ZINC15:current limitations - Revision history

Frodo: sdf

2015-10-10T14:52:14Z

sdf

← Older revision		Revision as of 14:52, 10 October 2015
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	Some things in ZINC15 are still not right. We are working as fast as we can.		Some things in ZINC15 are still not right. We are working as fast as we can.
	If any of these is impacting you, please write us and we will see what we can do to prioritize it.		If any of these is impacting you, please write us and we will see what we can do to prioritize it.
			{{TOCright}}
	== Incomplete loading ==		== Incomplete loading ==
	* We know that not all rings are loaded yet. We are about 90% complete. Estimate completion in October 2015.		* We know that not all rings are loaded yet. We are about 90% complete. Estimate completion in October 2015.

Frodo: /* Incomplete GUI implementation (see also ZINC15:Status) */ dsf

2015-10-10T14:24:33Z

Incomplete GUI implementation (see also ZINC15:Status): dsf

← Older revision		Revision as of 14:24, 10 October 2015
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	== Incomplete GUI implementation (see also [[ZINC15:Status]]) ==		== Incomplete GUI implementation (see also [[ZINC15:Status]]) ==
	* no GUI-based method to create "having" queries		* no GUI-based method to create "having" queries
	* missing ~~/home, /examples and other endpoints~~		* some detail endpoints (majorclass, subclass, organism) still missing.
	* some pages continue to be simplistic		* some pages (gene detail, ortholog detail, catalog detail) continue to be simplistic
	* Batch mode is not yet working. We estimate December 2015 for a beta version.		* Batch mode is not yet working. We estimate December 2015 for a beta version.

Frodo: /* Incomplete loading */ sdf

2015-10-10T14:23:06Z

Incomplete loading: sdf

← Older revision		Revision as of 14:23, 10 October 2015
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	== Incomplete loading ==		== Incomplete loading ==
	* We know that not all rings are loaded yet. We are about 85% complete. Estimate completion in October 2015.		* We know that not all rings are loaded yet. We are about 90% complete. Estimate completion in October 2015.
	* We do not have 3D models for every molecule in ZINC15. We estimate we will have 50% coverage of lead-like and 25% coverage of drug-like by Jan 1, 2016. The work around is to use ZINC 12 (zinc.docking.org) until ZINC15 3D loading is ready.		* We do not have 3D models for every molecule in ZINC15. We estimate we will have 50% coverage of lead-like and 25% coverage of drug-like by Jan 1, 2016. The work around is to use ZINC 12 (zinc.docking.org) until ZINC15 3D loading is ready.
	* Catalog updates are correct as of mid August 2015. We have a backlog that will be caught up by end October 2015.		* Catalog updates are correct as of mid August 2015. We have a backlog that will be caught up by end October 2015.
			* We know there is a problem with Sigma Aldrich purchasing codes. Oct 15th.
	* There are various problems with the ChEMBL and SEA loading, which will be fixed in October 2015.		* There are various problems with the ChEMBL and SEA loading, which will be fixed in October 2015.

Frodo: asdf

2015-10-02T00:26:48Z

asdf

@@ Line 18: / Line 18: @@
 * We know that some of the links to vendors need updating. If you tell us what they are (via discus, bottom of page) we will update them more quickly.
-== Visual SMARTS handling ==
+Surprisingly, no SEA predictions even though it is a drug.
-* We know that we are not displaying the SMARTS patterns correctly.
+* metformin 12859773  - has no SEA predictions and no targets < 10uM per ChEMBL 20.
 * We know that the JSME editor is not currently handling SMARTS correctly, and that this is our problem not theirs.

