Arthor Documentation for Future Developer: Difference between revisions

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(Adding new notes for building Arthor indexes and larger databases. Still in the rough draft stages)
 
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Written by Jennifer Young on December 16, 2019. Last edited January 30, 2020
== Introduction ==
[https://www.nextmovesoftware.com/downloads/arthor/documentation/Arthor.pdf Here is the link to Arthor's manual]
* Username: ucsf@nextmovesoftware.com
* Password: <Ask jjiteam@googlegroups.com>


==Install and Set Up on TomCat==
Arthor configurations and the frontend files are consolidated in '''/nfs/soft2/arthor_configs/'''.
Arthor currently runs on n-1-136, which runs CentOS Linux release 7.7.1908 (Core).  You can check the version of CentOS with the following command
    cat /etc/centos-release


Check your current version of Java with the following command:
'''/nfs/soft2/arthor_configs/start_arthor_script.sh''' can start/restart Arthor instances on respective machines.
    java -version


On n-1-136 we are running openjdk version "1.8.0_222", OpenJDK Runtime Environment (build 1.8.0_222-b10), and OpenJDK 64-Bit Server VM (build 25.222-b10, mixed mode)
Launch the script to see the options available.
If Java is not installed, install it using yum


==See this wiki page for more detailed information about installing Tomcat on our cluster==
== How To Download Arthor ==
http://wiki.docking.org/index.php/Tomcat_Installation
# Ssh to nfs-soft2 and become root. Prepare directory
#: <source> mkdir /export/soft2/arthor_configs/arthor-<version> && cd /export/soft2/arthor_configs/arthor-<version> </source>
# [https://www.nextmovesoftware.com/downloads/arthor/ 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
#: <source> wget --user ucsf@nextmovesoftware.com --password <Ask jjiteam@googlegroups.com> <link address> </source>
# Decompress the file
#* <source> tar -xvf <file_name> </source>


==Open port for Arthor==
== How To Launch Arthor For The First Time ==
In order for Arthor to be usable in the browser, the port you wish to run it on must be opened.
=== Prepare Files and Directories ===
https://www.thegeekdiary.com/how-to-open-a-ports-in-centos-rhel-7/
# Ssh to nfs-exc and become root
# Open a port in the firewall
#: <source>firewall-cmd --permanent --add-port=<port_number>/tcp
firewall-cmd --reload
</source>
# Go to Arthor Config directory
#: <source>cd /export/soft2/arthor_configs/arthor-<latest_version></source>
# Create an Arthor config file
#: <source>vim <name_of_file>.cfg</source>
#* Add these lines in the file. Check the manual for more options.
#: <source>
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
</source>
=== 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
#: <source>bash</source>
# Create a screen
#: <source>screen -S <screen_name></source>
# Prepare Arthor Config Path
#: <source>export ARTHOR_CONFIG="/nfs/soft2/arthor_configs/arthor-<version>/<name_of_config_file>.cfg"</source>
# Launch java
#: <source>java -jar -Dserver.port=<port_number> /nfs/soft2/arthor_configs/arthor-<version>/arthor-server-<version>.war</source>


===Step 1: Check Port Status===
=== Configuration Details ===
Check that the port is not open and that Apache is not showing that port.
    netstat -na | grep <port number you are checking>


    lsof -i -P |grep http
*'''DataDir''': This is the directory where the Arthor data files live.  Location where the index files will be created and loaded from.


===Step 2: Check Port Status in IP Tables===
*'''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.
    iptables-save | grep <port number you are checking>


I skipped Step 3 from the guide, because there was a lot of information in the /etc/services file and I didn't want to edit it and break something.
*'''MaxThreadsPerSearch''': The number of threads to use for both ATDB and ATFP searches


===Step 4: Open Firewall Ports===
*Set '''AutomaticIndex''' to false if you don't want new smiles files added to the data directory to be indexed automatically
I did not include the zone=public section because the stand-alone servers are usually used for private instances of Arthor and SmallWorld.
Run as root.
    firewall-cmd --add-port=<port number you are adding>/tcp --permanent


You need to reload the firewall after a change is made.
*'''AsyncHitCountMax''': The upper-bound for the number of hits to retrieve in background searches.
    firewall-cmd --reload


===Step 5: Check that port is working===
*'''Resolver''': Using Smallworld API, allows input box to take in a SMILE format and automatically draw on the board.
To check that the port is active, run.
    iptables -nL


You should see something along the lines of:
'''Check Arthor manual for more configuration options'''
    ACCEPT    tcp  --  0.0.0.0/0            0.0.0.0/0            tcp dpt:<port number you're adding> ctstate NEW,UNTRACKED


==How to run standalone Arthor instance==
== 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.


