News of 2022-01 Jan - Revision history

Frodo: Frodo moved page News of 2021-01 Jan to News of 2022-01 Jan

2024-11-22T16:24:10Z

Frodo moved page News of 2021-01 Jan to News of 2022-01 Jan

← Older revision

Revision as of 16:24, 22 November 2024

Frodo: Frodo moved page ZINC-22 Clean Up in Jan 2022 to News of 2021-01 Jan

2024-11-22T16:23:18Z

Frodo moved page ZINC-22 Clean Up in Jan 2022 to News of 2021-01 Jan

← Older revision

Revision as of 16:23, 22 November 2024

Frodo: asdf

2024-05-23T16:29:05Z

asdf

← Older revision		Revision as of 16:29, 23 May 2024
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	Questions to jjiteam at googlegroups dot com.		Questions to jjiteam at googlegroups dot com.

	[[Category:~~ZINC-22-news~~]]		[[Category:News]]

Frodo: asdf

2022-02-01T17:18:48Z

asdf

← Older revision		Revision as of 17:18, 1 February 2022
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			==Background ==

	We started building ZINC-22 before all of the cataloging apparatus was ready. As a result of mistakes we made, a few tranches were damaged, have been lost, and must be rebuilt.		We started building ZINC-22 before all of the cataloging apparatus was ready. As a result of mistakes we made, a few tranches were damaged, have been lost, and must be rebuilt.

			== Actions taken ==
	We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.		We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.

			== What was affected ==
	The affected molecules are:		The affected molecules are:
	* H24P200-230 which have the prefix oq, or, os, ot after ZINC. Only per the table below.		* H24P200-230 which have the prefix oq, or, os, ot after ZINC. Only per the table below.
Line 19:		Line 23:
	zinc-22u \| H22P320_390 \| 1097048		zinc-22u \| H22P320_390 \| 1097048

			== Impact ==
	Molecules in these tranches will NOT be findable by ZINC code in Cartblanche22.docking.org.		Molecules in these tranches will NOT be findable by ZINC code in Cartblanche22.docking.org.
	However, they CAN be found by searching the SMILES in the swp.docking.org service.		However, they CAN be found by searching the SMILES in the swp.docking.org service.
	So you can still likely buy them.		So you can still likely buy them.

			== Other news ==
	* We are building/updating new smallworld and arthor indexes based on ZINC-22 2d-12. H04-H26		* We are building/updating new smallworld and arthor indexes based on ZINC-22 2d-12. H04-H26
	* We are working to complete H27-H29. Maybe Feb 1. Until then, looking up molecules in cartblanche22 H27-H29 may fail.		* We are working to complete H27-H29. Maybe Feb 1. Until then, looking up molecules in cartblanche22 H27-H29 may fail.

Frodo: sdf

2022-02-01T17:17:08Z

sdf

← Older revision		Revision as of 17:17, 1 February 2022
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	Questions to jjiteam at googlegroups dot com.		Questions to jjiteam at googlegroups dot com.

			[[Category:ZINC-22-news]]

Frodo: asdf

2022-01-12T18:32:21Z

asdf

← Older revision		Revision as of 18:32, 12 January 2022
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	We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.		We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.

	H24P200-230 have the prefix oq, or, os, ot after ZINC.		The affected molecules are:
			* H24P200-230 which have the prefix oq, or, os, ot after ZINC. Only per the table below.
	H22P320-380 have the prefix mC, mD, mE, mF, mG, mH, mI, mJ after ZINC.		* H22P320-380 which have the prefix mC, mD, mE, mF, mG, mH, mI, mJ after ZINC. per the table below.

	generation tranche. count		generation tranche. count
Line 23:		Line 23:
	So you can still likely buy them.		So you can still likely buy them.

	* We are building/updating a new smallworld and arthor ~~index~~ based on ZINC-22 2d-12. H04-H26 ~~(JJ, Ben)~~		* We are building/updating new smallworld and arthor indexes based on ZINC-22 2d-12. H04-H26
			* We are working to complete H27-H29. Maybe Feb 1. Until then, looking up molecules in cartblanche22 H27-H29 may fail.
	* We are ~~aware of remaining problems with~~ H27, ~~H28 and~~ H29. ~~working~~. ~~Maybe mid January?~~		workaround is to look up in smallworld private.

