DISI - Recent changes [en]

Cluster 7:Libraries

Frodo — Wed, 13 May 2026 19:59:49 GMT

30B under HAC30 (4): asdf

← Older revision		Revision as of 19:59, 13 May 2026
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	\|}		\|}

	== Fvn ~~QQQ~~ (3) ==		== FS5 Fvn (4) ==

	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
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	\|-		\|-
	\| FS5_F5fvn_H30_34.smi \|\| 10 B \|\| 9B \|\| XXXM. ()		\| FS5_F5fvn_H30_34.smi \|\| 10 B \|\| 9B \|\| XXXM. ()
			\|-
			\| FS5_F5fvn_H35_39.smi \|\| 1 B \|\| 900M \|\| 1.086B ( 770M unique)
			\|-
			\| FS5_F5fvn_H40_72.smi \|\| 1 B \|\| 900M \|\| 1.201B (955M unique)
			\|-
			\| Total (expected) \|\| 5 B \|\|
			\|}

			== FS5 - 30B under HAC30 (4) ==

			{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped->arthor (%unique)
			\|-
			\| fs5a_H10_23 \|\| 100 B \|\| 90.9B (80.1) \|\| 19.1M (12.5M unique)
			\|-
			\| fs5a_H24 \|\| 10 B \|\| 9B \|\| XXXM. ()
	\|-		\|-
	\| FS5_F5fvn_H35_39.smi \|\| 1 B \|\| 900M \|\| 1.086B ( 770M unique)		\| FS5_F5fvn_H35_39.smi \|\| 1 B \|\| 900M \|\| 1.086B ( 770M unique)

Group Meeting

Yvonne Munchua — Wed, 13 May 2026 17:50:26 GMT

MEETING SCHEDULE

← Older revision		Revision as of 17:50, 13 May 2026
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	*5/1/26: Joe Pepe
	*5/8/26: NO lab mtg (BKS out)
	*5/15/26 NO lab mtg (BKS out)		*5/15/26 NO lab mtg (BKS out)
	*5/22/26: Andrii Kyrylchuk		*5/22/26: Andrii Kyrylchuk
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			*6/5/26: Katie Holland
			*6/12/26: Brian Dick
			*6/19/26: NO lab mtg (UC Holiday - Juneteenth)
			*6/26/26: Weixiu Xu


Line 52:		Line 54:
	*Andrii Kyrylchuk		*Andrii Kyrylchuk
	*Katie Holland		*Katie Holland
			*Brian Dick (Schedule on June 12 = Last day in lab is June 15, 2026)
	*Weixiu Xu (Start Date: 2/2/26)		*Weixiu Xu (Start Date: 2/2/26)
	*Brian Dick (Schedule on June 12 = Last day in lab is June 15, 2026)
	*Jongbin Kim		*Jongbin Kim
	*Zoey Dingman		*Zoey Dingman

Filter xREAL by Heavy Atom Count

Zdingman — Tue, 12 May 2026 22:29:18 GMT

updated path

← Older revision		Revision as of 22:29, 12 May 2026
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	1. Copy the script to your working directory, and make a log dir:		1. Copy the script to your working directory, and make a log dir:
	cd /wynton/group/bks/work/zdingman/GAT1/zwitterion_scripts/HAC_filter_xREAL.sh .		cd /wynton/group/bks/work/zdingman/GAT1/zwitterion_scratch/zwitterion_scripts/HAC_filter_xREAL.sh .
	mkdir logs		mkdir logs
	2. Modify the header variables defined in the header: ''HACMIN'', ''HACMAX'', ''outpath''. (When xREAL inevitably changes locations, modify ''inpath'' as well.		2. Modify the header variables defined in the header: ''HACMIN'', ''HACMAX'', ''outpath''. (When xREAL inevitably changes locations, modify ''inpath'' as well.

