SmallWorld Documentation for Future Developer: Difference between revisions
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= Introduction = | |||
[https://www.nextmovesoftware.com/downloads/smallworld/documentation/SmallWorld.pdf Here is the link to Smallworld's manual] | [https://www.nextmovesoftware.com/downloads/smallworld/documentation/SmallWorld.pdf Here is the link to Smallworld's manual] | ||
* Username: ucsf@nextmovesoftware.com | * Username: ucsf@nextmovesoftware.com | ||
Line 10: | Line 10: | ||
Execute command '''start_smallworld''' to see options on which smallworld instance to start/restart. | Execute command '''start_smallworld''' to see options on which smallworld instance to start/restart. | ||
= How to Download Smallworld = | |||
# Ssh to abacus and become root. Prepare directory | # Ssh to abacus and become root. Prepare directory | ||
#: <source> mkdir /opt/nextmove/smallworld-<version> && cd /opt/nextmove/smallworld-<version> </source> | #: <source> mkdir /opt/nextmove/smallworld-<version> && cd /opt/nextmove/smallworld-<version> </source> | ||
Line 22: | Line 22: | ||
#* <source> tar -xvf <file_name> </source> | #* <source> tar -xvf <file_name> </source> | ||
= How to Launch Smallworld For The First Time = | |||
== Prepare Files and Directories == | |||
# Ssh to abacus and become root | # Ssh to abacus and become root | ||
# Open a port in the firewall | # Open a port in the firewall | ||
Line 72: | Line 72: | ||
#* '''SearchTimeOut''' should be the only option you'll change in the future. It caps search time to lessen strain on machine. | #* '''SearchTimeOut''' should be the only option you'll change in the future. It caps search time to lessen strain on machine. | ||
#Place any *.anon.maps you've already compiled for testing into the maps sub-directory. | #Place any *.anon.maps you've already compiled for testing into the maps sub-directory. | ||
== Start Smallworld Instance == | |||
# Go to smallworld extract directory | # Go to smallworld extract directory | ||
#: <source>cd /export/db3/smallworld_extract</source> | #: <source>cd /export/db3/smallworld_extract</source> | ||
Line 82: | Line 82: | ||
#: <source>java -jar /opt/nextmove/smallworld-<version>/sw-ws-<version>.jar --httpPort=<port_number></source> | #: <source>java -jar /opt/nextmove/smallworld-<version>/sw-ws-<version>.jar --httpPort=<port_number></source> | ||
= How to Build Smallworld Maps/Databases = | |||
Consolidate smiles into '''/export/db3/temp_mapping'''. | Consolidate smiles into '''/export/db3/temp_mapping'''. | ||
Line 103: | Line 103: | ||
end | end | ||
</source> | </source> | ||
== Command Details == | |||
'''setenv''' sets the environment where the anon master map is | '''setenv''' sets the environment where the anon master map is | ||
Line 114: | Line 114: | ||
'''tee''' will log the progress of the process | '''tee''' will log the progress of the process | ||
== Splitting Databases == | |||
[[http://wiki.docking.org/index.php/Creating_Maps_on_SmallWorld| Follow this page if John has asked you to split the database into smaller slices.]] | [[http://wiki.docking.org/index.php/Creating_Maps_on_SmallWorld| Follow this page if John has asked you to split the database into smaller slices.]] | ||
= Active Smallworld Instances = | |||
{| class="wikitable" | {| class="wikitable" | ||
|+ Caption text | |+ Caption text | ||
Line 135: | Line 135: | ||
|} | |} | ||
= Customize Smallworld FrontEnd To Our Needs (Smallworld 5.5) = | |||
'''These instructions only worked and compiled for me in the machine called epyc which is running Rocky 8 Linux operating system.''' | '''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 swsearch.js: | Summary of changes in swsearch.js: | ||
* Conditional hyperlinks attached to smallworld hits. Leads to zinc20, cartblanche22, or nothing. | * Conditional hyperlinks attached to smallworld hits. Leads to zinc20, cartblanche22, or nothing. | ||
* Adding clipboard icon to copy SMILES of hits. | |||
Summary of changes in search.html: | Summary of changes in search.html: | ||
* Add 'Ask Questions' and contact info | * Add 'Ask Questions' and contact info | ||
* Add 'Database Information' hyperlink | |||
* Pre-toggle Advanced Option | |||
Summary of changes in smallworld-swagger.yaml: | |||
