Arthor Documentation for Future Developer: Difference between revisions

Latest revision as of 20:23, 22 November 2024

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

Ssh to nfs-soft2 and become root. Prepare directory

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

Download Software with this link
- Username: ucsf@nextmovesoftware.com
- Password: <Ask jjiteam@googlegroups.com>
Go to releases. Look for smallworld-java-<version>.tar.gz and copy the link address.

Download using wget

 wget --user ucsf@nextmovesoftware.com --password <Ask jjiteam@googlegroups.com> <link address>

Decompress the file
- ```
 tar -xvf <file_name>
```

How To Launch Arthor For The First Time

Prepare Files and Directories

Ssh to nfs-exc and become root

Open a port in the firewall

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

Go to Arthor Config directory

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

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

Now ssh into a machine you wish to run an Arthor instance on and become root
Change your shell to bash if you havn't already
```
bash
```
Create a screen
```
screen -S <screen_name>
```

Prepare Arthor Config Path

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

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

Ssh to nfs-soft2 and become root

Open a port in the firewall

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

Go to Arthor Config Directory

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

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

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

Now ssh into a machine you wish to run the round table head on and become root
Change your shell to bash if you havn't already
```
bash
```
Create a screen
```
screen -S <screen_name>
```

Prepare Arthor Config Path

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

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

Install Apache Maven
- ```
dnf install maven -y
```
Install Node Package Manager (NPM)
- ```
dnf install npm -y
```
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
```
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

Extract contents from the tar.gz files

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

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

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

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?title=Arthor_Databases" target="_blank">Database Information Link</a>
      </div>

Remove Similarity and Formula Buttons

vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server-ui/src/index.html
Search for 'arthor_search_list'
```
 ?arthor_search_list
```

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

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

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

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

Search this
```
?parser
```

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>')));

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

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

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
Search for "servers"
- ```
?basePath
```
Remove "arthor" and keep argument as "/"

Compile/Minify Code through NPM

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

If the npx commands don't work, try updating node and npm version to the latest one.

Build the war file

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

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)

Create service files

touch /etc/systemd/system/arthor.service

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

Change "ExecStart" to other Arthor Instances

Restarting Arthor Instance(s) Instructions

Public, Private Arthor, and Super Private Arthor

ssh to "arthor" server and run

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

ArthorBB, ArthorCC, and ArthorCovalent

ssh to "epyc-a40" server and run

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