Selecting tranches in ZINC22 - Revision history

Frodo: asdf

2024-06-12T17:56:51Z

asdf

← Older revision		Revision as of 17:56, 12 June 2024
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	If you are on another platform, we suggest using and adapting one of these three.		If you are on another platform, we suggest using and adapting one of these three.

	== ~~arbitrary~~ subsets ==		== Prepared subsets in "sets" ==
	~~We have created subsets for you (see below, but you can select subsets at a very fine grain level:~~
	* by HAC by number of atoms		* by HAC by number of atoms
	* by calculated LogP within 0.1 units.		* by calculated LogP within 0.1 units.
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	Look in /nfs/exd/zinc-22/sets/		Look in /nfs/exd/zinc-22/sets/

	~~== lead-like ==~~		e.g. to dock neutrals (N), H17, lead-like, on Wynton, you would use
	* if you want to dock lead-like, you ~~want~~		/wynton/group/bks/sets/N-H17.lead-like.wyn
	/sets/H17~~-19~~.lead-like.~~<suffix> where <suffix> is txt,~~ wyn ~~or s3 as above~~		similarly, to dock mono cations, H23-H25, lead-like, on our cluster, use
	~~/sets/H20~~-~~23.~~lead-like~~.<suffix>~~		/nfs/exd/sets/O-H2[345].lead-like.txt
	~~Then~~, ~~depending~~ on ~~whether you want to include H24 and H25~~, ~~you can optionally include~~		and to dock all charges of fragment-like, H07 to H16, on AWS, use
	/sets/~~H24~~.lead-like.~~<suffix>~~		sets/?-H0[789].frag-like.s3 sets/?-H1[0-6].frag-like.s3
	/sets/~~H25~~.~~lead~~-like.~~<suffix>~~
	~~If you want to add on compounds from calculated LogP from 4.0 to 4.9~~
	/sets/~~H17~~-19.~~greasy~~-~~leads~~.~~<suffix> and so on as above~~

	== ~~fragment-like~~ ==		== more granularity use "dirs" ==
	* if you want to dock fragments H10-H16, ~~LogP<4~~		Thus, use /wynton/group/bks/sets/dirs/ or /nfs/exd/sets/dirs.
	/sets/~~frag-like~~.~~<suffix>~~

	~~== greasy molecules ==~~		The format is <charge>-<logPbin>-<Hbin>.<layer>.<suffix>
	* if you want to dock calculated logP > 5		where
	~~/sets/H04~~-~~H19.greasy.~~<~~suffix~~>		* suffix is one of s3, wyn, txt
	~~/sets/H20~~-29.~~greasy~~.<suffix>		* layer is a-z see [[ZINC22:Layers]]
			* Hbin is H04 to H49
	* ~~if you want~~ to ~~dock big monsters (not recommended~~, ~~but who knows)~~		* charge is N=0, O=+1, M=-1, etc from J to R.
	~~/sets/H26-H29~~.~~big~~.<~~suffix>~~		* logP bin is
	~~/sets/H26-H29~~.~~big-greasy~~.~~<suffix~~>		** P359 = LogP 3.5 to 3.99
			** P304 = logP 3.0 to 3.49
			** P012 = LogP 0-2
			** M = LogP < 0
			** P4 = LogP 4.0 to 4.99
			** P56789 = logP > 5.0

	You can learn about how the sets were assembled using make-sets.csh		You can learn about how the sets were assembled using make-sets.csh
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	We can adjust these subsets based on what people want. It is easy, we just need to do it.		We can adjust these subsets based on what people want. It is easy, we just need to do it.


	~~== real life example ==~~
	~~So, supposing I want to dock lead-like (H17-H25) in AWS using my S3 bucket results2021.~~
	~~I assemble a file database210325.txt from four files:~~

	~~cat H17-19.lead-like.s3 H20-23.lead-like.s3 H24.lead-like.s3 H25.lead-like.s3 > database210325.txt~~
	~~I upload this to s3~~
	~~aws s3 cp database210325.txt s3://results2021/~~
	~~Then I go on AWS and I follow the instructions in [[DOCK on AWS]].~~

	~~I monitor the job as it runs.~~

	~~Then I harvest the results and download them to my computer.~~


	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:DOCK3.8]]		[[Category:DOCK3.8]]

Frodo: /* platforms */ asdf

2024-06-12T17:47:18Z

platforms: asdf

← Older revision		Revision as of 17:47, 12 June 2024
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	* Wynton, .wyn suffix		* Wynton, .wyn suffix
	* AWS, .s3 suffix		* AWS, .s3 suffix
	If you are on another platform, suggest using one of these three.		If you are on another platform, we suggest using and adapting one of these three.