===Step 1: Use or start a bash shell===
Just use the script located at '''/nfs/home/jjg/scripts/arthor_index_script.sh''' at the directory where you stored the smiles.
You can check your default shell using
    echo $SHELL


If your default shell is csh, use
Here is the content of the script:
    bash
<source>
to start a new bash shell in the current terminal window.  Note that echo $SHELL will show you your default shell regardless of the current shell.
#!/bin/bash


===Step 2: Set your environment variables===
target="*.smi"
    export ARTHOR_DIR=/opt/nextmove/arthor/arthor-3.0-rt-beta-linux
threads='48'
    export PATH=$ARTHOR_DIR/bin/:$PATH
version="3.6.1"


Make sure the ARTHOR_DIR variable is set to the directory for the latest version of Arthor or whichever version you would like to test.
The PATH environment variable is needed if you wish to use the Arthor tools from the command line


===Step 3: Run the arthor-server.jar===
export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-$version/arthor-$version-centos8/
    java -jar /opt/nextmove/arthor/arthor-3.0-rt-beta-linux/java/arthor-server.jar --httpPort <your httpPort>
export PATH=$ARTHOR_DIR/bin/:$PATH


==Setting environment variables for TomCat Server==
for j in $target
Set the environment variables in the setenv.sh file. Note: Be sure to edit the file in the directory corresponding to the latest version of TomCat. As of December 2019, we are running 9.0.27 on n-1-136.
do
        echo 'smi2atdb -v -r -j '$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


  vim  /opt/tomcat/apache-tomcat-9.0.27/bin/setenv.sh
for i in $target*atdb
do
echo 'atdb2fp -j '$threads' '$i
        time atdb2fp -j $threads $i
chmod 744 $i.fp
done
</source>


Add the line below to the setenv.sh file above, or substitute the path to wherever you currently store the arthor.cfg file
=== Command Details ===
  export ARTHOR_CONFIG=/usr/local/tomcat/arthor.cfg
'''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


Here is an example of the arthor.cfg file:
'''smi2atfp''' creates atfp files for similarity searching
  # Arthor generated config file
  BINDIR=/opt/nextmove/arthor/arthor-2.1.2-centos7/bin
  DATADIR=/usr/local/tomcat/arthor_data
  STAGEDIR=/usr/local/arthor_data/stage
  NTHREADS=64 .
  NODEAFFINITY=true
  SearchAsYouDraw=true
  AutomaticIndex=true
  DEPICTION=./depict/bot/svg?w=%w&h=%h&svgunits=px&smi=%s&zoom=0.8&sma=%m&smalim=1
  RESOLVER=


'''Important parts of the arthor.cfg file'''
==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
#: <source>firewall-cmd --permanent --add-port=<port_number>/tcp
firewall-cmd --reload
</source>
# Go to Arthor Config Directory
#: <source>cd /export/soft2/arthor_configs/arthor-<version></source>
# Create Round Table Head configuration file. Here is an example:
# <source>
[RoundTable]
RemoteClient=http://10.20.0.41:8008
RemoteClient=http://10.20.5.19:8008
Resolver=https://sw.docking.org/util/smi2mol?smi=%s
</source>
# 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
#: <source>bash</source>
# Create a screen
#: <source>screen -S <screen_name></source>
# Prepare Arthor Config Path
#: <source>export ARTHOR_CONFIG="/nfs/soft2/arthor_configs/arthor-<version>/<round_table_head>.cfg"</source>
# Launch java
#: <source>java -jar /nfs/soft2/arthor_configs/arthor-<version>/arthor-<version>-centos7/java/arthor.jar --httpPort=<port_number></source>
 
== Active Arthor Instances ==
===Public Arthor===
{| class="wikitable"
|-
! Rocky Linux Machine
! Port
! Round Table Data Directory
! Which Arthor
|-
| arthor
| 10.20.200.100:8080
| /local3/public_arthor/
| Public Arthor
|-
|}
 
===Private Arthor===
{| class="wikitable"
|-
! Rocky Linux Machine
! Port
! Round Table Data Directory
! Which Arthor
|-
| arthor
| 10.20.200.100:8081
| /local3/private_arthor/
| Private Arthor
|-
|}
 