Group Meeting

Yvonne Munchua — Tue, 12 May 2026 19:50:41 GMT

MEETING SCHEDULE

← Older revision		Revision as of 19:50, 12 May 2026
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	*5/1/26: Joe Pepe		*5/1/26: Joe Pepe
	*5/8/26: NO lab mtg (BKS out)		*5/8/26: NO lab mtg (BKS out)
	*5/15/26 ~~Andrii Kyrylchuk~~		*5/15/26 NO lab mtg (BKS out)
	*5/22/26: ~~Katie Holland~~		*5/22/26: Andrii Kyrylchuk
	*5/29/26: NO lab mtg (BKS out)		*5/29/26: NO lab mtg (BKS out)

Cluster 7:Libraries

Frodo — Tue, 12 May 2026 06:06:24 GMT

REAL M HAC 05-29: asdf

← Older revision		Revision as of 06:06, 12 May 2026
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	\| M_H27.smi \|\| 7.522B \|\| 7.412B (99.8%) \|\| 110.8M (13.4M unique)		\| M_H27.smi \|\| 7.522B \|\| 7.412B (99.8%) \|\| 110.8M (13.4M unique)
	\|-		\|-
	\| M_H28.smi \|\| 8.079B \|\| 7.99B?? \|\| 10.1M (~~552K~~ unique)		\| M_H28.smi \|\| 8.079B \|\| 7.99B?? \|\| 186.4M (22.3M unique)
	\|-		\|-
	\| M_H29.smi \|\| 7.704B \|\| 7.69B?? \|\| 10.1M (552K unique)		\| M_H29.smi \|\| 7.704B \|\| 7.69B?? \|\| 10.1M (552K unique)
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	! File !! Size !! mapped !! unmapped->arthor (#unique)		! File !! Size !! mapped !! unmapped->arthor (#unique)
	\|-		\|-
	\| M_H30.smi \|\| 6.891B \|\| ~~90M~~ \|\| ~~10M~~		\| M_H30.smi \|\| 6.891B \|\| ?? \|\| 502.1M (54.2M unique)
	\|-		\|-
	\| M_H31.smi \|\| 6.245B \|\| 90M \|\| 10M		\| M_H31.smi \|\| 6.245B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H32.smi \|\| 5.959B \|\| 90M \|\| 10M		\| M_H32.smi \|\| 5.959B \|\| 90M \|\| 10M. runs
	\|-		\|-
	\| M_H33.smi \|\| 5.~~5? B~~ \|\| 90M \|\| 10M		\| M_H33.smi \|\| 5.610B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H34.smi \|\| 5.126B \|\| 90M \|\| 10M		\| M_H34.smi \|\| 5.126B \|\| 90M \|\| 10M
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	\| M_H39.smi \|\| 1.775B \|\| 90M \|\| 10M		\| M_H39.smi \|\| 1.775B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H40_41.smi \|\| 2.268B \|\| ~~90M~~ \|\| 950.9M (#unique)		\| M_H40_41.smi \|\| 2.268B \|\| 1.317B (58.1%) \|\| 950.9M (235.7M unique).
	\|-		\|-
	\| M_H42_65.smi \|\| 1.893B \|\| 90M \|\| 725.6M (# unique 40.5B)		\| M_H42_65.smi \|\| 1.893B \|\| 90M \|\| 725.6M (# unique 40.5B)

Running ChemSTEP

Kholland — Thu, 07 May 2026 22:54:15 GMT

← Older revision		Revision as of 22:54, 7 May 2026
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	last update: ~~dec 16 2025~~ katie. current ver = ~~0.3.1.5~~ (~~automatic resubmission of failed SGE jobs~~).		last update: may 07 2026 katie. current ver = 03 (integrated IFP).

	ChemSTEP (Chemical Space Traversal and Exploration Procedure) is an open-source, transparent acceleration algorithm for molecular docking capable of dealing with virtual libraries of several trillion compounds. This wiki page is a guide for BKS lab members to run ChemSTEP on Wynton HPC, using a ~~drug-like~~ subset of ZINC (22B) or 13.3B library from Enamine REAL. '''for detailed instructions on the 13B space, see 'Running ChemSTEP on the 13B space' wiki page'''. For more general use directions, please refer to [ChemSTEP Read-the-Docs].		ChemSTEP (Chemical Space Traversal and Exploration Procedure) is an open-source, transparent acceleration algorithm for molecular docking capable of dealing with virtual libraries of several trillion compounds. This wiki page is a guide for BKS lab members to run ChemSTEP on Wynton HPC, using a subset of ZINC (22B or 72B) or 13.3B library from Enamine REAL. '''for detailed instructions on the 13B space, see 'Running ChemSTEP on the 13B space' wiki page'''. For more general use directions, please refer to [ChemSTEP Read-the-Docs].