Frodo: /* Incomplete curation */ asdf

2015-10-01T23:12:22Z

Incomplete curation: asdf

← Older revision		Revision as of 23:12, 1 October 2015
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	== Incomplete curation ==		== Incomplete curation ==
	* We know that we have not curated all patterns correctly yet. By incomplete curation, we mean that the patterns have not yet been correctly assigned to the "reactivity" axis. As a result, some compounds are currently incorrectly classified on the reactivity axis. We are aware of this, we are working on it, and we hope to have better curation available in October 2015.		* We know that we have not curated all patterns correctly yet. By incomplete curation, we mean that the patterns have not yet been correctly assigned to the "reactivity" axis. As a result, some compounds are currently incorrectly classified on the reactivity axis. We are aware of this, we are working on it, and we hope to have better curation available in October 2015.
			* We know the codes for Sigma Aldrich and Tocris need to be corrected.
			* We know that some of the links to vendors need updating. If you tell us what they are (via discus, bottom of page) we will update them more quickly.

	== Visual SMARTS handling ==		== Visual SMARTS handling ==

Frodo: /* Incomplete loading */ j

2015-10-01T11:42:53Z

Incomplete loading: j

← Older revision		Revision as of 11:42, 1 October 2015
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	== Incomplete loading ==		== Incomplete loading ==
	* We know that not all rings are loaded yet. We are about 85% complete. Estimate completion in October 2015.		* We know that not all rings are loaded yet. We are about 85% complete. Estimate completion in October 2015.
	* We do not have 3D models for every molecule in ZINC15. We estimate we will have 50% coverage of lead-like and 25% coverage of drug-like by Jan 1, 2016.		* We do not have 3D models for every molecule in ZINC15. We estimate we will have 50% coverage of lead-like and 25% coverage of drug-like by Jan 1, 2016. The work around is to use ZINC 12 (zinc.docking.org) until ZINC15 3D loading is ready.
	* Catalog ~~loading is~~ correct as of August 2015. We have a backlog that will be caught up in October 2015 ~~post release~~.		* Catalog updates are correct as of mid August 2015. We have a backlog that will be caught up by end October 2015.
	* There are various problems with the ChEMBL and SEA loading, which will be fixed in October 2015.		* There are various problems with the ChEMBL and SEA loading, which will be fixed in October 2015.

Frodo: /* Incomplete curation */ asdf

2015-09-29T19:01:52Z

Incomplete curation: asdf

← Older revision		Revision as of 19:01, 29 September 2015
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	== Incomplete curation ==		== Incomplete curation ==
	* We know that we have not curated all patterns correctly yet		* We know that we have not curated all patterns correctly yet. By incomplete curation, we mean that the patterns have not yet been correctly assigned to the "reactivity" axis. As a result, some compounds are currently incorrectly classified on the reactivity axis. We are aware of this, we are working on it, and we hope to have better curation available in October 2015.

	== Visual SMARTS handling ==		== Visual SMARTS handling ==

Frodo: asdf

2015-09-28T22:27:11Z

asdf

← Older revision		Revision as of 22:27, 28 September 2015
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	* We know that the JSME editor is not currently handling SMARTS correctly, and that this is our problem not theirs.		* We know that the JSME editor is not currently handling SMARTS correctly, and that this is our problem not theirs.

	== Incomplete GUI implementation (see also [[ZINC15:~~status~~]]) ==		== Incomplete GUI implementation (see also [[ZINC15:Status]]) ==
	* no GUI-based method to create "having" queries		* no GUI-based method to create "having" queries
	* missing /home, /examples and other endpoints		* missing /home, /examples and other endpoints

Frodo: asdf

2015-09-28T22:26:39Z

asdf

← Older revision		Revision as of 22:26, 28 September 2015
Line 2:		Line 2:
	If any of these is impacting you, please write us and we will see what we can do to prioritize it.		If any of these is impacting you, please write us and we will see what we can do to prioritize it.

