Api15 - Revision history

Frodo: asd

2015-10-02T00:14:11Z

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	where list1 and list2 is a previously created subset using the zinc api and reaction smarts is a chemical reaction to combine molecule from list1 with molecules from list2 to create a new combinatorial library.		where list1 and list2 is a previously created subset using the zinc api and reaction smarts is a chemical reaction to combine molecule from list1 with molecules from list2 to create a new combinatorial library.

	covalent docking. prepare hot covalent docking library.		covalent docking. prepare hot covalent docking library.


	~~[[Category:ZINC15]]~~

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2015-04-16T15:57:15Z

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	This is a ~~description~~ of ~~the 2015 api~~ to docking.org ~~services~~.		We offer an application programming interface to carry out complex queries. In general, queries are asynchronous. That is:
			* make a request
			* wait
			* retrieve the results

			This is the 2015 version of this service. To get a list of services offered, please browse to [api15.docking.org api15.docking.org]. Requests may be invoked starting from a web page, or by using curl or wget. As much as possible, each operation is atomic, that is, you make the request and get the response, and that is the end of it. We plan to support a hand-off model in which the results of one request may be used by a following request without downloading the files to your client computer.

	{{TOCright}}		{{TOCright}}
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	* covalent - covalent docking		* covalent - covalent docking
	* zinc - database preparation and processing, including covalent docking libraries		* zinc - database preparation and processing, including covalent docking libraries
	* ~~dude~~ - decoys as sanity checks, when actives are available		* decoys - decoys as sanity checks, when actives are available
			* action - other cheminformatics operations such as clustering
	This API aims to allow all simple transactions to be run under program control on our servers. The user may then elect to download the materials (docking prep files, databases) for local fine tuning on the user's machines, or to continue the calculation with less control on our servers.		This API aims to allow all simple transactions to be run under program control on our servers. The user may then elect to download the materials (docking prep files, databases) for local fine tuning on the user's machines, or to continue the calculation with less control on our servers.

			= Services offered =
			* currently no services are available.

			= Services planned for 2015 =
			* build library for docking - non-covalent
			* build library for docking - covalent
			* prepare receptor for docking - non-covalent
			* prepare receptor for docking - covalent
			* run docking controls - non-covalent
			* run docking controls - covalent
			* dock a library - non-covalent
			* dock a library - covalent
			* tanimoto lower triangular
			* chemical clustering

			= Service planned for 2016 =


	= Syntax =		= Syntax =
	The URL takes one of two forms		The URL takes one of two forms

	~~1. api~~.docking.org~~/vX~~/application/action~~/arguments~~		* api15.docking.org/application/action?arguments
			where application is one of: docking, covalent, zinc, decoys, or action, and action and arguments are defined in the relevant section of this page.
	~~1. api.docking.org/vX/job_number/application/subaction/~~arguments

	~~Where~~ application is one of: docking, covalent, zinc, decoys~~. We take up~~ the ~~arguments~~ of ~~each of these below:~~

	= Applications =		= Applications =

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2014-12-08T18:57:54Z

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	{{TOCright}}		{{TOCright}}

			= Background =
			Docking remains too difficult for many people, even experts. One of the reasons is that it requires a complex software and hardware environment that requires much effort and ongoing maintenance. The purpose of this API is to make important steps in the docking process more accessible. The major application areas are:
			* docking - non covalent docking
			* covalent - covalent docking
			* zinc - database preparation and processing, including covalent docking libraries
			* dude - decoys as sanity checks, when actives are available
			This API aims to allow all simple transactions to be run under program control on our servers. The user may then elect to download the materials (docking prep files, databases) for local fine tuning on the user's machines, or to continue the calculation with less control on our servers.

	= Syntax =		= Syntax =

Frodo: /* Use Case examples */

2014-12-08T18:49:11Z

Use Case examples

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	api.docking.org/v1/122334/download/db2		api.docking.org/v1/122334/download/db2

			Upload a structure of unknown function and unknown binding site, identify binding site
			api.docking.org/v1/dock/upload/rec=rec.pdb # implies pocket picking since no binding site specified
			Uploads as dock jobs 32234

			Download the pockets picked above together with basic cleanup and normalization of the structure
			api.docking.org/v1/dock/32234/download/all

			Upload a structure and a binding site specification, but still request that pockets be picked:
			api.docking.org/v1/dock/upload/rec=rec.pdb&lig=xtal-lig.pdb&pick=true

			Covalent docking. Upload a structure, and scan for eligible covalent attachment points.
			api.docking.org/v1/covalent/rec=rec.pdb

			covalent docking. Upload a structure and a covalent attachment point.
			api.docking.org/v1/covalent/rec=rec.pdb&site=Asp A 234

			Covalent docking. Prepare library for covalent docking.
			api.docking.org/v1/covalent/library/list1/list2/reactionsmarts
			where list1 and list2 is a previously created subset using the zinc api and reaction smarts is a chemical reaction to combine molecule from list1 with molecules from list2 to create a new combinatorial library.

			covalent docking. prepare hot covalent docking library.


	[[Category:ZINC15]]		[[Category:ZINC15]]

Frodo: blah

2014-12-08T18:14:41Z

blah

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	This is a description of the 2015 api to docking.org services.		This is a description of the 2015 api to docking.org services.