* Change API route to be just "/" | |||
== Install Prerequisite Packages == | |||
# Install Apache Maven | # Install Apache Maven | ||
#* <source>dnf install maven -y</source> | #* <source>dnf install maven -y</source> | ||
Line 161: | Line 167: | ||
</source> | </source> | ||
== Customizing swsearch.js == | |||
Location: /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/js/swsearch.js | Location: /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/js/swsearch.js | ||
=== Conditional Hyperlinks === | |||
# vim /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/js/swsearch.js | # vim /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/js/swsearch.js | ||
# Search for this | # Search for this | ||
Line 173: | Line 179: | ||
div.append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>"); | div.append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>"); | ||
} else if(id.substring(0,4) == "ZINC" && id.substring(4,6) != "00") { | } else if(id.substring(0,4) == "ZINC" && id.substring(4,6) != "00") { | ||
div.append("<b><a target='_blank' href='https://cartblanche22.docking.org/ | div.append("<b><a target='_blank' href='https://cartblanche22.docking.org/substance/"+id+"'>" + id + "</a></b>"); | ||
} else { | } else { | ||
div.append("<b>" + id + "</b>"); | div.append("<b>" + id + "</b>"); | ||
} | } | ||
</source> | </source> | ||
=== Copy SMILES of Hits === | |||
# Search for this | |||
#: <source>?var $props</source> | |||
# Add this line at the end of the appends | |||
#: <source> | |||
.append('<br/><a href="#" onclick="copySmiles(\'' + get_smiles_parts(data.hitSmiles)[0] + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>'); | |||
</source> | |||
# It should look like this | |||
#: <source> | |||
var $props = $('<div>').append('<b>SWIDX:</b> ' + data.anonIdx) | |||
.append('<br/><b>MW:</b> ' + data.mw) | |||
.append('<br/><b>MF:</b> ' + data.mf) | |||
.append('<br/><b>Copy SMILES: </b><a href="#" onclick="copySmiles(\'' + get_smiles_parts(data.hitSmiles)[0] + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>'); | |||
</source> | |||
# Then add this function anywhere except inside another function's scope | |||
#: <source> | |||
function copySmiles(smiles) { | |||
navigator.clipboard.writeText(smiles); | |||
} | |||
</source> | |||
== Customizing search.html == | |||
Location: /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/search.html | Location: /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/search.html | ||
=== Add 'Ask Questions' and 'Database Information' === | |||
# vim /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/search.html | # vim /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/search.html | ||
# Search 'Scoring Methods' | # Search 'Scoring Methods' | ||
#: <source>?Scoring Methods</source> | #: <source>?Scoring Methods</source> | ||
# At the end of that big block of 'div', add | # At the end of that big block of 'div', add these: | ||
#: <source> | #: <source> | ||
<div class="section-head"> | <div class="section-head"> | ||
Line 192: | Line 218: | ||
<table class="swopt searchasyoudraw" style="width: 100%"> | <table class="swopt searchasyoudraw" style="width: 100%"> | ||
<th style="text-align: left">Email us: jjiteam@googlegroups.com</th> | <th style="text-align: left">Email us: jjiteam@googlegroups.com</th> | ||
</table> | |||
</div> | |||
<div class="section-head"> | |||
Database Descriptions | |||
<table class="swopt searchasyoudraw" style="width: 100%"> | |||
<th style="text-align: left"> | |||
<a href="https://wiki.docking.org/index.php/Smallworld_and_Arthor_Databases#Smallworld_Databases" target="_blank">Database Information Link</a> | |||
</th> | |||
</table> | </table> | ||
</div> | </div> | ||
Line 210: | Line 244: | ||
</table> | </table> | ||
</div> | </div> | ||
<div class="section-head"> | |||
Database Descriptions | |||
<table class="swopt searchasyoudraw" style="width: 100%"> | |||
<th style="text-align: left"> | |||
<a href="https://wiki.docking.org/index.php/Smallworld_and_Arthor_Databases#Smallworld_Databases" target="_blank">Database Information Link</a> | |||
</th> | |||
</table> | |||
</div> | |||
</source> | |||
=== Pre-toggle Advanced Option === | |||
# Inside the script element, add this function | |||
#: <source> | |||