	At a high-level, ChemSTEP is an iterative process that identifies molecules from the larger virtual library to prioritize for docking. First, we identify a random sample of the total library (termed "seed set", round zero) and dock those molecules to the target of interest. From this seed set, we can calculate total-library pProp values (-log rank percentages) and the number of "virtual hits" in the total library (high-scoring molecules). ChemSTEP will identify a set of maximally diverse molecules that score above the desired pProp threshold ("beacons") from the seed set. These beacons guide prioritization, where molecules chosen and output by ChemSTEP are close in chemical space to the beacons. Prioritized molecules are then built, docked, and returned to ChemSTEP for a second round of prioritization. This process is iterated until you reach desired virtual hit recovery, or you are no longer recovering virtual hits.		At a high-level, ChemSTEP is an iterative process that identifies molecules from the larger virtual library to prioritize for docking. First, we identify a random sample of the total library (termed "seed set", round zero) and dock those molecules to the target of interest. From this seed set, we can calculate total-library pProp values (-log rank percentages) and the number of "virtual hits" in the total library (high-scoring molecules). ChemSTEP will identify a set of maximally diverse molecules that score above the desired pProp threshold ("beacons") from the seed set. These beacons guide prioritization, where molecules chosen and output by ChemSTEP are close in chemical space to the beacons. Prioritized molecules are then built, docked, and returned to ChemSTEP for a second round of prioritization. This process is iterated until you reach desired virtual hit recovery, or you are no longer recovering virtual hits.
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	= Running ChemSTEP (Auto DOCK and Build) =		= Running ChemSTEP (Auto DOCK and Build) =

	ChemSTEP is configured to run on Wynton with libraries of '''13B''' and '''~~22B~~'''. This page covers the full workflow for running ChemSTEP with automatic submission of docking and building jobs.		ChemSTEP is configured to run on Wynton with libraries of '''13B''', '''22B''' (HAC 17-26, cLogP <= 3.5), and '''72B''' (HAC4-49, cLogP <=4.0). This page covers the full workflow for running ChemSTEP with automatic submission of docking and building jobs.

	__TOC__		__TOC__
Line 15:		Line 15:

	<pre>		<pre>
	source /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/bin/activate		source /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/bin/activate
	</pre>		</pre>

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	! Library !! Path		! Library !! Path
	\|-		\|-
	\| 13B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/libraries/13B/13M_seeds.sdi</code>		\| 13B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/13B/13M_seeds.wynton.sdi</code>
	\|-		\|-
	\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/libraries/22B/22M_seeds.sdi</code>		\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/22B/22M_seeds.sdi</code>
			\|-
			\| 72B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/72B/72M_seeds.sdi</code>
	\|}		\|}

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	Once docking is complete, run the following from the directory '''one level above''' your docking output (<code>MOLECULES_DIR_TO_BIND</code>).		Once docking is complete, run the following from the directory '''one level above''' your docking output (<code>MOLECULES_DIR_TO_BIND</code>).

	'''22B library:'''		'''22B/72B library:'''
	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/get_scores.py 0		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/get_scores.py 0
	</pre>		</pre>

	'''13B library:'''		'''13B library:'''
	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/~~get_scores_13B~~.py 0 MOL		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/get_scores.py 0 MOL
	</pre>		</pre>

	{{Note\|You must specify the molecule ID prefix for the 13B library (<code>MOL</code>)~~.}}~~		Note: You must specify the molecule ID prefix for the 13B library (<code>MOL</code>)

	Verify that <code>scores_round_0.txt</code> was correctly written:		Verify that <code>scores_round_0.txt</code> was correctly written:
Line 58:		Line 60:

	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/convert_scores_to_npy.py 0 <mol_id_prefix>		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/convert_scores_to_npy.py 0 <mol_id_prefix>
	</pre>		</pre>

