Arthor Documentation for Future Developer

Introduction

Here is the link to Arthor's manual

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 the right OS 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

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

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

   bash

7. Create a screen

   screen -S <screen_name>

8. Prepare Arthor Config Path

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

9. Launch java

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

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.

Just use the script located at /nfs/home/jjg/scripts/arthor_index_script.sh

Here is the content of the script:

#!/bin/bash

version="3.4.2"

# EXPORT THESE FIRST
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

This is a new feature in Arthor 3.0 and is currently beta (January 2020). See section 2.4 in the manual As explained in the manual, "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.

Since Arthor requires CentOS 7, as of January 2020 we have 6 servers that are capable of running Arthor with Round Table.

Setting up Host Server

If we want to add machines to the Round Table, for example 'nun' and 'samekh', we need to edit their arthor.cfg file so that when our Local Machine passes commands these secondary servers know to perform the search they are given.

  $ cat arthor.cfg
  MaxThreadsPerSearch=4 
  AutomaticIndex=false 
  DATADIR=<Directory where smiles are located>

We then run the jar server on each of these host machines containing data on any available port.

  java -jar /nfs/ex9/work/xyz/psql/arthor-3.3-centos7/java/arthor.jar --httpPort <port>

For our local machine, the arthor.cfg file will look different.

  $ cat arthor.cfg
  [RoundTable] 
  RemoteClient=http://skynet:<port number where jar server is running>/ 
  RemoteClient=http://hal:<port number where jar server is running>/

Please refer to Section 2 in the RoundTable Documentation file (pages 6-8) for more useful information on configuration.

Then run the following command on n-1-136:

  java -jar /nfs/ex9/work/xyz/psql/arthor-3.3-centos7/java/arthor.jar --httpPort <port>

Public Arthor

CentOS 7 Machine	Port	Round Table Data Directory	Active
samekh	10.20.0.41:8000	/local2/public_arthor/	active
nun	10.20.0.40:8000	/local2/public_arthor/	active
n-9-22	10.20.9.22:8000	/export/db4/public_arthor/	active

Arthor Round Table Head

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

Arthor Round Table Nodes

CentOS 7 Machine	Port	Round Table Data Directory	Active
samekh	10.20.0.41:8008	/local2/arthor_database/	active
nun	10.20.0.40:8008	/local2/arthor_database/	active
n-1-17	10.20.1.17:8008	/local2/arthor_database/	not active
n-5-32	10.20.5.32:8008	/local2/arthor_database/	not active
n-5-33	10.20.5.33:8008	/local2/arthor_database/	not active

Arthor Local 8081 (Datasets all local to samekh/nun)

CentOS 7 Machine	Port	Round Table Data Directory	Active
samekh	10.20.0.41:8081	/local2/arthor_local_8081/	not active
nun	10.20.0.40:8081	/local2/arthor_local_8081/	not active

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;

Restarting Arthor Instance(s) Instructions

Public, Private, and SuperPrivate Arthors are all started the same way.

Public Arthor lives and runs on both samekh and nun.

Private Arthor lives and runs on samekh.

Super Private Arthor lives and runs on nun.

Instructions

• To start an instance

1. ssh into appropriate machine
2. become root
3. cat run_arthors_on_reboot.sh
4. copy and run screen command
   • Public Arthor only needs one line.
     • /usr/bin/screen -dmS public_arthor /root/screen_public_arthor.sh
   • Private and Super Private needs two lines.
     • /usr/bin/screen -dmS private_arthor /root/screen_private_arthor.sh
     • /usr/bin/screen -dmS private_arthor_rt_head /root/screen_private_round_table_head.sh

• To stop an instance

1. ssh into appropriate machine
2. become root
3. One Way
   • screen -ls
   • screen -r <instance_screen_name or instance_screen_number>
   • ctrl + C
4. Second Way
   • screen -ls, find instance name or number
   • screen -X -S <instance_screen_name or instance_screen_number> kill
   • screen -ls, to double check