===Super Private Arthor===
{| class="wikitable"
|-
! CentOS 7 Machine
! Port
! Round Table Data Directory
! Which Arthor
|-
| nun
| 10.20.0.40:8080
| Round table head has no directory
| Super Private Arthor Round Table Head Node
|-
| nun
| 10.20.0.40:8008
| /local2/public_arthor/
| Super Private Arthor Database Node
|-
| samekh
| 10.20.0.41:8008
| /local2/public_arthor/
| Super Private Arthor Database Node
|-
|}
 
===Arthor BB and CC===
{| class="wikitable"
|-
! 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
|-
|}
 
== Customizing Arthor Frontend To Our Needs (Arthor 3.6.1) ==
'''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
 
Summary of changes in sketcher.js:
*Input box should be updated as user draws molecule


'''BINDIR''' is the location of the Arthor command line binaries. These are used to generate the Arthor index files and to perform searches directly on n-1-136. An example of this would be using atdbgrep for substructure search.
Summary of changes in arthor-swagger.yaml.js:
*Input box should be updated as user draws molecule


'''DATADIR''' This is the directory where the Arthor data files live.  Location where the index files will be created and loaded from.


'''STAGEDIR''' Location where the index files will be built before being moved into the DATADIR.
=== Install Prerequisite Packages ===
# Install Apache Maven
#* <source>dnf install maven -y</source>
# Install Node Package Manager (NPM)
#* <source>dnf install npm -y</source>
# In your home directory, create a new directory to hold the files for the upcoming procedures
#* <source>mkdir /mnt/nfs/home/jjg/arthor_build_from_source</source>
# Download these latest Arthors and store them in 'arthor_build_from_source/'. [[Arthor Documentation for Future Developer#How To Download Arthor|Here's how to download Arthor.]]
#* arthor-3.6.1-source.tar.gz
#* arthor-3.6.1-centos7.tar.gz
# Extract contents from the tar.gz files
#* <source>tar -xvf arthor-3.6.1-source.tar.gz
tar -xvf arthor-3.6.1-centos7.tar.gz</source>
# Install Apache Maven Arthor dependencies through this script
#* <source>
#!/bin/bash


'''NTHREADS''' The number of threads to use for both ATDB and ATFP searches
export ARTHOR_DIR=/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1-centos8/java
export OS=linux
export VERSION=3.6.1


Set '''AutomaticIndex''' to false if you don't want new smiles files added to the data directory to be indexed automatically
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
</source>
=== Customizing Index.html ===
Location: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-source/server/src/main/webapp/WEB-INF/static/index.html


==Building Arthor Indexes==
==== Add contact info and tldr ====
# vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-source/server/src/main/webapp/WEB-INF/static/index.html
# Search for 'arthor_table_list'
#* <source>?arthor_table_list</source>
# 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
#* <source>
      <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>
</source>


===Checking Memory Usage===
==== Add Database Information Link ====
Before building arthor indexes, it's always a good thing to check what percent of the memory is being used. Try to be cautious with how much memory you have left, and make sure to check while building indexes to make sure that you have enough space. To check, run the following command:


  df -h /<directory with disc>


===Downloading Arthor and RoundTable documentation====
==== Remove Similarity and Formula Buttons ====
# vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-source/server/src/main/webapp/WEB-INF/static/index.html
# Search for 'arthor_search_list'
#* <source> ?arthor_search_list </source>
# Delete and Replace the whole 'ul' element block with this
#* <source>
          <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>-->
</source>


===Building Arthor Indexes===
=== Customize Index.js ===
Location /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1-source/server-ui/src/index.js


===Search Queries===
# Add the zinc20 hyperlink to the Arthor results. Search for this
#* <source>
"<b>" + id + "</b>"
</source>
# Delete the contents of the whole else block and replace it with this
#* <source>
            if (id.substring(0, 6) == "ZINC00") {
                $info.append(
                  $('<tr>').append(
                    $('<td>').append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>",
                                    "<span class='table_name'>" + table_name + "</span>")));
            } else if (id.substring(0,4) == "ZINC" && id.substring(4,6) != "00") {
                $info.append(
                  $('<tr>').append(
                    $('<td>').append("<b><a target='_blank' href='https://cartblanche22.docking.org/substance/"+id+"'>" + id + "</a></b>",
                                    "<span class='table_name'>" + table_name + "</span>")));
            } else {
                $info.append(
                  $('<tr>').append(
                    $('<td>').append("<b>" + id + "</b>")));
            }
</source>


===Uploading Indexes to the Web Application===
=== Customize Sketcher.js ===
Location: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1-source/server-ui/src/sketcher.js


