How to use Arthor API - Revision history

Jgutierrez6: /* Data Tables */

2023-02-16T20:50:34Z

Data Tables

← Older revision		Revision as of 20:50, 16 February 2023
Line 9:		Line 9:

	Example command:		Example command:
	curl 'http://arthor.docking.org/dt/data'		curl http://arthor.docking.org/dt/data

	Produces the following JSON:		Produces the following JSON:

Jyoung at 23:42, 8 January 2020

2020-01-08T23:42:32Z

← Older revision		Revision as of 23:42, 8 January 2020
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	[[Category:Arthor]]		[[Category:Arthor]]
	[[Category:API]]		[[Category:API]]
			[[Category: NextMove]]

Jyoung at 23:41, 8 January 2020

2020-01-08T23:41:02Z

← Older revision		Revision as of 23:41, 8 January 2020
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	After some time the background count will have completed and the hasMore will now be false meaning the hit count is correct. The time taken to do the count is set on the time field.		After some time the background count will have completed and the hasMore will now be false meaning the hit count is correct. The time taken to do the count is set on the time field.

			[[Category:Arthor]]
			[[Category:API]]

Jyoung at 00:16, 18 December 2019

2019-12-18T00:16:20Z

← Older revision		Revision as of 00:16, 18 December 2019
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	==Similarity Search==		==Similarity Search==

	curl 'http://arthor.docking.org/dt/~~now_bb~~/search?query=c1ccccc1&type=SIM&start=0&length=5'		curl 'http://arthor.docking.org/dt/In-Stock-19Q4-13.8M/search?query=c1ccccc1&type=SIM&start=0&length=5'

	{"query":"c1ccccc1","		{"query":"c1ccccc1","
Line 84:		Line 84:
	A substructure or SMARTS search has some additional complexity. A parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total number of hits. The idea is the server can be pooled until the count is finished.		A substructure or SMARTS search has some additional complexity. A parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total number of hits. The idea is the server can be pooled until the count is finished.

	curl 'http://arthor.docking.org/dt/~~now_bb~~/search?query=c1ccccc1&type=SUB&start=0&length=5'		curl 'http://arthor.docking.org/dt/In-Stock-19Q4-13.8M/search?query=c1ccccc1&type=SUB&start=0&length=5'

	{"query":"c1:c:c:c:c:c:1","data":[		{"query":"c1:c:c:c:c:c:1","data":[

Jyoung at 22:04, 11 December 2019

2019-12-11T22:04:11Z

@@ Line 12: / Line 12: @@
 Produces the following JSON:
 [{"displayName":"wait-ok.smi","location":"/usr/local/tomcat/arthor_data/wait-ok.smi","urlFormatStr":null,"idxTypes":["SUB"]},{"displayName":"for-sale.smi","location":"/usr/local/tomcat/arthor_data/for-sale.smi","urlFormatStr":null,"idxTypes":["SUB"]},{"displayName":"now_bb.smi","location":"/usr/local/tomcat/arthor_data/now_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"wait-ok_bb.smi","location":"/usr/local/tomcat/arthor_data/wait-ok_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"for-sale_bb.smi","location":"/usr/local/tomcat/arthor_data/for-sale_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"in-stock.smi","location":"/usr/local/tomcat/arthor_data/in-stock.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"bb-all.smi","location":"/usr/local/tomcat/arthor_data/bb-all.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"bb-now.smi","location":"/usr/local/tomcat/arthor_data/bb-now.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"interesting.smi","location":"/usr/local/tomcat/arthor_data/interesting.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"on-demand.smi","location":"/usr/local/tomcat/arthor_data/on-demand.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"wuxi.smi","location":"/usr/local/tomcat/arthor_data/wuxi.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]}]
 ===/dt/${db_name}/data===

Jyoung at 23:57, 6 December 2019

2019-12-06T23:57:49Z

← Older revision		Revision as of 23:57, 6 December 2019
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	Response: The search returns a JSON object containing the result set as a data property		Response: The search returns a JSON object containing the result set as a data property

