SmallWorld Documentation for Future Developer - Revision history

Jgutierrez6: /* Update Smallworld Start Script */

2026-02-03T22:46:17Z

Update Smallworld Start Script

← Older revision		Revision as of 22:46, 3 February 2026
Line 295:		Line 295:

	= Update Smallworld Start Script =		= Update Smallworld Start Script =
	Become Root on abacus. The script that the daemon uses is located in ~~```~~/root/start_smallworld_service.sh~~```.~~		Become Root on abacus. The script that the daemon uses is located in
			<source>
			/root/start_smallworld_service.sh
			</source>

	[[Category:Smallworld]]		[[Category:Smallworld]]
	[[Category:Developer]]		[[Category:Developer]]

Jgutierrez6 at 22:45, 3 February 2026

2026-02-03T22:45:50Z

← Older revision		Revision as of 22:45, 3 February 2026
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	</source>		</source>

			= Update Smallworld Start Script =
			Become Root on abacus. The script that the daemon uses is located in ```/root/start_smallworld_service.sh```.

	[[Category:Smallworld]]		[[Category:Smallworld]]
	[[Category:Developer]]		[[Category:Developer]]

Jgutierrez6: /* Start Smallworld Instance */

2024-12-10T20:43:50Z

Start Smallworld Instance

← Older revision		Revision as of 20:43, 10 December 2024
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	#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 ==		== Start Smallworld Instance ==
	~~# Go to smallworld extract directory~~
	~~#: <source>cd /export/db3/smallworld_extract</source>~~
	# Create a screen		# Create a screen
	#: <source>screen -S <screen_name></source>		#: <source>screen -S <screen_name></source>
	# Export the smallworld directory you've made		# Export the smallworld directory you've made
	#: <source>export SWDIR=/export/~~db3~~/<smallworld_dir></source>		#: <source>export SWDIR=/export/db5/<smallworld_dir></source>
	# Launch java		# Launch java
	#: <source>java -jar ~~/opt/nextmove~~/smallworld-<version>/sw-ws-<version>.~~jar --httpPort=<port_number>~~</source>		#: <source>java -jar -Dserver.port=9999 sw_source/smallworld-<version>/sw-ws-<version>.war</source>

	= How to Build Smallworld Maps/Databases =		= How to Build Smallworld Maps/Databases =

Jgutierrez6: /* Copy SMILES of Hits */

2024-06-25T00:57:20Z

Copy SMILES of Hits

← Older revision		Revision as of 00:57, 25 June 2024
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	# Add this line at the end of the appends		# Add this line at the end of the appends
	#: <source>		#: <source>
	.append('<br/><a href="#" onclick="copySmiles(\'' + get_smiles_parts(data.hitSmiles)[0] + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>');		.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>		</source>
	# It should look like this		# It should look like this

Frodo: asdf

2024-05-31T23:29:55Z

asdf

← Older revision		Revision as of 23:29, 31 May 2024
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	systemctl <start\|stop\|restart> <sw\|swp\|swc\|swbb\|swcc>		systemctl <start\|stop\|restart> <sw\|swp\|swc\|swbb\|swcc>
	</source>		</source>


			[[Category:Smallworld]]
			[[Category:Developer]]

Jgutierrez6: /* Copy SMILES of Hits */

2024-05-01T23:38:29Z

Copy SMILES of Hits

← Older revision		Revision as of 23:38, 1 May 2024
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	.append('<br/><b>MW:</b> ' + data.mw)		.append('<br/><b>MW:</b> ' + data.mw)
	.append('<br/><b>MF:</b> ' + data.mf)		.append('<br/><b>MF:</b> ' + data.mf)
	.append('<br/><a href="#" onclick="copySmiles(\'' + get_smiles_parts(data.hitSmiles)[0] + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>');		.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>		</source>
	# Then add this function anywhere except inside another function's scope		# Then add this function anywhere except inside another function's scope

Jgutierrez6: /* Customize Smallworld FrontEnd To Our Needs (Smallworld 5.5) */

2024-04-03T04:36:30Z

Customize Smallworld FrontEnd To Our Needs (Smallworld 5.5)

@@ Line 140: / Line 140: @@
 Summary of changes in swsearch.js:
 * Conditional hyperlinks attached to smallworld hits. Leads to zinc20, cartblanche22, or nothing.
 Summary of changes in search.html:
@@ Line 183: / Line 184: @@
+                 }
 </source>
 == Customizing search.html ==