==== Input Box Updates as User Draws ====
#vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1-source/server-ui/src/sketcher.js
#Search for this line "var smiles = event.src.smiles();"
#* <source>?var smiles = event.src.smiles();</source>
#Add this new line below it
#* <source>$('#ar_text_input').val(smiles);</source>


==Building Large Databases==
=== Customize arthor-swagger.yaml ===
At the moment, we are building databases of size 500M molecules by merging smile files. There are multiple methods of trying to create large databases, one being merging based off of the same H?? prefix and stopping once the database reaches > 500M molecules (or whatever upperbound you want to use). Here is some python code that simulates this merging process. Essentially the program takes all of the .smi files within an input directory, sorts them lexiographically, and begins merging these .smi files together in order until the size reaches > 500M molecules.
Location: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-source/server/src/main/webapp/WEB-INF/static/swagger/arthor-swagger.yaml
 
Feel free to modify it if you think a better method exists.
 
  import subprocess
  import sys
  import os                                                                                                                                                                         
 
  from os import listdir
  from os.path import isfile, join
 
  mypath = "<Path to directory holding .smi files>"
  onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]
  onlyfiles.sort()
 
  create_fp = True
  cur_mols = 0
  lower_bound = 450000000
  upper_bound = 500000000
  files_to_merge = []
 
  def merge_files(f_t_m):
      arr = f_t_m[0].split(".")
      arr2 = f_t_m[len(f_t_m) - 1].split(".")
      file_name_merge = (arr[0] + "_" + arr2[0] + ".smi")
      print ("File being created: " + file_name_merge)
 
      for file in f_t_m:
        tmp = file.split(".")
        process = subprocess.Popen("cat " + join(mypath, file) + " >> " + file_name_merge, shell=True)
        process.wait()
 
  for file in onlyfiles:
      arr = file.split(".")
 
      if (arr[len(arr) - 1] == "smi"):
        print("Working with " + file)
        mol = sum(1 for line in open(join(mypath, file)))
        print(file, mol, cur_mols)
 
        if (cur_mols + mol > lower_bound):
            if (cur_mols + mol < upper_bound):
              files_to_merge.append(file)
              merge_files(files_to_merge)
              cur_mols = 0
              files_to_merge.clear()
            else:
              merge_files(files_to_merge)
              files_to_merge.clear()
              files_to_merge.append(file)
              merge_files(files_to_merge)
              cur_mols = 0
              files_to_merge.clear()
        else:
            cur_mols += mol
            files_to_merge.append(file)
 
  if (len(files_to_merge) != 0):
      merge_files(files_to_merge)


==Setting up Round Table==
==== Change URL Base Path for API Call ====
This is a new feature in Arthor 3.0 and is currently beta (January 2020). See section 2.4 in the manual
# vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-source/server/src/main/webapp/WEB-INF/static/swagger/arthor-swagger.yaml
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.
# Search for "servers"
#* <source>?basePath</source>
# Remove "/arthor" and keep argument empty
 
=== Compile/Minify Code through NPM ===
# Install NPM packages and Minify Code
#* <source>
cd /nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-source/server-ui
npm install
npx webpack-dev-server
npx webpack --mode=production
</source>
# If the npx commands don't work, try updating node and npm version to the latest one.
# Build the war file
#* <source>
cd /nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-source/server
mvn install -Pbootable
</source>
# If it works, then the path to new war file is at /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.4.7/arthor-3.4.7-source/server/target/arthor-server-3.4.7.war
 
== Adding Arthor to Systemd (example) ==
# Create service files
#: <source>
touch /etc/systemd/system/arthor.service
</source>
# Add this code block in the service file
#: <source>
 
[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 -public
ExecStop=/bin/kill -15 $MAINPID
 
[Install]
WantedBy=multi-user.target
</source>
# Change "ExecStart" to other Arthor Instances
 
== Restarting Arthor Instance(s) Instructions ==
=== Public and Private Arthor ===
# ssh to "arthor" server and run
#: <source>
systemctl <start|stop|restart> <arthor|arthorp>
</source>