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	\| <code>hit_pprop</code> \|\| Defines a "virtual hit." pProp = −log(rank%) within the total library score distribution. E.g., pProp 4 in 13B space ≈ top 0.01% (~1.3M molecules); pProp 5 ≈ 0.001% (~132K). The seed set should contain at least 10<sup>(pProp+2)</sup> molecules.		\| <code>hit_pprop</code> \|\| Defines a "virtual hit." pProp = −log(rank%) within the total library score distribution. E.g., pProp 4 in 13B space ≈ top 0.01% (~1.3M molecules); pProp 5 ≈ 0.001% (~132K). The seed set should contain at least 10<sup>(pProp+2)</sup> molecules.
	\|-		\|-
	\| <code>n_docked_per_round</code> \|\| Number of molecules prioritized per round. All must be built and docked between rounds. Too many slows throughput and may reduce diversity; too few slows virtual hit recovery.		\| <code>n_docked_per_round</code> \|\| Number of molecules prioritized per round. All must be built and docked between rounds. Too many slows throughput and may reduce diversity; too few slows virtual hit recovery. Recommended: 1-2 million
	\|-		\|-
	\| <code>max_beacons</code> \|\| Diverse, well-scoring molecules used to guide prioritization. All molecules above the pProp threshold are candidates. Too many ~~reduces~~ inter-beacon diversity; too few ~~hinders~~ space exploration. Fewer beacons than specified may be assigned if insufficient molecules clear the threshold.		\| <code>max_beacons</code> \|\| Diverse, well-scoring molecules used to guide prioritization. All molecules above the pProp threshold are candidates. Too many reduce inter-beacon diversity; too few hinder space exploration. Fewer beacons than specified may be assigned if an insufficient number of molecules clear the threshold. Recommended: 100
	\|-		\|-
	\| <code>bundle_size</code> \|\| In auto docking mode, number of molecules submitted as a single build job.		\| <code>bundle_size</code> \|\| In auto docking mode, number of molecules submitted as a single build job.
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	! Library !! Path		! Library !! Path
	\|-		\|-
	\| 13B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/libraries/13B/boltz_fplib.pickle</code>		\| 13B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/13B/boltz_fplib.pickle</code>
	\|-		\|-
	\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/libraries/22B/22B_fplib.pickle</code>		\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/22B/22B_fplib.pickle</code>
			\|-
			\| 72B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/72B/72B_fplib.pickle</code>
	\|}		\|}

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	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/get_beacon_smiles.py /path/to/library/pickle chemstep_algo.log		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/get_beacon_smiles.py /path/to/library/pickle chemstep_algo.log
	</pre>		</pre>

	Use the library pickle path from [[#7. Edit run_chemstep.py\|Step 7]].		Use the library pickle path from [[#7. Edit run_chemstep.py\|Step 7]].

	== 11. Get Poses After Docking ==		== 11. Plot Hit Recovery ==

			In your ChemSTEP directory containing <code>chemstep_algo.log</code> and score files,
			<pre>
			bash /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/submit_hit_recovery.sh
			</pre>

			== 12. Get Poses After Docking ==

	Make a list of <code>test.mol2.gz.0</code> files from docking:		Make a list of <code>test.mol2.gz.0</code> files from docking:

Cluster 7:Libraries

Frodo — Thu, 07 May 2026 20:29:35 GMT

REAL M (HAC 30+): asdf

← Older revision		Revision as of 20:29, 7 May 2026
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	So Far seven indexed : 1) ChemSpace, 2) Enamine, 3) WuXi, 4) XtalPi, 5) OnePot, 6) KzChBr, 7) MolPort.		* So Far seven indexed : 1) ChemSpace, 2) Enamine, 3) WuXi, 4) XtalPi, 5) OnePot, 6) KzChBr, 7) MolPort.
	* Last update: May 5, 2026		* So far, total molecules (pre stereochemical expansion). HAC 05-29: 57.9 B, HAC 30+: 94.6 B
			* This excludes xREAL, which are ugly anyway.