			==Similarity Search==

	curl 'http://arthor.docking.org/dt/now_bb/search?query=c1ccccc1&type=SIM&start=0&length=5'		curl 'http://arthor.docking.org/dt/now_bb/search?query=c1ccccc1&type=SIM&start=0&length=5'
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	}		}


			==Substructure or SMARTS Search==
	A substructure or SMARTS search has some additional complexity. A parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total number of hits. The idea is the server can be pooled until the count is finished.		A substructure or SMARTS search has some additional complexity. A parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total number of hits. The idea is the server can be pooled until the count is finished.

Jyoung at 23:56, 6 December 2019

2019-12-06T23:56:45Z

← Older revision		Revision as of 23:56, 6 December 2019
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	//matches UI		//matches UI
	let DEFAULT_FLAGS = QueryFlags.AROMATISE \|		let DEFAULT_FLAGS = QueryFlags.AROMATISE \|
	QueryFlags.LOCK_CHARGES \|		QueryFlags.LOCK_CHARGES \|
	QueryFlags.LOCK_ISOTOPES \|		QueryFlags.LOCK_ISOTOPES \|
	QueryFlags.LOCK_CONNECTIVITY;		QueryFlags.LOCK_CONNECTIVITY;

Jyoung at 23:56, 6 December 2019

2019-12-06T23:56:12Z

Jyoung: Created page with "=Introduction= This information was taken from the Arthor version 2.1.2 documentation. RESTful API: The current server implementation utilizes the Data Tables JS library to ..."

2019-12-06T23:55:16Z

Created page with "=Introduction= This information was taken from the Arthor version 2.1.2 documentation. RESTful API: The current server implementation utilizes the Data Tables JS library to ..."

New page

=Introduction=

This information was taken from the Arthor version 2.1.2 documentation. RESTful API: The current server implementation utilizes the Data Tables JS library to display hits. The current API therefore reflects some requirements of this library and all URLs are organised under the /dt/ (for data tables) path, in future there may be new URLs introduced to match other clients (e.g. /jchem/).

==Data Tables==

===/dt/data===
List all available databases and the types of search available, note a “SUB” in idxTypes means both “SUB” and “SMA” search can be performed:

Example command:
curl 'http://arthor.docking.org/dt/data'

Produces the following JSON:
[{"displayName":"wait-ok.smi","location":"/usr/local/tomcat/arthor_data/wait-ok.smi","urlFormatStr":null,"idxTypes":["SUB"]},{"displayName":"for-sale.smi","location":"/usr/local/tomcat/arthor_data/for-sale.smi","urlFormatStr":null,"idxTypes":["SUB"]},{"displayName":"now_bb.smi","location":"/usr/local/tomcat/arthor_data/now_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"wait-ok_bb.smi","location":"/usr/local/tomcat/arthor_data/wait-ok_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"for-sale_bb.smi","location":"/usr/local/tomcat/arthor_data/for-sale_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"in-stock.smi","location":"/usr/local/tomcat/arthor_data/in-stock.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"bb-all.smi","location":"/usr/local/tomcat/arthor_data/bb-all.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"bb-now.smi","location":"/usr/local/tomcat/arthor_data/bb-now.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"interesting.smi","location":"/usr/local/tomcat/arthor_data/interesting.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"on-demand.smi","location":"/usr/local/tomcat/arthor_data/on-demand.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},{"displayName":"wuxi.smi","location":"/usr/local/tomcat/arthor_data/wuxi.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]}]

===/dt/${db_name}/data===
Access information on a single database, the virtual memory status is also reported for Similarity and Substructure indexes:

===/dt/${db_name}/search/===
Search a database with a query SMILES/SMARTS.