window.onload = function() { | |||
$('#advPanel').css('display', $(this).prop('checked', true) && 'block'); update_visible_columns(); | |||
} | |||
</source> | |||
# Then search for "update_visible_columns" and scroll till you find the input checkbox element | |||
#:<source>?update_visible_columns</source> | |||
# In the input box element, add the checked option. Should look like this | |||
#:<source> | |||
<input name="optAdv" type="checkbox" | |||
onchange="$('#advPanel').css('display', $(this).prop('checked') ? 'block' : 'none'); update_visible_columns();" checked> | |||
</source> | </source> | ||
=== Compile Code To Make WAR File | === Change API Route to "/" === | ||
# path smallworld-java-src/web/target/sw-ws-5.6.1/WEB-INF/static/swagger/smallworld-swagger.yaml | |||
== Compile Code To Make WAR File == | |||
#Build WAR File | #Build WAR File | ||
#: <source> | #: <source> | ||
cd /nfs/home/jjg/smallworld_build_from_source/smallworld-java-src | cd /nfs/home/jjg/smallworld_build_from_source/smallworld-java-src | ||
mvn install -Pbootable | mvn install -Pbootable | ||
</source> | </source> | ||
#If it works, then the new WAR File is located at '''/mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/target/sw-ws-5.5.war''' | #If it works, then the new WAR File is located at '''/mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/target/sw-ws-5.5.war''' | ||
= Restarting Smallworld Instance(s) = | |||
=== Old Way === | |||
# Ssh to abacus and become root | # Ssh to abacus and become root | ||
# execute '''run_sw_on_reboot.sh''' to show restart all instances on the machine | # execute '''run_sw_on_reboot.sh''' to show restart all instances on the machine | ||
Line 230: | Line 290: | ||
start_smallworld | start_smallworld | ||
</source> | </source> | ||
=== New Way === | |||
== | # Ssh to abacus and become root. Then run | ||
#: <source> | |||
systemctl <start|stop|restart> <sw|swp|swc|swbb|swcc> | |||
# | |||
# | |||
< | |||
</source> | </source> |
Revision as of 23:38, 1 May 2024
Introduction
Here is the link to Smallworld's manual
- Username: ucsf@nextmovesoftware.com
- Password: <Ask jjiteam@googlegroups.com>
All smallworld databases live in abacus' db3.
Smallworld frontend files are consolidated and located at /export/db3/smallworld_extract/.extract.
Execute command start_smallworld to see options on which smallworld instance to start/restart.
How to Download Smallworld
- Ssh to abacus and become root. Prepare directory
mkdir /opt/nextmove/smallworld-<version> && cd /opt/nextmove/smallworld-<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 Smallworld For The First Time
Prepare Files and Directories
- Ssh to abacus and become root
- Open a port in the firewall
firewall-cmd --permanent --add-port=<port_number>/tcp firewall-cmd --reload
- Go to smallworld databases directory
cd /export/db3/
- Create a Smallworld directory and go to it
mkdir <smallworld_dir> && cd <smallworld_dir>
- Inside that directory, create these
- a symbolic link to the smallworld anon map
ln -s /export/db2/smallworld_anon_21Q4 anon
- a sub-directory called maps to store databases
mkdir maps
- a smallworld config file
vim smallworld.cfg
- Add this block of code inside the config file
[WebApp] DepictionUrl=./depict/svg?w=%w&h=%h&smi=%s&qry=%q&cols=%c&cmap=%m ResolverUrl=./util/smi2mol?smi=%s SearchTimeOut=5000 SearchAsYouDraw=true [Score] Name=Atom Alignment Description=Aligns and scores each hit relative to the query atom types, differences are categorised as MAJ, MIN, HYB, SUB Class=com.nmsoftware.smallworld.score.SimpleAtomAlignment EnabledByDefault=false MappingMode=EditMap [Score] Name=SMARTS Alignment Description=Treat input as SMARTS and align and score each hit relative to the query atom expressions in the input Class=com.nmsoftware.smallworld.score.SmartsAtomAlignment EnabledByDefault=false [Score] Name=ECFP4 Description=Extended Connectivity Circular Fingerprint Class=com.nmsoftware.smallworld.score.EcfpTanimoto Radius=2 EnabledByDefault=true [Score] Name=Daylight Description=Path based fingerprint Class=com.nmsoftware.smallworld.score.DaylightTanimoto EnabledByDefault=true
- SearchTimeOut should be the only option you'll change in the future. It caps search time to lessen strain on machine.
