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>

How to run standalone Arthor instance

Step 1: Use or start a bash shell

You can check your default shell using

   echo $SHELL

If your default shell is csh, use

   bash

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.

Step 2: Set your environment variables

   export ARTHOR_DIR=/opt/nextmove/arthor/arthor-3.3-centos7
   export PATH=$ARTHOR_DIR/bin/:$PATH

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

   java -jar /opt/nextmove/arthor/arthor-3.3-centos7/java/arthor.jar --httpPort <your httpPort>

Setting environment variables for an Arthor Server

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.

  vim  /opt/tomcat/apache-tomcat-9.0.27/bin/setenv.sh

Add the line below to the setenv.sh file above, or substitute the path to wherever you currently store the arthor.cfg file

  export ARTHOR_CONFIG=/usr/local/tomcat/arthor.cfg

Here is an example of the arthor.cfg file:

  BinDir=/opt/nextmove/arthor/arthor-3.3-centos7/bin
  DataDir=/local2/arthor_local_8081/
  MaxConcurrentSearches=6
  MaxThreadsPerSearch=8
  AutomaticIndex=false
  AsyncHitCountMax=1000000
  Resolver=https://sw.docking.org/util/smi2mol?smi=%s

Configuration Details

• 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.

• 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.

Background

Before working with Arthor, it is recommended that you familiarize yourself with the Arthor documentation. Some useful pages to look at include 3-5, 22-25 and 33-39. Of course, reading everything would be the best!

Checking Disk Space Usage

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>

Building Large Databases

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.

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 = 500000000
  upper_bound = 600000000
  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)

Building Arthor Indexes

Once you've merged the .smi files together, it's time to start building the databases themselves. To do this we use the command

  smi2atdb -j 0 -p <The .smi file> <The .atdb> 

The flag "-j 0" enables parallel generation and utilizes all available processors to generate the .atdb file. The "-p" flag stores the offset position in the ATDB file. Since we're building indexes for the Web Application, you must use the "-p" flag when building indexes. Please note that the name of the .smi file should also be the name of the .atdb file. That way, the Web Application knows to use these files together and correctly display the required images. Refer to pages 33-34 in the Arthor documentation for more information.

If there are too many large .smi files and you do not want to manually build each .atdb file, you can use this python script which takes all of the .smi files in the current directory and converts them to .atdb files. Make sure to modify mypath to the directory containing the .smi files. You can change the variable "create_fp" to false if you don't want to create .atdb.fp files (refer to page 9 in the Arthor documentation).

  import subprocess
  import sys
  import os
  
  from os import listdir
  from os.path import isfile, join
  
  mypath = "<Path containing the .smi files"
  onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]
  
  create_fp = True
  
  for file in onlyfiles:
     arr = file.split(".")
  
     if (arr[len(arr) - 1] == "smi"):
        process = subprocess.Popen("/nfs/ex9/work/xyz/psql/arthor-3.3-centos7/bin/smi2atdb -j 0 -p {0} {1}.atdb".format(join(mypath, file), arr[0]), shell=True)
        process.wait()
  
        print("SUCCESS! {0}.atdb file was created!".format(arr[0]))
  
        if (create_fp):
           process = subprocess.Popen("/nfs/ex9/work/xyz/psql/arthor-3.3-centos7/bin/atdb2fp -j 0 {0}.atdb".format(arr[0]), shell=True)
           process.wait()
     
           print("SUCCESS! {0}.atdb.fp file was created!".format(arr[0]))

Uploading Indexes to the Web Application

One can upload indexes to the Web Application by changing the "DATADIR" variable in the arthor.cfg file to the directory holding the .atdb files. This is already set up on n-1-136 and n-5-34.

Virtual Memory

In addition to modifying the arthor.cfg file, virtual memory can also be used to make queries faster. There can still be More information can be found in pages 10-16 in the Arthor Documentation.

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