			{{TOCright}}

	= Syntax =		= Syntax =

Frodo at 18:14, 8 December 2014

2014-12-08T18:14:11Z

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	This is a description of the 2015 api to docking.org services. The URL takes one of two forms		This is a description of the 2015 api to docking.org services.

			= Syntax =
			The URL takes one of two forms

	1. api.docking.org/vX/application/action/arguments		1. api.docking.org/vX/application/action/arguments

	2. api.docking.org/vX/job_number/~~action~~/arguments		1. api.docking.org/vX/job_number/application/subaction/arguments

			Where application is one of: docking, covalent, zinc, decoys. We take up the arguments of each of these below:

	~~Where application is one of: zinc, docking, covalent, decoys, dude, advisor. We take up the arguments of each of these below:~~		= Applications =
			== application:docking ==
	= application:docking =
	Supported actions are: pdb, upload, listpdb, jobs, myjobs		Supported actions are: pdb, upload, listpdb, jobs, myjobs

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	== ~~Actions~~ for operating on a docking job ==		== Sub-actions for operating on a docking job ==

	info : display what kind of job it is, when submitted, current status.		info : display what kind of job it is, when submitted, current status.
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	= application:covalent =		== application:covalent ==
	supported actions are: upload, jobs, myjobs		supported actions are: upload, jobs, myjobs

	upload: specify receptor and covalent attachment point.		upload: specify receptor and covalent attachment point.

	== actions for operating on a covalent docking job ==		== Sub-actions for operating on a covalent docking job ==
	info: display what kind of job it is, when submitted, current status		info: display what kind of job it is, when submitted, current status
	library: specify library for docking		library: specify library for docking


	= application: decoys =		== application: decoys ==
	Supported actions are: make, get, list		Supported actions are: make, get, list

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	list: list all genes for which decoys (and actives) are available.		list: list all genes for which decoys (and actives) are available.

	= application: zinc =		== Subactions for acting on a decoys job ==
			Supported subactions are: download


			== application: zinc ==
	supported actions: upload, download, prepare, subset, hotsubset		supported actions: upload, download, prepare, subset, hotsubset

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	hotsubset: prepare covalent docking database		hotsubset: prepare covalent docking database

			== Sub-actions for application: zinc ==
	= application: ~~advisor~~ =		Supported subactions are: download




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	Download the arylsulfonamide database created above in db2 format		Download the arylsulfonamide database created above in db2 format
	api.docking.org/v1/122334/download/db2		api.docking.org/v1/122334/download/db2




	[[Category:ZINC15]]		[[Category:ZINC15]]

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2014-12-08T17:42:25Z

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	= application: advisor =		= application: advisor =




			= Use Case examples =

			Create a database of in stock commercially available arylsulfonamides for docking =
			api.docking.org/v1/zinc/subset/substances/smiles,sub_id/substance contains c1ccccc1S(=O)(=O)N&catalog.purchasable gt 20
			This is created as job # 122334

			Now find a upload a structure and docking this library to it
			api.docking.org/v1/dock/upload/rec=rec.pdb,lig=xtal-lig.pdb,lib=122334
			This is created as job # 556677

			Download the docking results for docking on the client
			api.docking.org/v1/556677/download/all

			Download the arylsulfonamide database created above in db2 format
			api.docking.org/v1/122334/download/db2

	[[Category:ZINC15]]		[[Category:ZINC15]]

Frodo: Created page with "This is a description of the 2015 api to docking.org services. The URL takes one of two forms 1. api.docking.org/vX/application/action/arguments 2. api.docking.org/vX/job_nu..."

2014-12-08T17:20:04Z

Created page with "This is a description of the 2015 api to docking.org services. The URL takes one of two forms 1. api.docking.org/vX/application/action/arguments 2. api.docking.org/vX/job_nu..."

New page

This is a description of the 2015 api to docking.org services. The URL takes one of two forms

1. api.docking.org/vX/application/action/arguments

2. api.docking.org/vX/job_number/action/arguments

Where application is one of: zinc, docking, covalent, decoys, dude, advisor. We take up the arguments of each of these below:

= application:docking =
Supported actions are: pdb, upload, listpdb, jobs, myjobs

pdb: specify pdb code for automatic (be_blasti) docking

upload: specify receptor and binding site. if binding site not specified, pockets are picked.

list: list all pdb codes supported

jobs: list all recent jobs in system

myjobs: list my recent jobs (based on apikey)

== Actions for operating on a docking job ==

info : display what kind of job it is, when submitted, current status.
pickpockets : pick pockets
library: specify library for docking

= application:covalent =
supported actions are: upload, jobs, myjobs

upload: specify receptor and covalent attachment point.

== actions for operating on a covalent docking job ==
info: display what kind of job it is, when submitted, current status
library: specify library for docking

= application: decoys =
Supported actions are: make, get, list

make: make decoys based on uploaded molecules

get: specify gene, get both actives and decoys from chembl for that gene

list: list all genes for which decoys (and actives) are available.

= application: zinc =
supported actions: upload, download, prepare, subset, hotsubset

upload: upload molecules for standard preparation using zinc pipeline. Libraries uploaded in this way may be used by docking

download: download large custom subset in any format.

prepare: make sure 3D versions of a subset are ready for download (this may take weeks)

subset: create a subset for docking,

hotsubset: prepare covalent docking database

= application: advisor =

[[Category:ZINC15]]