${db_name} Required path variable, the database name is specified in the URL path as ${db_name}. For one of the databases above, ‘ChEMBL 23’ would be searched as /dt/ ChEMBL%2023/search.
query=<string> The query to run either a valid SMILES or SMARTS, depending on search type.
type=SUB|SIM|SMA The search type to perform (SUB=Substructure, SMA=SMARTS, SIM=Similarity), these primarily differ by what input is expected in the query= string. Both “SUB” and “SIM” expect a valid SMILES to be provided, “SMA” expects a SMARTS.
The SMILES provided to “SUB” is aromatized to be consistent with the database (if flag provided) and converted to a query with any flags specified.
This parameter is optional, the default is “SIM”.

start=<num> Optional start offset for the result set to allow paging. The default value is 0 mean- ing the result start at the first hit.
length=<num> Optional length of the result set to allow paging. The default is 10.
draw=<num> Echoed value to maintain consistent ordering of asynchronous events. A number is provided to this parameter that is returned with the result set.
If when the response is received by the client the draw value doesn’t match the current draw value the result can be considered “out of date” and should be ignored.
This value is client specific and optional.
qopts=<opts> Specify the query options to run the Substructure or SMARTS search with. For example “qopts=RC” would lock the rings and chains of the query. See Arthor::ParseQuery for more info.
If your query is an MDL file then you must specify “Mdl” in the qopts.

//matches server side constants
let QueryFlags = {
AROMATISE: 0x0100,
LOCK_RINGS: 0x0200,
LOCK_CHAINS: 0x0400,
LOCK_CHARGES: 0x0800
LOCK_ISOTOPES: 0x1000,
LOCK_CONNECTIVITY 0x2000
};

//matches UI
let DEFAULT_FLAGS = QueryFlags.AROMATISE |
QueryFlags.LOCK_CHARGES |
QueryFlags.LOCK_ISOTOPES |
QueryFlags.LOCK_CONNECTIVITY;

To "lock" means don't allow it to change

Response: The search returns a JSON object containing the result set as a data property

curl 'http://arthor.docking.org/dt/now_bb/search?query=c1ccccc1&type=SIM&start=0&length=5'

{"query":"c1ccccc1","
data":[
[1,"c1ccccc1\tZINC000000967532","1.000"],
[2,"c1ccccccccccccccccc1\tZINC000100074375","1.000"],
[3,"c1ncncn1\tZINC000001718513","0.498"],
[4,"c1cncnc1\tZINC000000895216","0.427"],
[5,"Ic1cc(I)cc(I)c1\tZINC000057266212","0.373"]],
"draw":0,"recordsFiltered":1649789,"recordsTotal":1649789,"time":79,"hasMore":false,"error":null
}

A substructure or SMARTS search has some additional complexity. A parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total number of hits. The idea is the server can be pooled until the count is finished.

curl 'http://arthor.docking.org/dt/now_bb/search?query=c1ccccc1&type=SUB&start=0&length=5'

{"query":"c1:c:c:c:c:c:1","data":[
[1,"C[C@@]1(c2ccccc2)OC(C(=O)O)=CC1=O\tZINC000000000010",""],
[2,"COc1cc(Cc2cnc(N)nc2N)cc(OC)c1N(C)C\tZINC000000000011",""],
[3,"O=C(C[S@@](=O)C(c1ccccc1)c1ccccc1)NO\tZINC000000000012",""],
[4,"CCC[S@](=O)c1ccc2[nH]/c(=N\\C(=O)OC)[nH]c2c1\tZINC000000000017",""],
[5,"C=C(C)CNc1ccc([C@H](C)C(=O)O)cc1\tZINC000000000022",""]],
"draw":0,"recordsFiltered":1162074,"recordsTotal":1162074,"time":1090,"hasMore":false,"error":null
}

After some time the background count will have completed and the hasMore will now be false meaning the hit count is correct. The time taken to do the count is set on the time field.

