Arthor Documentation for Future Developer: Difference between revisions
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#* <source>$('<td>').append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>",</source> | #* <source>$('<td>').append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>",</source> | ||
==== Compile/Minify Code through NPM ==== | ==== Compile/Minify Code through NPM ==== | ||
# | # Install NPM packages and Minify Code | ||
#* <source> | |||
cd /nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server-ui | |||
npm install | |||
npx webpack-dev-server | |||
npx webpack --mode=production | |||
</source> | |||
# Build the war file | |||
#* <source> | |||
cd /nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server | |||
mvn install -Pbootable | |||
</source> | |||
# If it works, then the path to new war file is at /nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server/target | |||
== Restarting Arthor Instance(s) Instructions == | == Restarting Arthor Instance(s) Instructions == |
Revision as of 01:13, 24 September 2022
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 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
- 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
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
- 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-3.4.7-source.tar.gz
- arthor-3.4.7-centos7.tar.gz
- 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
- 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
Change download options
Summary of changes needed:
- Add download options
- Add contact info
- Advertise TLDR
- Remove buttons for Similarity and Formula
- vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server/src/main/webapp/WEB-INF/static/index.html
- Search for 'arthor_tsv_link'
?arthor_tsv_link
- 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>
- 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>
Add contact info and tldr
- vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server/src/main/webapp/WEB-INF/static/index.html
- Search for 'arthor_table_list'
?arthor_table_list
- 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>
Remove Similarity and Formula Buttons
- vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server/src/main/webapp/WEB-INF/static/index.html
- Search for 'arthor_search_list'
- ?arthor_search_list
- Delete and Replace the whole 'ul' element block with this
<ul id="arthor_search_list"> <li class="first" value="Substructure" onclick="setSearchType(this)"> Substructure </li><li value="SMARTS" onclick="setSearchType(this)" class="last"> SMARTS </li> </ul>
Customize Index.js
Location /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server-ui/src/index.js
Summary of changes needed:
- Add download options
- Hyperlink the results to zinc20
Add download option logic
- vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server-ui/src/index.js
- Comment out these lines of code
if (setDownloadLinks) setDownloadLinks(hist_limit);
let limit = arthor.config.WebApp.DefaultDownloadLimit; if (!limit) limit = 500;
- Search for 'setDownloadLinks(limit)', both the function call and the function call argument, and remove the argument 'limit'.
?setDownloadLinks(limit)
- As for the function, add all the logic for the download sizes
function setDownloadLinks() { //100 Download Size var limit = 100; var params = $.param({ query: arthor.query, type: arthor.type, draw: 0, start: 0, length: limit, flags: arthor.flags }); var base_url = arthor.url + '/dt/' + normTableNames(arthor.table) + '/search'; $('#arthor_sdf_link_100').attr('href', base_url + '?fmt=sdf&' + params); $('#arthor_tsv_link_100').attr('href', base_url + '?fmt=tsv&' + params); $('#arthor_csv_link_100').attr('href', base_url + '?fmt=csv&' + params); //1k Download Size var limit = 1000; var params = $.param({ query: arthor.query, type: arthor.type, draw: 0, start: 0, length: limit, flags: arthor.flags }); var base_url = arthor.url + '/dt/' + normTableNames(arthor.table) + '/search'; $('#arthor_sdf_link_1k').attr('href', base_url + '?fmt=sdf&' + params); $('#arthor_tsv_link_1k').attr('href', base_url + '?fmt=tsv&' + params); $('#arthor_csv_link_1k').attr('href', base_url + '?fmt=csv&' + params); //10k Download Size var limit = 10000; var params = $.param({ query: arthor.query, type: arthor.type, draw: 0, start: 0, length: limit, flags: arthor.flags }); var base_url = arthor.url + '/dt/' + normTableNames(arthor.table) + '/search'; $('#arthor_sdf_link_10k').attr('href', base_url + '?fmt=sdf&' + params); $('#arthor_tsv_link_10k').attr('href', base_url + '?fmt=tsv&' + params); $('#arthor_csv_link_10k').attr('href', base_url + '?fmt=csv&' + params); //100k Download Size var limit = 100000; var params = $.param({ query: arthor.query, type: arthor.type, draw: 0, start: 0, length: limit, flags: arthor.flags }); var base_url = arthor.url + '/dt/' + normTableNames(arthor.table) + '/search'; $('#arthor_sdf_link_100k').attr('href', base_url + '?fmt=sdf&' + params); $('#arthor_tsv_link_100k').attr('href', base_url + '?fmt=tsv&' + params); $('#arthor_csv_link_100k').attr('href', base_url + '?fmt=csv&' + params); //200k Download Size var limit = 200000; var params = $.param({ query: arthor.query, type: arthor.type, draw: 0, start: 0, length: limit, flags: arthor.flags }); var base_url = arthor.url + '/dt/' + normTableNames(arthor.table) + '/search'; $('#arthor_sdf_link_200k').attr('href', base_url + '?fmt=sdf&' + params); $('#arthor_tsv_link_200k').attr('href', base_url + '?fmt=tsv&' + params); $('#arthor_csv_link_200k').attr('href', base_url + '?fmt=csv&' + params); //300k Download Size var limit = 300000; var params = $.param({ query: arthor.query, type: arthor.type, draw: 0, start: 0, length: limit, flags: arthor.flags }); var base_url = arthor.url + '/dt/' + normTableNames(arthor.table) + '/search'; $('#arthor_sdf_link_300k').attr('href', base_url + '?fmt=sdf&' + params); $('#arthor_tsv_link_300k').attr('href', base_url + '?fmt=tsv&' + params); $('#arthor_csv_link_300k').attr('href', base_url + '?fmt=csv&' + params); /* var params = $.param({ query: arthor.query, type: arthor.type, draw: 0, start: 0, length: limit, flags: arthor.flags }); var base_url = arthor.url + '/dt/' + normTableNames(arthor.table) + '/search'; $('#arthor_sdf_link').attr('href', base_url + '?fmt=sdf&' + params); $('#arthor_tsv_link').attr('href', base_url + '?fmt=tsv&' + params); $('#arthor_csv_link').attr('href', base_url + '?fmt=csv&' + params); */ }
- Lastly, add the zinc20 hyperlink to the Arthor results. Search for this
"<b>" + id + "</b>"
- Delete that whole line and replace it with this
$('<td>').append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>",
Compile/Minify Code through NPM
- Install NPM packages and Minify Code
cd /nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server-ui npm install npx webpack-dev-server npx webpack --mode=production
- Build the war file
cd /nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server mvn install -Pbootable
- If it works, then the path to new war file is at /nfs/home/jjg/arthor_build_from_source/arthor-3.4.7-source/server/target
Restarting Arthor Instance(s) Instructions
- Ssh to machine with respective Arthor instance and become root
- execute run_arthors_on_reboot.sh to show restart all instances on the machine
bash /root/run_arthors_on_reboot.sh
- 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