	* We have found a bug in which a few thousand molecules - mostly N-oxides or other uncommon functional groups - have been incorrectly treated as radicals. We are working to fix this. For now, ignore them if you see them.		* We have found a bug in which a few thousand molecules - mostly N-oxides or other uncommon functional groups - have been incorrectly treated as radicals. We are working to fix this. For now, ignore them if you see them.

	* ~~ZINC~~ in stock~~. is being~~ re-~~prepared~~.		* ZINC20 in stock in ZINC-22, called /zinc-22g/ has been completely re-created. The numbering of molecules may have changed.
	* We generated several versions of zinc-22g "ZINC 20 in stock" in 2021. They are all gone~~. We will reload and let you know~~.		We regret the impact this may cause. We had generated several versions of zinc-22g "ZINC 20 in stock" in 2021. They are all gone.

	If a ~~molecule does not look up correctly, you can always use its SMILES code~~.		We will try to minimize future disruption. The changes described here were essential to getting a high level of correctness in the database without delay.

	Questions to jjiteam at googlegroups dot com.		Questions to jjiteam at googlegroups dot com.

Frodo: dfgh

2022-01-07T05:22:17Z

dfgh

← Older revision		Revision as of 05:22, 7 January 2022
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	We started ~~builing~~ ZINC-22 before all of the cataloging apparatus was ready. As a result of mistakes we made, ~~some~~ tranches were damaged, have been lost, and must be rebuilt.		We started building ZINC-22 before all of the cataloging apparatus was ready. As a result of mistakes we made, a few tranches were damaged, have been lost, and must be rebuilt.

	We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.		We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.

			H24P200-230 have the prefix oq, or, os, ot after ZINC.

			H22P320-380 have the prefix mC, mD, mE, mF, mG, mH, mI, mJ after ZINC.

	generation tranche. count		generation tranche. count
Line 19:		Line 23:
	So you can still likely buy them.		So you can still likely buy them.

	* We are building/updating a new smallworld and arthor index based on ZINC-22 2d-12. (JJ, Ben)		* We are building/updating a new smallworld and arthor index based on ZINC-22 2d-12. H04-H26 (JJ, Ben)

	* We are aware of remaining problems with ~~H26-~~H29 ~~that we are aware of and are~~ working on.		* We are aware of remaining problems with H27, H28 and H29. working. Maybe mid January?
	~~We think H26 might be solved today (Jan 5), but H27-H29 will take a bit longer, maybe~~ mid ~~Jan.~~

	* We have found a bug in which a few thousand molecules - mostly N-oxides or other uncommon functional groups - have been incorrectly treated as radicals.		* We have found a bug in which a few thousand molecules - mostly N-oxides or other uncommon functional groups - have been incorrectly treated as radicals. We are working to fix this. For now, ignore them if you see them.
	We are working to fix this. For now, ignore them if you see them.

	* ZINC in stock. We generated several versions of zinc-22g "ZINC 20 in stock" in 2021. They are all gone. We will reload and let you know.		* ZINC in stock. is being re-prepared.
			* We generated several versions of zinc-22g "ZINC 20 in stock" in 2021. They are all gone. We will reload and let you know.

	If a molecule does not look up correctly, you can always use its SMILES code.		If a molecule does not look up correctly, you can always use its SMILES code.

	Questions to jjiteam at googlegroups dot com.		Questions to jjiteam at googlegroups dot com.

Frodo: update Jan 5

2022-01-05T17:44:31Z

update Jan 5

Frodo: asdf

2022-01-05T01:04:15Z

asdf

← Older revision		Revision as of 01:04, 5 January 2022
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	* We have found a bug in which a few thousand molecules have been incorrectly treated as radicals.		* We have found a bug in which a few thousand molecules have been incorrectly treated as radicals.
	We are working to fix this. For now, ignore.		We are working to fix this. For now, ignore.

			* ZINC in stock. We generated several versions of zinc-22g "ZINC 20 in stock" in 2021. They are all gone. We will reload.

	If a molecule does not look up correctly, you can always use its SMILES code.		If a molecule does not look up correctly, you can always use its SMILES code.

	Thank you for reading.		Thank you for reading.