			* Last update: May 7, 2026

	= All - All =		= All - All =
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	\| M_H26.smi \|\| 6.108 B \|\| 6.067B (99.32%) \|\| 41.1M (5.96M unique)		\| M_H26.smi \|\| 6.108 B \|\| 6.067B (99.32%) \|\| 41.1M (5.96M unique)
	\|-		\|-
	\| M_H27.smi \|\| 7.522B \|\| 7.~~422B~~ (99.86%) \|\| ~~100~~.1M (~~???K~~ unique)		\| M_H27.smi \|\| 7.522B \|\| 7.412B (99.8%) \|\| 110.8M (13.4M unique)
	\|-		\|-
	\| M_H28.smi \|\| 8.079B \|\| 7.99B?? \|\| 10.1M (552K unique)		\| M_H28.smi \|\| 8.079B \|\| 7.99B?? \|\| 10.1M (552K unique)
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	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! File !! Size !! mapped !! unmapped(~~arthor~~)		! File !! Size !! mapped !! unmapped->arthor (#unique)
	\|-		\|-
	\| M_H30.smi \|\| 6.891B \|\| 90M \|\| 10M		\| M_H30.smi \|\| 6.891B \|\| 90M \|\| 10M
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	\| M_H31.smi \|\| 6.245B \|\| 90M \|\| 10M		\| M_H31.smi \|\| 6.245B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H32.smi \|\| 5.~~9? B~~ \|\| 90M \|\| 10M		\| M_H32.smi \|\| 5.959B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H33.smi \|\| 5.5? B \|\| 90M \|\| 10M		\| M_H33.smi \|\| 5.5? B \|\| 90M \|\| 10M
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	\| M_H39.smi \|\| 1.775B \|\| 90M \|\| 10M		\| M_H39.smi \|\| 1.775B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H40_41.smi \|\| 2.268B \|\| 90M \|\| ~~10M~~		\| M_H40_41.smi \|\| 2.268B \|\| 90M \|\| 950.9M (#unique)
	\|-		\|-
	\| M_H42_65.smi \|\| 1.893B \|\| 90M \|\| ~~10M~~		\| M_H42_65.smi \|\| 1.893B \|\| 90M \|\| 725.6M (# unique 40.5B)
	\|-		\|-
	\| Total \|\| 51B \|\|		\| Total \|\| 51B \|\|

How to Use SWAG

Zdingman — Wed, 06 May 2026 19:44:21 GMT

← 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]]

Category:SWAG

Zdingman — Wed, 06 May 2026 19:44:05 GMT

Created blank page

New page

Using SWAG to search smaller vendors

Zdingman — Wed, 06 May 2026 19:43:04 GMT

← Older revision		Revision as of 19:43, 6 May 2026
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	- The above instructions here make use of SWAG's local map feature. More detail and uses for local maps can be [[Using SWAG to filter analogs by Graph Edit Distance\|found here]].		- The above instructions here make use of SWAG's local map feature. More detail and uses for local maps can be [[Using SWAG to filter analogs by Graph Edit Distance\|found here]].

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

Using SWAG to filter analogs by Graph Edit Distance

Zdingman — Wed, 06 May 2026 19:42:50 GMT

← Older revision		Revision as of 19:42, 6 May 2026
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	[[Category:Smallworld]]		[[Category:Smallworld]] [[Category:SWAG]]

Using SWAG to search smaller vendors

Zdingman — Wed, 06 May 2026 19:37:30 GMT

← Older revision		Revision as of 19:37, 6 May 2026
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	source /nfs/home/zdingman/environments/SWAG/bin/activate		source /nfs/home/zdingman/environments/SWAG/bin/activate
	cp /nfs/home/zdingman/scripts/~~SWAG_v1_3_0~~/SWAG.py .		cp /nfs/home/zdingman/scripts/SWAG_v1-3-1/SWAG.py .
	ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map local.anon.map		ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map local.anon.map
	ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map.blm local.anon.map.blm		ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map.blm local.anon.map.blm

Using SWAG to search smaller vendors

Zdingman — Wed, 06 May 2026 19:36:02 GMT

Created page.

New page

In addition to the included databases that SWAG can search by default ([[How to Use SWAG|see here]]), it is possible to search any other database with a SmallWorld mapping. Recent interest has been expressed by multiple lab members in searching the vendor OnePot's CORE database for potential compounds to purchase. The below instructions describe how to search OnePot specifically, but can be adapted for any other vendor whose catalog has been mapped with SmallWorld.