← Older revision		Revision as of 23:56, 6 December 2019
Line 54:		Line 54:
	Response: The search returns a JSON object containing the result set as a data property		Response: The search returns a JSON object containing the result set as a data property

	curl 'http://arthor.docking.org/dt/now_bb/search?query=c1ccccc1&type=SIM&start=0&length=5'		curl 'http://arthor.docking.org/dt/now_bb/search?query=c1ccccc1&type=SIM&start=0&length=5'

	{"query":"c1ccccc1","		{"query":"c1ccccc1","
	data":[		data":[
	[1,"c1ccccc1\tZINC000000967532","1.000"],		[1,"c1ccccc1\tZINC000000967532","1.000"],
	[2,"c1ccccccccccccccccc1\tZINC000100074375","1.000"],		[2,"c1ccccccccccccccccc1\tZINC000100074375","1.000"],
	[3,"c1ncncn1\tZINC000001718513","0.498"],		[3,"c1ncncn1\tZINC000001718513","0.498"],
	[4,"c1cncnc1\tZINC000000895216","0.427"],		[4,"c1cncnc1\tZINC000000895216","0.427"],
	[5,"Ic1cc(I)cc(I)c1\tZINC000057266212","0.373"]],		[5,"Ic1cc(I)cc(I)c1\tZINC000057266212","0.373"]],
	"draw":0,"recordsFiltered":1649789,"recordsTotal":1649789,"time":79,"hasMore":false,"error":null		"draw":0,"recordsFiltered":1649789,"recordsTotal":1649789,"time":79,"hasMore":false,"error":null
	}		}

	A substructure or SMARTS search has some additional complexity. A parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total number of hits. The idea is the server can be pooled until the count is finished.		A substructure or SMARTS search has some additional complexity. A parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total number of hits. The idea is the server can be pooled until the count is finished.

	curl 'http://arthor.docking.org/dt/now_bb/search?query=c1ccccc1&type=SUB&start=0&length=5'		curl 'http://arthor.docking.org/dt/now_bb/search?query=c1ccccc1&type=SUB&start=0&length=5'

	{"query":"c1:c:c:c:c:c:1","data":[		{"query":"c1:c:c:c:c:c:1","data":[
	[1,"C[C@@]1(c2ccccc2)OC(C(=O)O)=CC1=O\tZINC000000000010",""],		[1,"C[C@@]1(c2ccccc2)OC(C(=O)O)=CC1=O\tZINC000000000010",""],
	[2,"COc1cc(Cc2cnc(N)nc2N)cc(OC)c1N(C)C\tZINC000000000011",""],		[2,"COc1cc(Cc2cnc(N)nc2N)cc(OC)c1N(C)C\tZINC000000000011",""],
	[3,"O=C(C[S@@](=O)C(c1ccccc1)c1ccccc1)NO\tZINC000000000012",""],		[3,"O=C(C[S@@](=O)C(c1ccccc1)c1ccccc1)NO\tZINC000000000012",""],
	[4,"CCC[S@](=O)c1ccc2[nH]/c(=N\\C(=O)OC)[nH]c2c1\tZINC000000000017",""],		[4,"CCC[S@](=O)c1ccc2[nH]/c(=N\\C(=O)OC)[nH]c2c1\tZINC000000000017",""],
	[5,"C=C(C)CNc1ccc([C@H](C)C(=O)O)cc1\tZINC000000000022",""]],		[5,"C=C(C)CNc1ccc([C@H](C)C(=O)O)cc1\tZINC000000000022",""]],
	"draw":0,"recordsFiltered":1162074,"recordsTotal":1162074,"time":1090,"hasMore":false,"error":null		"draw":0,"recordsFiltered":1162074,"recordsTotal":1162074,"time":1090,"hasMore":false,"error":null
	}		}

	After some time the background count will have completed and the hasMore will now be false meaning the hit count is correct. The time taken to do the count is set on the time field.		After some time the background count will have completed and the hasMore will now be false meaning the hit count is correct. The time taken to do the count is set on the time field.