	== ~~incomplete~~ loading ==		== Incomplete loading ==
	* We know that not all rings are loaded yet. We are about 85% complete. Estimate completion in October 2015.		* We know that not all rings are loaded yet. We are about 85% complete. Estimate completion in October 2015.
	* We do not have 3D models for every molecule in ZINC15. We estimate we will have 50% coverage of lead-like and 25% coverage of drug-like by Jan 1, 2016.		* We do not have 3D models for every molecule in ZINC15. We estimate we will have 50% coverage of lead-like and 25% coverage of drug-like by Jan 1, 2016.
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	== ~~incomplete~~ curation ==		== Incomplete curation ==
	* We know that we have not curated all patterns correctly yet		* We know that we have not curated all patterns correctly yet

	== ~~visual~~ SMARTS handling ==		== Visual SMARTS handling ==
	* We know that we are not displaying the SMARTS patterns correctly.		* We know that we are not displaying the SMARTS patterns correctly.
	* We know that the JSME editor is not currently handling SMARTS correctly, and that this is our problem not theirs.		* We know that the JSME editor is not currently handling SMARTS correctly, and that this is our problem not theirs.

	== ~~incomplete~~ GUI implementation		== Incomplete GUI implementation (see also [[ZINC15:status]]) ==
	* no GUI-based method to create "having" queries		* no GUI-based method to create "having" queries
	* missing /home, /examples and other endpoints		* missing /home, /examples and other endpoints

Frodo: dsfg

2015-09-28T22:14:54Z

dsfg

← Older revision		Revision as of 22:14, 28 September 2015
Line 1:		Line 1:
	Some things in ZINC15 are still not right. We are working as fast as we can. If any of these is impacting you ~~in your work~~, please write us and we will see what we can do to prioritize it.		Some things in ZINC15 are still not right. We are working as fast as we can.
			If any of these is impacting you, please write us and we will see what we can do to prioritize it.

	* We do not have 3D models for every molecule in ZINC15. We estimate we will have 50% coverage of lead-like and 25% coverage of drug-like by Jan 1, 2016.		== incomplete loading ==
	* ~~Batch mode~~ is ~~not yet working~~. We ~~estimate December~~ 2015 ~~for a beta version~~.		* We know that not all rings are loaded yet. We are about 85% complete. Estimate completion in October 2015.
			* We do not have 3D models for every molecule in ZINC15. We estimate we will have 50% coverage of lead-like and 25% coverage of drug-like by Jan 1, 2016.
			* Catalog loading is correct as of August 2015. We have a backlog that will be caught up in October 2015 post release.
			* There are various problems with the ChEMBL and SEA loading, which will be fixed in October 2015.

	== ~~timeout~~ problems ==		== Timeout problems ==
	* We are aware of timeout problems on long running queries. We have a solution for this expected Dec 2015. In the meantime, there are workarounds. Ask us.		* We are aware of timeout problems on long running queries. We have a solution for this expected Dec 2015. In the meantime, there are workarounds. Ask us.
	* We know about performance problems under heavy load. We have more hardware standing by to ~~add and will revisit this~~ in November.		* We know about performance problems under heavy load. We have more hardware standing by. Expect to deploy (doubling website performance) in November 2015.

	~~== incomplete loading ==~~
	* We know that not all rings are loaded yet. We are about 85% complete. Estimate completion in October 2015.

	== incomplete curation ==		== incomplete curation ==
	* We know that we have not curated all patterns correctly yet		* We know that we have not curated all patterns correctly yet

			== visual SMARTS handling ==
	* We know that we are not displaying the SMARTS patterns correctly.		* We know that we are not displaying the SMARTS patterns correctly.

	* We know that the JSME editor is not currently handling SMARTS correctly, and that this is our problem not theirs.		* We know that the JSME editor is not currently handling SMARTS correctly, and that this is our problem not theirs.

			== incomplete GUI implementation
			* no GUI-based method to create "having" queries
			* missing /home, /examples and other endpoints
			* some pages continue to be simplistic
			* Batch mode is not yet working. We estimate December 2015 for a beta version.

	* 3D models for every molecule in ZINC.		== detailed reports of problems to be investigated ==
	* no GUI-based method to create "having" queries.

	== reports of problems to be investigated ==
	* Trent says: here is a mol that does not work for me in db2 generation:		* Trent says: here is a mol that does not work for me in db2 generation:
	c1ccc2c(c1)[nH]c3scc[n+]23 ZINC01648614		c1ccc2c(c1)[nH]c3scc[n+]23 ZINC01648614