== Instructions ==

Connect to either epyc or epyc2 on the lab cluster. Make a working directory in the location of your choice, open that directory, and copy query.smi (your SMILES of interest) into the directory. Copy and paste the following code:

source /nfs/home/zdingman/environments/SWAG/bin/activate
cp /nfs/home/zdingman/scripts/SWAG_v1_3_0/SWAG.py .
ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map local.anon.map
ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map.blm local.anon.map.blm
python SWAG.py -f query.smi -o lookup -d local -p [0]

SWAG will begin to lookup your SMILES. The file lookup_responses.csv contains the compounds that were successfully found in the vendor's catalog. Don't be surprised if the coverage is subpar for larger compounds; at larger HAC tranches, the overlap between ZINC22 and OnePot is fairly minimal.

== Notes ==

- If you're willing to explore single-atom changes, you can instead specify -p [1] when running SWAG.

- The above instructions here make use of SWAG's local map feature. More detail and uses for local maps can be [[Using SWAG to filter analogs by Graph Edit Distance|found here]].

Cluster 7:Libraries

Frodo — Wed, 06 May 2026 17:47:50 GMT

REAL M (HAC 30+): aSD

← Older revision		Revision as of 17:47, 6 May 2026
(11 intermediate revisions by the same user not shown)
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	= Enamine =		= Enamine =

			== Collections ==
			{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
			\|-
			\| REAL_stock.smi \|\| 5 M \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| REAL_H05_29-all.smi \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| REAL_all.smi \|\| ??? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
			\|}

	== REAL S ==		== REAL S ==
Line 92:		Line 104:
	! File !! Size !! mapped !! unmapped->arthor (unique) !! Comments		! File !! Size !! mapped !! unmapped->arthor (unique) !! Comments
	\|-		\|-
	\| S_H11_25.smi \|\| 2.150B \|\| 2.149B (99.95%) \|\| 1.13M (306.6K unique) ~~\|\| one mistake. Arthor atdb.fp file missing. regenerate.~~		\| S_H11_25.smi \|\| 2.150B \|\| 2.149B (99.95%) \|\| 1.13M (306.6K unique)
	\|-		\|-
	\| S_H26_29.smi \|\| 1.683B \|\| 1.668B (99.1%) \|\| 15.4M (5.2M unique)		\| S_H26_29.smi \|\| 1.683B \|\| 1.668B (99.1%) \|\| 15.4M (5.2M unique)
Line 98:		Line 110:
	\| S_30_50.smi \|\| 1.786B \|\| 1.647B (92.2%) \|\| 139M (60.0M unique)		\| S_30_50.smi \|\| 1.786B \|\| 1.647B (92.2%) \|\| 139M (60.0M unique)
	\|-		\|-
	\| Total \|\| 5.619 B \|\| 5.464 B \|\| - \|\| 5.~~6 billion~~ inexpensive from Enamine "S". ~~This is a HUGE improvement over previous versions with only 800 M x S.~~		! Total !! 5.619 B !! 5.464 B !! - \|\| 5.6B inexpensive from Enamine "S".
	\|}		\|}
			This is a HUGE improvement over previous versions, which had only 800 M x S.

	== REAL M HAC 05-29 ==		== REAL M HAC 05-29 ==
Line 115:		Line 128:
	\| M_H26.smi \|\| 6.108 B \|\| 6.067B (99.32%) \|\| 41.1M (5.96M unique)		\| M_H26.smi \|\| 6.108 B \|\| 6.067B (99.32%) \|\| 41.1M (5.96M unique)
	\|-		\|-
	\| M_H27.smi \|\| 7.522B \|\| 7.~~512B~~ (99.86%) \|\| 10.1M (???K unique)		\| M_H27.smi \|\| 7.522B \|\| 7.422B (99.86%) \|\| 100.1M (???K unique)
	\|-		\|-
	\| M_H28.smi \|\| 8.~~00B??~~ \|\| 7.99B?? \|\| 10.1M (552K unique)		\| M_H28.smi \|\| 8.079B \|\| 7.99B?? \|\| 10.1M (552K unique)
	\|-		\|-
	\| M_H29.smi \|\| 9.~~00B??~~ \|\| 8.~~99B~~?? \|\| 10.1M (552K unique)		\| M_H29.smi \|\| 7.704B \|\| 7.69B?? \|\| 10.1M (552K unique)
	\|-		\|-
	\| Total (est) ~~\|\| 39B~~		! Total (est) !! 39.48B !! 38.5B?? !!
	\|}		\|}