Frodo: Update

2022-01-05T01:01:38Z

Update

← Older revision		Revision as of 01:01, 5 January 2022
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	We started builing ZINC-22 before ~~we really had~~ all of the ~~catalogging~~ apparatus ready. As a result, some tranches were damaged, have been lost, and must be rebuilt.		We started builing ZINC-22 before all of the cataloging apparatus was ready. As a result, some tranches were damaged, have been lost, and must be rebuilt.

	We cleaned up ZINC-22 in the first week of January 2022 ~~as follows:~~		We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.

	generation tranche. count		generation tranche. count
Line 15:		Line 15:
	zinc-22u \| H22P320_390 \| 1097048		zinc-22u \| H22P320_390 \| 1097048

	~~A total of 47.6 M 3D~~ molecules ~~were deleted. If you docked ZINC_22 before Jan 4, 2022, you may have docked~~ these ~~molecules.~~		molecules in these tranches will NOT be findable by ZINC code in Cartblanche22.docking.org.
	~~These molecules~~ will ~~not look up correctly~~ in Cartblanche22.docking.org. However, ~~you can still look for them using~~		However, they CAN be found by searching the SMILES in the swp.docking.org service.
	the SMILES ~~lookup feature~~.

	~~At the time of writing~~ (~~Jan 4 noon~~) ~~there are still problems with H26 to H29. These will be resolved asap.~~		* we still must build a new smallworld and arthor index based on ZINC-22 2d-12. (JJ, Ben)

	We are ~~currently investigating whether 2d~~-~~0? (1-8), representing the pre-2022 database,~~ are ~~complete~~ and ~~correct~~.		* there are remaining problems with H26-H29 that we are aware of and are working on.

	~~The current 2d database is /nfs/exb/zinc22/2d-12~~. We are ~~currently investigating whether anything from 2d-0? is missing~~.		* We have found a bug in which a few thousand molecules have been incorrectly treated as radicals.
			We are working to fix this. For now, ignore.

	~~There are~~ a ~~small number of molecules in the 3D production /nfs/exd/zinc-22? that are~~ not ~~present in 2d-0? and 2d-12.~~		If a molecule does not look up correctly, you can always use its SMILES code.
	~~We are working on figuring out how many~~, ~~and what to do about them~~.

	~~If a molecule does not look up correctly,~~ you ~~can always use its SMILES code~~.		Thank you for reading.

← Older revision		Revision as of 17:44, 5 January 2022
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	We started builing ZINC-22 before all of the cataloging apparatus was ready. As a result, some tranches were damaged, have been lost, and must be rebuilt.		We started builing ZINC-22 before all of the cataloging apparatus was ready. As a result of mistakes we made, some tranches were damaged, have been lost, and must be rebuilt.

	We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.		We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.
Line 15:		Line 15:
	zinc-22u \| H22P320_390 \| 1097048		zinc-22u \| H22P320_390 \| 1097048

	~~molecules~~ in these tranches will NOT be findable by ZINC code in Cartblanche22.docking.org.		Molecules in these tranches will NOT be findable by ZINC code in Cartblanche22.docking.org.
	However, they CAN be found by searching the SMILES in the swp.docking.org service.		However, they CAN be found by searching the SMILES in the swp.docking.org service.
			So you can still likely buy them.

	* ~~we still must build~~ a new smallworld and arthor index based on ZINC-22 2d-12. (JJ, Ben)		* We are building/updating a new smallworld and arthor index based on ZINC-22 2d-12. (JJ, Ben)

	* ~~there~~ are remaining problems with H26-H29 that we are aware of and are working on.		* We are aware of remaining problems with H26-H29 that we are aware of and are working on.
			We think H26 might be solved today (Jan 5), but H27-H29 will take a bit longer, maybe mid Jan.

	* We have found a bug in which a few thousand molecules have been incorrectly treated as radicals.		* We have found a bug in which a few thousand molecules - mostly N-oxides or other uncommon functional groups - have been incorrectly treated as radicals.
	We are working to fix this. For now, ignore.		We are working to fix this. For now, ignore them if you see them.

	* ZINC in stock. We generated several versions of zinc-22g "ZINC 20 in stock" in 2021. They are all gone. We will reload.		* ZINC in stock. We generated several versions of zinc-22g "ZINC 20 in stock" in 2021. They are all gone. We will reload and let you know.

	If a molecule does not look up correctly, you can always use its SMILES code.		If a molecule does not look up correctly, you can always use its SMILES code.

	~~Thank you for reading~~.		Questions to jjiteam at googlegroups dot com.