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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 | ||
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 = | |||
== application:docking == | |||
= application:docking = | |||
Supported actions are: pdb, upload, listpdb, jobs, myjobs | Supported actions are: pdb, upload, listpdb, jobs, myjobs | ||
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== | == 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: | Supported subactions are: download | ||
| Line 82: | Line 87: | ||
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]] | ||
Revision as of 18:14, 8 December 2014
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/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
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)
Sub-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.
Sub-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.
Subactions for acting on a decoys job
Supported subactions are: download
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
Sub-actions for application: zinc
Supported subactions are: download
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