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 c

Here is the content of the script:

#!/bin/bash

version="3.4.2"

export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-$version/arthor-$version-centos7/
export PATH=$ARTHOR_DIR/bin/:$PATH

target="*.smi"

for j in $target
do
        echo 'smi2atdb -j 4 -p '$j' '${j}'.atdb'
        smi2atdb -j 4 -p $j ${j}.atdb
        echo 'atdb2fp -j 4 '$j'.atdb'
	atdb2fp -j 4 ${j}.atdb
done

Command Details

smi2atdb creates the atdb files needed for Substructure searching.

• -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

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

CentOS 7 Machine	Port	Round Table Data Directory
samekh	10.20.0.41:8000	/local2/public_arthor/
nun	10.20.0.40:8000	/local2/public_arthor/

Arthor Round Table Head

CentOS 7 Machine	Port	Round Table Data Directory
samekh	10.20.0.41:8080	/local2/arthor_database/
nun	10.20.0.40:8080	/local2/arthor_database/

Arthor Round Table Nodes

CentOS 7 Machine	Port	Round Table Data Directory
samekh	10.20.0.41:8008	/local2/arthor_database/
nun	10.20.0.40:8008	/local2/arthor_database/
nfs-exd	10.20.1.113:8008	/export/exd/arthor_database/
nfs-exh	10.20.5.19:8008	/export/exh/arthor_database/

Customizing Arthor Frontend To Our Needs (Arthor 3.4.7)

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

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-3.4.7-source.tar.gz
   • arthor-3.4.7-centos7.tar.gz
5. 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

6. Install Apache Maven Arthor dependencies through this script

   • #!/bin/bash
     
     export ARTHOR_DIR=/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-centos7/java
     export OS=linux
     export VERSION=3.4.7
     
     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: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server/src/main/webapp/WEB-INF/static/index.html

Summary of changes needed:

• Add download options
• Add contact info
• Advertise TLDR
• Remove buttons for Similarity and Formula

Change download options

1. vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server/src/main/webapp/WEB-INF/static/index.html
2. Search for 'arthor_tsv_link'

   • ?arthor_tsv_link

3. Delete original download links

   •               <a id="arthor_tsv_link" href="#"> TSV</a>
                   <a id="arthor_csv_link" href="#"> CSV</a>
                   <a id="arthor_sdf_link" href="#"> SDF</a>

4. Add new download link options

   •               <a id="arthor_tsv_link_100" href="#"> TSV-100</a>
                   <a id="arthor_tsv_link_1k" href="#"> TSV-1,000</a>
                   <a id="arthor_tsv_link_10k" href="#"> TSV-10,000</a>
                   <a id="arthor_tsv_link_100k" href="#"> TSV-100,000</a>
                   <a id="arthor_tsv_link_200k" href="#"> TSV-200,000</a>
                   <a id="arthor_tsv_link_300k" href="#"> TSV-300,000</a>
                   <a id="arthor_csv_link_100" href="#"> CSV-100</a>
                   <a id="arthor_csv_link_1k" href="#"> CSV-1,000</a>
                   <a id="arthor_csv_link_10k" href="#"> CSV-10,000</a>
                   <a id="arthor_csv_link_100k" href="#"> CSV-100,000</a>
                   <a id="arthor_csv_link_200k" href="#"> CSV-200,000</a>
                   <a id="arthor_csv_link_300k" href="#"> CSV-300,000</a>
                   <a id="arthor_sdf_link_100" href="#"> SDF-100</a>
                   <a id="arthor_sdf_link_1k" href="#"> SDF-1,000</a>
                   <a id="arthor_sdf_link_10k" href="#"> SDF-10,000</a>
                   <a id="arthor_sdf_link_100k" href="#"> SDF-100,000</a>
                   <a id="arthor_sdf_link_200k" href="#"> SDF-200,000</a>
                   <a id="arthor_sdf_link_300k" href="#"> SDF-300,000</a>

5. Search for 'arthor_table_list'

   • ?arthor_table_list

6. Add contact info and a plug to tldr.docking.org 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>

Customizing Arthor Frontend to our needs

The frontend Arthor code is located at /nfs/exc/arthor_configs/* and the * is based on current running version.

Add Arthor Download Options

For Arthor 3.4:

1. vim .extract/webapps/ROOT/WEB-INF/static/index.html

2. search: arthor_tsv_link

3. in the div with the class=”dropdown-content”, add these link options and change the number accordingly:

              <a id="arthor_tsv_link" href="#"> TSV-500</a>
              <a id="arthor_tsv_link_5000" href="#"> TSV-5,000</a>
              <a id="arthor_tsv_link_50000" href="#"> TSV-50,000</a>
              <a id="arthor_tsv_link_100000" href="#"> TSV-100,000</a>
              <a id="arthor_tsv_link_max" href="#"> TSV-max</a>
              <a id="arthor_csv_link" href="#"> CSV-500</a>
              <a id="arthor_csv_link_5000" href="#"> CSV-5,000</a>
              <a id="arthor_csv_link_50000" href="#"> CSV-50,000</a>
              <a id="arthor_csv_link_100000" href="#"> CSV-100,000</a>
              <a id="arthor_csv_link_max" href="#"> CSV-max</a>
              <a id="arthor_sdf_link" href="#"> SDF-500</a>
              <a id="arthor_sdf_link_5000" href="#"> SDF-5,000</a>
              <a id="arthor_sdf_link_50000" href="#"> SDF-50,000</a>
              <a id="arthor_sdf_link_100000" href="#"> SDF-100,000</a>
              <a id="arthor_sdf_link_max" href="#"> SDF-max</a>