- Place any *.anon.maps you've already compiled for testing into the maps sub-directory.
Start Smallworld Instance
- Go to smallworld extract directory
cd /export/db3/smallworld_extract
- Create a screen
screen -S <screen_name>
- Export the smallworld directory you've made
export SWDIR=/export/db3/<smallworld_dir>
- Launch java
java -jar /opt/nextmove/smallworld-<version>/sw-ws-<version>.jar --httpPort=<port_number>
How to Build Smallworld Maps/Databases
Consolidate smiles into /export/db3/temp_mapping.
Use the script located in that directory called smallworld_map_script.
Here is the content of the script:
#!/bin/csh -f
setenv SWDIR /export/db3/public_smallworld_4th_gen/
alias sw 'time java -jar /opt/nextmove/smallworld-5.1/sw.jar'
set target = '*.smi'
foreach i ($target)
echo '(sw map' $i '-T tmp/ -o '${i}'.anon.map -u '${i}'.anon.unmapped) |& tee '${i}'_log'
(sw map $i -T tmp/ -o ${i}.anon.map -u ${i}.anon.unmapped) |& tee ${i}_log
echo 'sw blm -p 0.01 '${i}'.anon.map'
sw blm -p 0.01 ${i}.anon.map
end
Command Details
setenv sets the environment where the anon master map is
java -jar /opt/nextmove/smallworld-5.1/sw.jar shortened to sw via alias
map will map the smiles based on the current anon master map.
- -T stores temp files so /tmp does not get overloaded
- -o output with custom name you like
- -u will collect the unmapped molecules to send to Nextmove or to use swextend
tee will log the progress of the process
Splitting Databases
[Follow this page if John has asked you to split the database into smaller slices.]
Active Smallworld Instances
Type | URL | Machine:Port | Directory |
---|---|---|---|
Public | http://sw.docking.org/ | 10.20.0.5:5020 | /nfs/db3/public_smallworld_4th_gen |
Private | http://swp.docking.org/ | 10.20.0.5:8080 | /nfs/db3/private_smallworld_4th_gen |
Super Private | http://swc.docking.org/ | 10.20.0.5:5099 | /nfs/db3/super_private_smallworld_4th_gen |
SWBB | http://swbb.docking.org/ | 10.20.0.5:8081 | /nfs/db3/swbb_5th_gen |
SWCC | http://swcc.docking.org/ | 10.20.0.5:8082 | /nfs/db3/swcc_5th_gen |
Customize Smallworld FrontEnd To Our Needs (Smallworld 5.5)
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 swsearch.js:
- Conditional hyperlinks attached to smallworld hits. Leads to zinc20, cartblanche22, or nothing.
- Adding clipboard icon to copy SMILES of hits.
Summary of changes in search.html:
- Add 'Ask Questions' and contact info
- Add 'Database Information' hyperlink
- Pre-toggle Advanced Option
Summary of changes in smallworld-swagger.yaml:
- Change API route to be just "/"
Install Prerequisite Packages
- Install Apache Maven
dnf install maven -y
- In your home directory, create a new directory to hold the files for the upcoming procedures
mkdir /mnt/nfs/home/jjg/smallworld_build_from_source
- Download these latest Smallworlds and store them in 'smallworld_build_from_source/'. Here's how to download Smallworld.