	== arbitrary subsets ==		== arbitrary subsets ==

Frodo: asdf

2021-03-25T22:19:34Z

asdf

← Older revision		Revision as of 22:19, 25 March 2021
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	Current method to select tranches to dock in ZINC 22 .		Current method to select tranches to dock in ZINC 22 .

			== platforms ==
	We support three platforms:		We support three platforms:
	* our cluster, .txt suffix		* our cluster, .txt suffix
	* Wynton, .wyn suffix		* Wynton, .wyn suffix
	* AWS, .s3 suffix		* AWS, .s3 suffix
			If you are on another platform, suggest using one of these three.

	We have created subsets, but you can select subsets at a fine grain level, by HAC ~~and~~ calculated LogP within 0.1 units.		== arbitrary subsets ==
			We have created subsets for you (see below, but you can select subsets at a very fine grain level:
	Look in		* by HAC by number of atoms
	/nfs/exd/zinc-22/sets		* by calculated LogP within 0.1 units.
			* by charge -4 to +4.
			Look in /nfs/exd/zinc-22/sets/

			== lead-like ==
	* if you want to dock lead-like, you want		* if you want to dock lead-like, you want
	/sets/H17-19.lead-like.<suffix> where <suffix> is txt, wyn or s3 as above		/sets/H17-19.lead-like.<suffix> where <suffix> is txt, wyn or s3 as above
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	/sets/H17-19.greasy-leads.<suffix> and so on as above		/sets/H17-19.greasy-leads.<suffix> and so on as above

			== fragment-like ==
	* if you want to dock fragments H10-H16, LogP<4		* if you want to dock fragments H10-H16, LogP<4
	/sets/frag-like.<suffix>		/sets/frag-like.<suffix>

			== greasy molecules ==
	* if you want to dock calculated logP > 5		* if you want to dock calculated logP > 5
	/sets/H04-H19.greasy.<suffix>		/sets/H04-H19.greasy.<suffix>
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	We can adjust these subsets based on what people want. It is easy, we just need to do it.		We can adjust these subsets based on what people want. It is easy, we just need to do it.


			== real life example ==
			So, supposing I want to dock lead-like (H17-H25) in AWS using my S3 bucket results2021.
			I assemble a file database210325.txt from four files:

			cat H17-19.lead-like.s3 H20-23.lead-like.s3 H24.lead-like.s3 H25.lead-like.s3 > database210325.txt
			I upload this to s3
			aws s3 cp database210325.txt s3://results2021/
			Then I go on AWS and I follow the instructions in [[DOCK on AWS]].

			I monitor the job as it runs.

			Then I harvest the results and download them to my computer.


	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:DOCK3.8]]		[[Category:DOCK3.8]]

Frodo: asdf

2021-03-25T20:06:46Z

asdf

← Older revision		Revision as of 20:06, 25 March 2021
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	/sets/H26-H29.big-greasy.<suffix>		/sets/H26-H29.big-greasy.<suffix>

			You can learn about how the sets were assembled using make-sets.csh
			make-sets.csh in turn uses files in /nfs/exd/jjiwork/dirs/
			these in turn are created using make-files2.csh in /nfs/exd/jjiwork/

			We can adjust these subsets based on what people want. It is easy, we just need to do it.

	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:DOCK3.8]]		[[Category:DOCK3.8]]

Frodo: asdf

2021-03-25T20:01:42Z

asdf

New page

Current method to select tranches to dock in ZINC 22 .

We support three platforms:
* our cluster, .txt suffix
* Wynton, .wyn suffix
* AWS, .s3 suffix

We have created subsets, but you can select subsets at a fine grain level, by HAC and calculated LogP within 0.1 units.

Look in
/nfs/exd/zinc-22/sets

* if you want to dock lead-like, you want
/sets/H17-19.lead-like.<suffix> where <suffix> is txt, wyn or s3 as above
/sets/H20-23.lead-like.<suffix>
Then, depending on whether you want to include H24 and H25, you can optionally include
/sets/H24.lead-like.<suffix>
/sets/H25.lead-like.<suffix>
If you want to add on compounds from calculated LogP from 4.0 to 4.9
/sets/H17-19.greasy-leads.<suffix> and so on as above

* if you want to dock fragments H10-H16, LogP<4
/sets/frag-like.<suffix>

* if you want to dock calculated logP > 5
/sets/H04-H19.greasy.<suffix>
/sets/H20-29.greasy.<suffix>

* if you want to dock big monsters (not recommended, but who knows)
/sets/H26-H29.big.<suffix>
/sets/H26-H29.big-greasy.<suffix>

[[Category:ZINC22]]
[[Category:DOCK3.8]]