Jgutierrez6: /* Restarting Smallworld Instance(s) */

2024-04-01T23:48:42Z

Restarting Smallworld Instance(s)

← Older revision		Revision as of 23:48, 1 April 2024
Line 259:		Line 259:

	= Restarting Smallworld Instance(s) =		= 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
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	#: <source>		#: <source>
	start_smallworld		start_smallworld
			</source>
			=== New Way ===
			# Ssh to abacus and become root. Then run
			#: <source>
			systemctl <start\|stop\|restart> <sw\|swp\|swc\|swbb\|swcc>
	</source>		</source>

Jgutierrez6 at 23:44, 19 January 2024

2024-01-19T23:44:44Z

← Older revision		Revision as of 23:44, 19 January 2024
Line 1:		Line 1:
	== Introduction ==		= 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
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	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 ==		= 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>
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	#* <source> tar -xvf <file_name> </source>		#* <source> tar -xvf <file_name> </source>

	== How to Launch Smallworld For The First Time ==		= How to Launch Smallworld For The First Time =
	=== Prepare Files and Directories ===		== 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
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	#* '''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 ===		== 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>
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	#: <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 ==		= How to Build Smallworld Maps/Databases =
	Consolidate smiles into '''/export/db3/temp_mapping'''.		Consolidate smiles into '''/export/db3/temp_mapping'''.

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	end		end
	</source>		</source>
	=== Command Details ===		== Command Details ==
	'''setenv''' sets the environment where the anon master map is		'''setenv''' sets the environment where the anon master map is

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	'''tee''' will log the progress of the process		'''tee''' will log the progress of the process

	=== Splitting Databases ===		== 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 ==		= Active Smallworld Instances =
	{\| class="wikitable"		{\| class="wikitable"
	\|+ Caption text		\|+ Caption text
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	\|}		\|}

	== Customize Smallworld FrontEnd To Our Needs (Smallworld 5.5) ==		= 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.'''

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	* Change API route to be just "/"		* Change API route to be just "/"

	=== Install Prerequisite Packages ===		== Install Prerequisite Packages ==
	# Install Apache Maven		# Install Apache Maven
	#* <source>dnf install maven -y</source>		#* <source>dnf install maven -y</source>
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	</source>		</source>

	=== Customizing swsearch.js ===		== 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 ====		=== 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
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	</source>		</source>

	=== Customizing search.html ===		== 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' ====		=== 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'
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	</div>		</div>
	</source>		</source>
	==== Pre-toggle Advanced Option ====		=== Pre-toggle Advanced Option ===
	# Inside the script element, add this function		# Inside the script element, add this function
	#: <source>		#: <source>
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	</source>		</source>

	==== Change API Route to "/" ====		=== Change API Route to "/" ===
	# path smallworld-java-src/web/target/sw-ws-5.6.1/WEB-INF/static/swagger/smallworld-swagger.yaml		# path smallworld-java-src/web/target/sw-ws-5.6.1/WEB-INF/static/swagger/smallworld-swagger.yaml

	=== Compile Code To Make WAR File ===		== Compile Code To Make WAR File ==
	#Build WAR File		#Build WAR File
	#: <source>		#: <source>
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	#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) ==		= Restarting Smallworld Instance(s) =
	# 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

Jgutierrez6: /* Customize Smallworld FrontEnd To Our Needs (Smallworld 5.5) */

2024-01-19T23:41:23Z

Customize Smallworld FrontEnd To Our Needs (Smallworld 5.5)

← Older revision		Revision as of 23:41, 19 January 2024
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	* Add 'Database Information' hyperlink		* Add 'Database Information' hyperlink
	* Pre-toggle Advanced Option		* Pre-toggle Advanced Option

			Summary of changes in smallworld-swagger.yaml:
			* Change API route to be just "/"

	=== Install Prerequisite Packages ===		=== Install Prerequisite Packages ===
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	onchange="$('#advPanel').css('display', $(this).prop('checked') ? 'block' : 'none'); update_visible_columns();" checked>		onchange="$('#advPanel').css('display', $(this).prop('checked') ? 'block' : 'none'); update_visible_columns();" checked>
	</source>		</source>

			==== 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 ===		=== Compile Code To Make WAR File ===