- smallworld-java-5.5.tar.gz
- smallworld-java-src-5.5.tar.gz
- Extract contents from the tar.gz files
tar -xvf smallworld-java-5.5.tar.gz tar -xvf smallworld-java-src-5.5.tar.gz
- Install Apache Maven Smallworld Dependencies
cd /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java/lib/ bash mvn-install.sh
Customizing swsearch.js
Location: /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/js/swsearch.js
Conditional Hyperlinks
- vim /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/js/swsearch.js
- Search for this
?div.append("<b>" + id + "</b>");
- Replace the inside of the else statement with these lines of code
if (id.substring(0,6) == "ZINC00") { div.append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>"); } else if(id.substring(0,4) == "ZINC" && id.substring(4,6) != "00") { div.append("<b><a target='_blank' href='https://cartblanche22.docking.org/substance/"+id+"'>" + id + "</a></b>"); } else { div.append("<b>" + id + "</b>"); }
Copy SMILES of Hits
- Search for this
?var $props
- Add this line at the end of the appends
.append('<br/><a href="#" onclick="copySmiles(\'' + get_smiles_parts(data.hitSmiles)[0] + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>');
- It should look like this
var $props = $('<div>').append('<b>SWIDX:</b> ' + data.anonIdx) .append('<br/><b>MW:</b> ' + data.mw) .append('<br/><b>MF:</b> ' + data.mf) .append('<br/><b>Copy SMILES: </b><a href="#" onclick="copySmiles(\'' + get_smiles_parts(data.hitSmiles)[0] + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>');
- Then add this function anywhere except inside another function's scope
function copySmiles(smiles) { navigator.clipboard.writeText(smiles); }
Customizing search.html
Location: /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/search.html
Add 'Ask Questions' and 'Database Information'
- vim /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/src/main/webapp/WEB-INF/static/search.html
- Search 'Scoring Methods'
?Scoring Methods
- At the end of that big block of 'div', add these:
<div class="section-head"> Ask Questions <table class="swopt searchasyoudraw" style="width: 100%"> <th style="text-align: left">Email us: jjiteam@googlegroups.com</th> </table> </div> <div class="section-head"> Database Descriptions <table class="swopt searchasyoudraw" style="width: 100%"> <th style="text-align: left"> <a href="https://wiki.docking.org/index.php/Smallworld_and_Arthor_Databases#Smallworld_Databases" target="_blank">Database Information Link</a> </th> </table> </div>
- It should look like this
<div class="section-head"> Scoring Methods </div> <table id="swscore"> </table> </div> <div class="section-head"> Ask Questions <table class="swopt searchasyoudraw" style="width: 100%"> <th style="text-align: left">Email us: jjiteam@googlegroups.com</th> </table> </div> <div class="section-head"> Database Descriptions <table class="swopt searchasyoudraw" style="width: 100%"> <th style="text-align: left"> <a href="https://wiki.docking.org/index.php/Smallworld_and_Arthor_Databases#Smallworld_Databases" target="_blank">Database Information Link</a> </th> </table> </div>
Pre-toggle Advanced Option
- Inside the script element, add this function
window.onload = function() { $('#advPanel').css('display', $(this).prop('checked', true) && 'block'); update_visible_columns(); }
- Then search for "update_visible_columns" and scroll till you find the input checkbox element
?update_visible_columns
- In the input box element, add the checked option. Should look like this
<input name="optAdv" type="checkbox" onchange="$('#advPanel').css('display', $(this).prop('checked') ? 'block' : 'none'); update_visible_columns();" checked>
Change API Route to "/"
- path smallworld-java-src/web/target/sw-ws-5.6.1/WEB-INF/static/swagger/smallworld-swagger.yaml
Compile Code To Make WAR File
- Build WAR File
cd /nfs/home/jjg/smallworld_build_from_source/smallworld-java-src mvn install -Pbootable
- If it works, then the new WAR File is located at /mnt/nfs/home/jjg/smallworld_build_from_source/smallworld-java-src/web/target/sw-ws-5.5.war
Restarting Smallworld Instance(s)
Old Way
- Ssh to abacus and become root
- execute run_sw_on_reboot.sh to show restart all instances on the machine
bash /root/run_arthors_on_reboot.sh
- execute start_smallworld to restart specific Smallworld instance. It will show you options to choose from.
start_smallworld
New Way
- Ssh to abacus and become root. Then run
systemctl <start|stop|restart> <sw|swp|swc|swbb|swcc>