10.20.200.92:8082	/local2/arthorcc	ArthorCC
epyc-A40	10.20.200.92:8080	/local2/arthorcovalent	Arthor Covalent

Customizing Arthor Frontend To Our Needs (Arthor 4.1)

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 index.html:

• Add contact info
• Advertise TLDR
• Remove button for Formula
• Database Information Link

Summary of changes in index.js:

• Hyperlink the results to zinc20 or cartblanche22
• Copy SMILES with clipboard button

Summary of changes in sketcher.js:

• Input box should be updated as user draws molecule

Summary of changes in arthor-swagger.yaml.js:

• Make API point to "/"

Install Prerequisite Packages

1. Install Apache Maven

   • dnf install maven -y

2. Install Node Package Manager (NPM)

   • dnf install npm -y

3. 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

4. Download these latest Arthors and store them in 'arthor_build_from_source/'. Here's how to download Arthor.
   • arthor-4.1-source.tar.gz
   • arthor-4.1-centos8.tar.gz
5. Extract contents from the tar.gz files

   • tar -xvf arthor-4.1-source.tar.gz
     tar -xvf arthor-4.1-centos8.tar.gz

6. Install Apache Maven Arthor dependencies through this script located at nfs/home/jjg/arthor_build_from_source/mvn_build.sh

   • #!/bin/bash
     
     version=4.1
     
     export ARTHOR_DIR=/mnt/nfs/home/jjg/arthor_build_from_source/arthor-$version/arthor-$version-centos8/java/
     export OS=linux
     export VERSION=$version
     
     mvn install:install-file -Dfile=$ARTHOR_DIR/arthor-jni-${OS}.jar \
                              -Dpackaging=jar \
                              -DgeneratePom=true \
                              -DartifactId=arthor-jni-${OS} \
                              -DgroupId=com.nextmovesoftware.arthor \
                              -Dversion=$VERSION
     mvn install:install-file -Dfile=$ARTHOR_DIR/arthor-jni.jar \
                              -Dpackaging=jar \
                              -DgeneratePom=true \
                              -DartifactId=arthor-jni \
                              -DgroupId=com.nextmovesoftware.arthor \
                              -Dversion=$VERSION

Customizing Index.html

Location: /nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server-ui/src/index.html

Add contact info and tldr

1. vim /nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server-ui/src/index.html
2. Search for 'arthor_table_list'

   • ?arthor_table_list

3. Add contact info, a plug to tldr.docking.org, and database link after the div block where arthor_table_list is inside of. It should look like this

   •       <div class="opt-box-border">
             <label>Databases</label>
             <!-- This will be populated by available databases -->
             <ul id="arthor_table_list">
               <li class="placeholder">Please select a search type</li>
             </ul>
           </div>
           <div class="opt-box-border">
             <label>Ask Questions</label>
             Email us: jjiteam@googlegroups.com
           </div>
           <div class="opt-box-border">
             <label> To Download 100K+ Results</label>
             Sign up for <a href="http://tldr.docking.org/">tldr.docking.org</a> and use arthorbatch
           </div>
           <div class="opt-box-border">
             <label> Database Information</label>
             <a href="https://wiki.docking.org/index.php/Smallworld_and_Arthor_Databases#Smallworld_Databases" target="_blank">Database Information Link</a>
           </div>

Remove Similarity and Formula Buttons

1. vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server/src/main/webapp/WEB-INF/static/index.html
2. Search for 'arthor_search_list'

   •  ?arthor_search_list

3. Delete and Replace the whole 'ul' element block with this

   •           <li value="Similarity" onclick="setSearchType(this)" class="first">
                 Similarity
               </li><li value="Substructure" onclick="setSearchType(this)">
                 Substructure
               </li><li value="SMARTS" onclick="setSearchType(this)" class="last">
                 SMARTS
               </li>
               <!--<li value="Formula" onclick="setSearchType(this)" class="last">
                 Formula
               </li>-->

Customize Index.js

Conditional Hyperlinks

Location /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1-source/server-ui/src/index.js

1. Add the zinc20 hyperlink to the Arthor results. Search for this

   • $info.append($("<tr>").append($('<td class="identifier">').append(id)));

2. Delete the contents of the whole else block and replace it with this

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

Copy SMILES Clipboard

1. Search this

   ?parser

2. At the end of the the try block add this

           $info.append(
             $('<tr>').append(
               $('<td>').append('Copy SMILES: <a href="#" onclick="navigator.clipboard.writeText(\'' + parser.smi + '\');"  ><i class="fa fa-clipboard" aria-hidden="true"></i></a>')));

3. The whole try and catch block should look like this

   try {
         var parser = new SmiJs.Parser(data);
         if (parser.parse()) {
           $info.append(
             $('<tr>').append(
               $('<td>').append(parser.mf(true))));
           $info.append(
                   $('<tr>').append(
                     $('<td>').append(parser.mw())));
           $info.append(
             $('<tr>').append(
               $('<td>').append('Copy SMILES: <a href="#" onclick="navigator.clipboard.writeText(\'' + parser.smi + '\');"  ><i class="fa fa-clipboard" aria-hidden="true"></i></a>')));
         }
       } catch(err) {
         console.log(err);
       }

Customize Sketcher.js

Location: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1-source/server-ui/src/sketcher.js

Input Box Updates as User Draws

1. vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1-source/server-ui/src/sketcher.js
2. Search for this line "var smiles = event.src.smiles();"

   • ?var smiles = event.src.smiles();

3. Add this new line below it

   • $('#ar_text_input').val(smiles);

Customize arthor-swagger.yaml

Location: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server/src/main/webapp/WEB-INF/static/swagger/arthor-swagger.yaml

Change URL Base Path for API Call

1. vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server/src/main/webapp/WEB-INF/static/swagger/arthor-swagger.yaml
2. Search for "servers"

   • ?basePath

3. Remove "/arthor" and keep argument empty

Compile/Minify Code through NPM

1. Install NPM packages and Minify Code

   • cd /nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server-ui
     npm install
     npx webpack-dev-server
     npx webpack --mode=production

2. If the npx commands don't work, try updating node and npm version to the latest one.
3. Build the war file

   • cd /nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server
     mvn install -Pbootable

4. If it works, then the path to new war file is at /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server/target/arthor-server-4.1.war

Adding Arthor to Systemd (example)

1. Create service files

   touch /etc/systemd/system/arthor.service

2. Add this code block in the service file

   [Unit]
   Description=Arthor Public Instance
   After=network.target
   
   [Service]
   Type=exec
   Restart=always
   RestartSec=3
   User=root
   ExecStart=/usr/bin/bash /nfs/soft2/arthor_configs/start_arthor_service.sh -arthor
   ExecStop=/bin/kill -15 $MAINPID
   
   [Install]
   WantedBy=multi-user.target

3. Change "ExecStart" to other Arthor Instances

Restarting Arthor Instance(s) Instructions

Public, Private Arthor, and Super Private Arthor

1. ssh to "arthor" server and run

   systemctl <start|stop|restart> <arthor|arthorp|arthorc>

ArthorBB, ArthorCC, and ArthorCovalent

1. ssh to "epyc-a40" server and run

   systemctl <start|stop|restart> <arthorbb|arthorcc|arthorcovalent>