Line 130:		Line 143:
	! File !! Size !! mapped !! unmapped(arthor)		! File !! Size !! mapped !! unmapped(arthor)
	\|-		\|-
	\| M_H30.smi \|\| 6.~~891 B~~ \|\| 90M \|\| 10M		\| M_H30.smi \|\| 6.891B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H31.smi \|\| ~~10 B~~ \|\| 90M \|\| 10M		\| M_H31.smi \|\| 6.245B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H32.smi \|\| 9 B \|\| 90M \|\| 10M		\| M_H32.smi \|\| 5.9? B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H33.smi \|\| 7 B \|\| 90M \|\| 10M		\| M_H33.smi \|\| 5.5? B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H34.smi \|\| ~~6 B~~ \|\| 90M \|\| 10M		\| M_H34.smi \|\| 5.126B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H35.smi \|\| 4.~~486 B~~ \|\| 90M \|\| 10M		\| M_H35.smi \|\| 4.486B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H36.smi \|\| 3.751B \|\| 90M \|\| 10M		\| M_H36.smi \|\| 3.751B \|\| 90M \|\| 10M
Line 158:		Line 171:

	= WuXi =		= WuXi =

			== Collections ==

	{\| class="wikitable"		{\| class="wikitable"
Line 163:		Line 178:
	! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment		! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
	\|-		\|-
	\| ~~Phase1 05~~ \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29		\| WuXi_stock \|\| 5 M \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| WuXi_H05_29 \|\| 5 M \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| WuXi_H30_70 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| WuXi_all.smi\|\| ??? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
			\|}

			== GalaXi ==

			{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
			\|-
			\| WuXi_Ph1_HAC05-29 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| WuXi_Ph2_HAC05_29 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| WuXi_Ph3_HAC05-29 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| WuXi_Ph1_HAC30_70 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| WuXi_Ph2_HAC30_70 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| WuXi_Ph3_HAC30_70 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
	\|-		\|-
	\| ~~All_H30plus.smi~~ \|\| ?? B est.\|\| ~~55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated~~		\| Total (est) \|\| ?? B est.\|\|
	\|}		\|}

Line 210:		Line 250:
	\|-		\|-
	\| All_H30plus.smi \|\| ?? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated		\| All_H30plus.smi \|\| ?? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
			\|}


			= Stock =

			{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
			\|-
			\| Small_vendors_H05_29\|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| Small_vendors_H30_H99 \|\| ?? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
	\|}		\|}



	[[Cluster 7]]		[[Category:Cluster 7]]
	[[Libraries]]		[[Category:Libraries]]

Zack useful snippets

Zack — Wed, 06 May 2026 03:40:31 GMT

Useful DOCK3.8 binaries

← Older revision		Revision as of 03:40, 6 May 2026
Line 195:		Line 195:
	\| <code>OMEGA_MAX_SEARCH_TIME</code> \|\| 120.0 \|\| Previously hardcoded; now configurable		\| <code>OMEGA_MAX_SEARCH_TIME</code> \|\| 120.0 \|\| Previously hardcoded; now configurable
	\|}		\|}


			==Useful DOCK3.8 binaries==
			On gimel / bks cluster:
			<pre>
			(base) -sh-4.2$ pwd
			/nfs/home/zack/software/dock_binaries
			(base) -sh-4.2$ ls
			dock64_light_mol2 dock64_no_maxnode_limit_divya dock64_verbose_no_viable_poses dock64_verbose_no_viable_poses_and_safe_db2_load_fail
			</pre>

Cluster 7:Libraries

Frodo — Wed, 06 May 2026 00:43:12 GMT

MolPort: asdf

← Older revision		Revision as of 00:43, 6 May 2026
(10 intermediate revisions by the same user not shown)
Line 90:		Line 90:
	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! File !! Size !! mapped !! unmapped(~~arthor~~) !! Comments		! File !! Size !! mapped !! unmapped->arthor (unique) !! Comments
	\|-		\|-
	\| S_H11_25.smi \|\| 2.150B \|\| 2.149B (99.95%) \|\| 1.13M (306.6K unique) \|\| one mistake. Arthor atdb.fp file missing. regenerate.		\| S_H11_25.smi \|\| 2.150B \|\| 2.149B (99.95%) \|\| 1.13M (306.6K unique) \|\| one mistake. Arthor atdb.fp file missing. regenerate.
Line 102:		Line 102:

	== REAL M HAC 05-29 ==		== REAL M HAC 05-29 ==
			Over 99% coverage in Smallworld upto HAC29
	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
Line 108:		Line 109:
	\| M_H11_23.smi \|\| 3.037 B \|\| 3.0365 B (99.97%) \|\| 546K (193K unique)		\| M_H11_23.smi \|\| 3.037 B \|\| 3.0365 B (99.97%) \|\| 546K (193K unique)
	\|-		\|-
	\| M_H24.smi \|\| 2.702 B \|\| ~~??B~~ \|\| 2.1M (%unique)		\| M_H24.smi \|\| 2.702 B \|\| 2.700B (99.92%) \|\| 2.1M (552K unique)
	\|-		\|-
	\| M_H25.smi \|\| 4.328 B \|\| 4.318 B (99.77%) \|\| 10.1M (~~552K~~ unique)??		\| M_H25.smi \|\| 4.328 B \|\| 4.318 B (99.77%) \|\| 10.1M (1.96M unique)
	\|-		\|-
	\| M_H26.smi \|\| 6.108 B \|\| 6.~~097B~~ (99.83%) \|\| 10.1M (~~552K~~ unique)??		\| M_H26.smi \|\| 6.108 B \|\| 6.067B (99.32%) \|\| 41.1M (5.96M unique)
	\|-		\|-
	\| M_H27.smi \|\| 7.522B \|\| 7.512B (99.86%) \|\| 10.1M (~~552K~~ unique)??		\| M_H27.smi \|\| 7.522B \|\| 7.512B (99.86%) \|\| 10.1M (???K unique)
	\|-		\|-
	\| M_H28.smi \|\| 8.00B?? \|\| 7.99B?? \|\| 10.1M (552K unique)		\| M_H28.smi \|\| 8.00B?? \|\| 7.99B?? \|\| 10.1M (552K unique)
Line 124:		Line 125:

	== REAL M (HAC 30+) ==		== REAL M (HAC 30+) ==
			Coverage in Smallworld anon falls off sharply after HAC30
	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! File !! Size !! mapped !! unmapped(arthor)		! File !! Size !! mapped !! unmapped(arthor)
	\|-		\|-
	\| M_H30.smi \|\| 10 B \|\| 90M \|\| 10M		\| M_H30.smi \|\| 6.891 B \|\| 90M \|\| 10M
	\|-		\|-
	\| M_H31.smi \|\| 10 B \|\| 90M \|\| 10M		\| M_H31.smi \|\| 10 B \|\| 90M \|\| 10M
Line 157:		Line 159:
	= WuXi =		= WuXi =

	= XtalPi =		{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
			\|-
			\| Phase1 05 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| All_H30plus.smi \|\| ?? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
			\|}

			= XtalPi =

	= ~~OnePot =~~		{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
			\|-
			\| Phase1 05 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| All_H30plus.smi \|\| ?? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
			\|}

	= KzChBr =		= OnePot =

			{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
			\|-
			\| Phase1 05 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| All_H30plus.smi \|\| ?? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
			\|}

			= KzChBr =

			{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
			\|-
			\| Phase1 05 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| All_H30plus.smi \|\| ?? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
			\|}

	= MolPort =		= MolPort =

			{\| class="wikitable"
			\|-
			! File !! Size !! mapped !! unmapped -> arthor (%unique) !! Comment
			\|-
			\| Phase1 05 \|\| ??? B \|\| 5.559 B (99.0 %) \|\| 55M (23.2M unique) \|\| 100% enumeration to HAC29
			\|-
			\| All_H30plus.smi \|\| ?? B est.\|\| 55 B(99%) est \|\| 248M (UNK unique) \|\| from HAC30 and beyond, not all enumerated
			\|}



	[[Cluster 7]]		[[Cluster 7]]
	[[Libraries]]		[[Libraries]]