4. then vim .extract/webapps/ROOT/WEB-INF/static/js/index.js

5. search: function $(t){

6. in the function $(t), add these lines:

if(document.getElementById("arthor_tsv_link")) {
       var e=i.a.param({query:s.b.query,type:s.b.type,draw:0,start:0,length:t,flags:s.b.flags}),n=s.b.url+"/dt/"+E(s.b.table)+"/search";i()("#arthor_sdf_link").attr("href",n+".sdf?"+e),i() ("#arthor_tsv_link").attr("href",n+".tsv?"+e),i()("#arthor_csv_link").attr("href",n+".csv?"+e)
}
if (document.getElementById("arthor_tsv_link_5000")) {
       var e=i.a.param({query:s.b.query,type:s.b.type,draw:0,start:0,length:5000,flags:s.b.flags}),n=s.b.url+"/dt/"+E(s.b.table)+"/search";i()("#arthor_sdf_link_5000").attr("href",n+".sdf?"+e),i()("#arthor_tsv_link_5000").attr("href",n+".tsv?"+e),i()("#arthor_csv_link_5000").attr("href",n+".csv?"+e)
}
if (document.getElementById("arthor_tsv_link_50000")) {
       var e=i.a.param({query:s.b.query,type:s.b.type,draw:0,start:0,length:50000,flags:s.b.flags}),n=s.b.url+"/dt/"+E(s.b.table)+"/search";i()("#arthor_sdf_link_50000").attr("href",n+".sdf?"+e),i()("#arthor_tsv_link_50000").attr("href",n+".tsv?"+e),i()("#arthor_csv_link_50000").attr("href",n+".csv?"+e)
}
if (document.getElementById("arthor_tsv_link_100000")) {
       var e=i.a.param({query:s.b.query,type:s.b.type,draw:0,start:0,length:100000,flags:s.b.flags}),n=s.b.url+"/dt/"+E(s.b.table)+"/search";i()("#arthor_sdf_link_100000").attr("href",n+".sdf?"+e),i()("#arthor_tsv_link_100000").attr("href",n+".tsv?"+e),i()("#arthor_csv_link_100000").attr("href",n+".csv?"+e)
}
if (document.getElementById("arthor_tsv_link_max")) {
       var e=i.a.param({query:s.b.query,type:s.b.type,draw:0,start:0,length:1000000000,flags:s.b.flags}),n=s.b.url+"/dt/"+E(s.b.table)+"/search";i()("#arthor_sdf_link_max").attr("href",n+".sdf?"+e),i()("#arthor_tsv_link_max").attr("href",n+".tsv?"+e),i()("#arthor_csv_link_max").attr("href",n+".csv?"+e)
}

Take out Similarity Button

vim .extract/webapps/ROOT/WEB-INF/static/index.html
search: Similarity

Comment out this line < li value="Similarity" onclick="setSearchType(this)" class="first"> Similarity //added spaces at the beginning and end so prevent wiki from converting it Then add "first" in Substructure's class

Hyperlink to zinc20

vim .extract/webapps/ROOT/WEB-INF/static/js/index.js
search: table_name
*find this line "< b>" + d + "< /b>"
*replace with "< b><a target='_blank' href='https://zinc20.docking.org/substances/"+d+"'>" + d + "</a>" //added spaces at the beginning and end so prevent wiki from converting it

Make Input Box Work

At the end of the Arthor config file add this:
   Resolver=https://sw.docking.org/util/smi2mol?smi=%s
To copy smiles in the input box:
   vim .extract/webapps/ROOT/WEB-INF/static/js/index.js
   search this: “var e=t.src.smiles()”
   add this after the semi-colon
       document.getElementById("ar_text_input").value = e;

Add Ask Questions

1. Go to frontend directory

   vim /export/soft2/arthor_configs/arthor-3.4.2/.extract/webapps/ROOT/WEB-INF/static/index.html

2. Search opt-box-border
3. Create another div in the compass of two big divs
4. Add this

   <div class="opt-box-border">
           <label>Ask Questions</label>
           Email us: jjiteam@googlegroups.com
   </div>

Restarting Arthor Instance(s) Instructions

1. Ssh to machine with respective Arthor instance and become root
2. execute run_arthors_on_reboot.sh to show restart all instances on the machine

   bash /root/run_arthors_on_reboot.sh

3. execute start_arthor_script.sh to restart specific Arthor instance. It will show you options to choose from.

   bash /nfs/soft2/arthor_configs/start_arthor_script.sh