ZINC-22 Clean Up in Jan 2022: Difference between revisions

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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.
==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.
== 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:
* H24P200-230 which have the prefix oq, or, os, ot after ZINC.  Only per the table below.
* 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 15: Line 23:
  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.  
== Impact ==
However, they CAN be found by searching the SMILES in the swp.docking.org service.  
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.
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)
== Other news ==
* 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.
workaround is to look up in smallworld private.


* there are remaining problems with H26-H29 that we are aware of and are working on.  
* 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 have been incorrectly treated as radicals.  
* ZINC20 in stock in ZINC-22, called /zinc-22g/ has been completely re-created. The numbering of molecules may have changed.
We are working to fix this. For now, ignore.  
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.  


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


If a molecule does not look up correctly, you can always use its SMILES code.
Questions to jjiteam at googlegroups dot com.


Thank you for reading.
[[Category:News]]

Latest revision as of 16:29, 23 May 2024

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.

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.

What was affected

The affected molecules are:

  • H24P200-230 which have the prefix oq, or, os, ot after ZINC. Only per the table below.
  • H22P320-380 which have the prefix mC, mD, mE, mF, mG, mH, mI, mJ after ZINC. per the table below.
generation tranche.        count
-----------------------------------
zinc-22x | H24P200_230   | 38034845
zinc-22u | H24P200_230   | 2105987
zinc-22k | H24P200_230   | 81295
zinc-22l | H24P200_230   | 39679
zinc-22m | H24P200_230   | 52743
zinc-22o | H24P200_230   | 751764
zinc-22p | H24P200_230   | 2105987
zinc-22x | H22P320_390   | 3895304
zinc-22u | H22P320_390   | 1097048

Impact

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. 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 working to complete H27-H29. Maybe Feb 1. Until then, looking up molecules in cartblanche22 H27-H29 may fail.

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.
  • ZINC20 in stock in ZINC-22, called /zinc-22g/ has been completely re-created. The numbering of molecules may have changed.

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.

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.

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