How to Use SWAG - Revision history

Zdingman at 19:44, 6 May 2026

2026-05-06T19:44:21Z

← Older revision		Revision as of 19:44, 6 May 2026
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	https://www.nextmovesoftware.com/downloads/smallworld/documentation/		https://www.nextmovesoftware.com/downloads/smallworld/documentation/

	[[Category:Smallworld]]		[[Category:Smallworld]] [[Category:SWAG]]

Zdingman: Added link to analog filtering page.

2026-03-14T00:58:45Z

Added link to analog filtering page.

← Older revision		Revision as of 00:58, 14 March 2026
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	* local: Checks the current directory for a local mapfile called 'local.anon.map'		* local: Checks the current directory for a local mapfile called 'local.anon.map'

	Unlike the first four databases that refer to existing databases, specifying 'local' will search the current working directory for a map file. This is useful if you have a specific list of molecules that you want to search within. For example, you can search your top million docking vActives to find close analogs of your selected hits, or search a list of compounds from Infinisee/xREAL to find analogs by edit distance.		Unlike the first four databases that refer to existing databases, specifying 'local' will search the current working directory for a map file. This is useful if you have a specific list of molecules that you want to search within. For example, you can search your top million docking vActives to find close analogs of your selected hits, or search a list of compounds from Infinisee/xREAL to find analogs by edit distance. You can read more at [[Using SWAG to filter analogs by Graph Edit Distance]].

	[~~An easy way for creating map files will be covered in a not-yet-written wiki page~~.]

	== Advanced Usage ==		== Advanced Usage ==

Zdingman at 20:39, 23 January 2026

2026-01-23T20:39:49Z

← Older revision		Revision as of 20:39, 23 January 2026
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	== Usage Instructions ==		== Usage Instructions ==

	SWAG ~~can~~ be run in a working directory ~~with~~ the following commands:		SWAG must be run on one either epyc/epyc2, and will not run on gimel/gimel2/etc. To run SWAG in a working directory, use the following commands:

	source /nfs/home/zdingman/environments/SWAG/bin/activate		source /nfs/home/zdingman/environments/SWAG/bin/activate

Zdingman at 04:49, 22 January 2026

2026-01-22T04:49:40Z

← Older revision		Revision as of 04:49, 22 January 2026
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	SWAG is a python interface for the ~~[[Category:Smallworld\|~~SmallWorld chemical database search tool]], enabling users to submit a list of SMILES formatted molecules for exhaustive analog searching.		SWAG is a python interface for the SmallWorld chemical database search tool, enabling users to submit a list of SMILES formatted molecules for exhaustive analog searching.

	SWAG produces two output files: output_ascores.csv and output_responses.csv. The first file contains each query molecule from the input, as well as the corresponding number of analogs found within the database. The second file lists every analog found for every query molecule, and includes the SMILES, name, and edit distance.		SWAG produces two output files: output_ascores.csv and output_responses.csv. The first file contains each query molecule from the input, as well as the corresponding number of analogs found within the database. The second file lists every analog found for every query molecule, and includes the SMILES, name, and edit distance.
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	For further details on SmallWorld, please see the official documentation:		For further details on SmallWorld, please see the official documentation:
	https://www.nextmovesoftware.com/downloads/smallworld/documentation/		https://www.nextmovesoftware.com/downloads/smallworld/documentation/

			[[Category:Smallworld]]

Zdingman: Created page. Documentation based on that in README.txt

2026-01-22T04:44:21Z

Created page. Documentation based on that in README.txt

New page

SWAG is a python interface for the [[Category:Smallworld|SmallWorld chemical database search tool]], enabling users to submit a list of SMILES formatted molecules for exhaustive analog searching.

SWAG produces two output files: output_ascores.csv and output_responses.csv. The first file contains each query molecule from the input, as well as the corresponding number of analogs found within the database. The second file lists every analog found for every query molecule, and includes the SMILES, name, and edit distance.

== Usage Instructions ==

SWAG can be run in a working directory with the following commands:

source /nfs/home/zdingman/environments/SWAG/bin/activate
cp /nfs/home/zdingman/scripts/SWAG_v1-3-1/* .
python SWAG.py [arguments]

SWAG has several requirements that must be specified at run time. These are:

* The input smiles file, given with -f [YOUR_INPUT.smi]
* The prefix for output files, given with -o [YOUR_OUTPUT]
* The database for querying, given with -d [DATABASE_NAME]
* The maximum distance, given with -p [NUMBER]

If we wanted to find all the compounds in ZINC22, within 4 edits of the compounds listed in our file ligands.smi, we would run the following command:
python SWAG.py -f ligands.smi -o ligands -d ZINC22 -p [4]

== Database Selection ==

The databases used by SmallWorld are (in most cases) pre-computed by the Irwin lab for our usage, and are hard-coded into the python environment we source. The following are available to query with SWAG:

* 480K: 480 thousand building blocks from ChemSpace
* Accessible-BB: 94 million building blocks from ChemSpace + Enamine FastMADE
* REAL: 70 billion compounds from 2024 Enamine REAL Space
* ZINC22: 96 billion commercial compounds listed in ZINC22
* local: Checks the current directory for a local mapfile called 'local.anon.map'

Unlike the first four databases that refer to existing databases, specifying 'local' will search the current working directory for a map file. This is useful if you have a specific list of molecules that you want to search within. For example, you can search your top million docking vActives to find close analogs of your selected hits, or search a list of compounds from Infinisee/xREAL to find analogs by edit distance.

[An easy way for creating map files will be covered in a not-yet-written wiki page.]

== Advanced Usage ==

By default, SWAG takes a single integer value for the distance parameter. However, you can also pass a list of 7 integers instead as [d,d,d,d,d,d,d] which corresponds to the maximum allowed number of edits for each of the following:

* Maximum distance
* Ring count additions
* Ring count removals
* Linker length additions
* Linker length removals
* Terminal group additions
* Terminal group removals

SmallWorld will return similar compounds, beginning with the fewest number of ring/linker/terminal modifications, up to the maximum distance specified for both specific changes and overall distance.

Additional runtime flags are as follows:

--skipInputStandardization

--includeStereo

--excludeStereo

--storeQueryTime

By default, input SMILES are converted to the uncharged parent version of their largest species. Recommended to use input standardization. Otherwise, similar molecules may not be found due to differing counterions or protonation state.

By default, results found from SWAG will count differing stereoisomers as different compounds. If you would like to treat all stereoisomers as a single compound and remove them from the output, use the excludeStereo flag.

By default, SWAG does not write the per-query search time. If you would like to output the max_dist and query_time to ascores.csv, use the storeQueryTime flag.

== Final Notes ==

SWAG is built using the Cython wrapper for the SmallWorld C++ API, which relies on the gnu c compiler (GCC) to run. If running SWAG.py returns "ImportError: CXXABI_1.3.9 not found" then you must use a machine with an updated GCC version. On the Shoichet cluster, these machines are epyc and epyc2.

For further details on SmallWorld, please see the official documentation:
https://www.nextmovesoftware.com/downloads/smallworld/documentation/