Since Arthor requires CentOS 7, as of January 2020 we have 6 servers that are capable of running Arthor with Round Table.  See the table below for the machines currently involved in Round Table
=== ArthorBB, ArthorCC, and ArthorCovalent ===
{| class="wikitable"
# ssh to "epyc-a40" server and run
|-
#: <source>
! CentOS 7 Machine
systemctl <start|stop|restart> <arthorbb|arthorcc|arthorcovalent>
! Private IP
</source>
! Arthor Install Location
! Round Table Data Directory
|-
| n-1-136
| 10.20.10.136
| /opt/nextmove/arthor/arthor-3.0-rt-beta-linux
| N/A. Round Table Server
|-
| abacus
| 10.20.0.5
| /opt/nextmove/arthor/arthor-3.0-rt-beta-linux
| /export/db2/arthor_round_table_abacus
|-
| shin
| 10.20.0.1
| /opt/nextmove/arthor/arthor-3.0-rt-beta-linux
| /export/db/arthor
|-
| zayin
| 10.20.0.2
| /opt/nextmove/arthor/arthor-3.0-rt-beta-linux
| /export/exa/work/jyoung/arthor_round_table_zayin
|-
| qof
| 10.20.9.29
| /opt/nextmove/arthor/arthor-3.0-rt-beta-linux
| /export/ex9/work/jyoung/arthor_data_qof/data
|-
| lamed
| 10.20.9.15
| /opt/nextmove/arthor/arthor-3.0-rt-beta-linux
| /export/ex6/work/jyoung
|-
|}


/opt/nextmove/arthor/arthor-3.0-rt-beta-linux
=== Super Private Arthor ===
# Ssh to machine with respective Arthor instance and become root
# execute '''run_arthors_on_reboot.sh''' to show restart all instances on the machine
#: <source>
bash /root/run_arthors_on_reboot.sh
</source>
# execute '''start_arthor_script.sh''' to restart specific Arthor instance. It will show you options to choose from.
#: <source>
bash /nfs/soft2/arthor_configs/start_arthor_script.sh
</source>

Latest revision as of 22:22, 19 March 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

  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

CentOS 7 Machine Port Round Table Data Directory Which Arthor
nun 10.20.0.40:8080 Round table head has no directory Super Private Arthor Round Table Head Node
nun 10.20.0.40:8008 /local2/public_arthor/ Super Private Arthor Database Node
samekh 10.20.0.41:8008 /local2/public_arthor/ Super Private Arthor Database Node

Arthor BB and CC

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

Customizing Arthor Frontend To Our Needs (Arthor 3.6.1)

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

Summary of changes in sketcher.js:

  • Input box should be updated as user draws molecule

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

  • Input box should be updated as user draws molecule


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-3.6.1-source.tar.gz
    • arthor-3.6.1-centos7.tar.gz
  5. Extract contents from the tar.gz files
    • tar -xvf arthor-3.6.1-source.tar.gz
      tar -xvf arthor-3.6.1-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-3.6.1-centos8/java
      export OS=linux
      export VERSION=3.6.1
      
      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-3.6.1/arthor-3.6.1-source/server/src/main/webapp/WEB-INF/static/index.html

Add contact info and tldr

  1. vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-source/server/src/main/webapp/WEB-INF/static/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>

Add Database Information Link

Remove Similarity and Formula Buttons

  1. vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1/arthor-3.6.1-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

Location /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1-source/server-ui/src/index.js

  1. Add the zinc20 hyperlink to the Arthor results. Search for this
    • "<b>" + id + "</b>"
  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>').append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>",
                                           "<span class='table_name'>" + table_name + "</span>")));
                  } else if (id.substring(0,4) == "ZINC" && id.substring(4,6) != "00") {
                      $info.append(
                        $('<tr>').append(
                          $('<td>').append("<b><a target='_blank' href='https://cartblanche22.docking.org/substance/"+id+"'>" + id + "</a></b>",
                                           "<span class='table_name'>" + table_name + "</span>")));
                  } else {
                      $info.append(
                        $('<tr>').append(
                          $('<td>').append("<b>" + id + "</b>")));
                  }

Customize Sketcher.js

Location: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1-source/server-ui/src/sketcher.js

Input Box Updates as User Draws

  1. vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-3.6.1-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-3.6.1/arthor-3.6.1-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-3.6.1/arthor-3.6.1-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-3.6.1/arthor-3.6.1-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-3.6.1/arthor-3.6.1-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-3.4.7/arthor-3.4.7-source/server/target/arthor-server-3.4.7.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 -public
    ExecStop=/bin/kill -15 $MAINPID
    
    [Install]
    WantedBy=multi-user.target
  3. Change "ExecStart" to other Arthor Instances

Restarting Arthor Instance(s) Instructions

Public and Private Arthor

  1. ssh to "arthor" server and run
    systemctl <start|stop|restart> <arthor|arthorp>

ArthorBB, ArthorCC, and ArthorCovalent

  1. ssh to "epyc-a40" server and run
    systemctl <start|stop|restart> <arthorbb|arthorcc|arthorcovalent>

Super Private Arthor

  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