ZINC:Command language: Difference between revisions

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You can control ZINC-12 remotely by hand writing URLs.  This document is a guide to how to use them.
You can control ZINC-12 remotely by hand writing URLs.  This document is a guide to how to use them. A subset of these qualify as RESTful.  There are more pages about controlling ZINC via various kinds of APIs we've experimented with at [[ZINC api]].


= Quick Search Bar =  
URLs are generally of the form:  http://zinc.docking.org/results?category.field=argument&category2.field2=argument2
We interpret the text in the quick search bar in the following order.  Wildcards are supported


1) If it is a number, interpret as a ZINC ID. To force this behavior, prefix with zinc:
Multiple queries and format instructions may be supplied in a single transaction.  


e.g. zinc:32768 and 32768 and 32768+55535+7  and 3933993*  ; are all supported
= Quick Search Bar =
You can access all the functionality of the [[Quick Search Bar]] (QSB) using the /find/ command to form a valid RESTful query.   


2) If it is of the form number-number-number, interpret as a CAS number. For force this behavior, prefix with cas:
e.g.  http://zinc.docking.org/find/12346+3432+3343    ; search for 3 ZINC IDs
e.g.  http://zinc.docking.org/find/drug:ibuprofen            ; interpreted as in the interactive Quick Search Bar


  e.g. cas:5-6-10 and 6-54-2 and 3-5-6+3-4-2    ; are all supported
The commands supported in the QSB (before the :, no spaces)  in the quick search bar are zinc, cas, smiles, drug, target, catalog and vendor. See the [[QSB]] article for examples.


3) If it is a valid SMILES, interpret as "90% similar to".  To force this behavior, prefix with smiles:
= Structure =
3a) Optionally after SMILES (SMARTS) add identical, exact, substructure, 80% or 0.8 (or any value) for corresponding searches.
The SMILES and SMARTS must be URL encoded.


  e.g. smiles:O=C1CCN1 substructure     and    smiles:O=C1CCN1 77%    and  C1CCNCC1 exact    ; are all supported
  structure.similarity=n where 0<=n<=1
structure.smiles=<SMILES>
structure.substructure=<SMARTS>


4) Attempt to interpret as name of molecule. To force this behavior, prefix with name: or drug:
e.g. http://zinc.docking.org/results.?structure.smiles=C1CCCCC1&structure.similarity=1.0  ; search for exactly cyclohexane


  e.g. drug:cetirizine    and    drug:*pram  and    ibuprofen    ; are all supported
= Catalog =
  catalog.purchasability={not-for-sale, in-stock, on-demand, boutique, agent, collabocules>
catalog.name=<name>


5) Attempt to interpret as target name. Uniprot and SwissProt codes as well as target names are supported.   To force this behavior, prefix with target:
e.g. http://zinc.docking.org/results?catalog.purchasablity=in-stock
e.g. http://zinc.docking.org/results?catalog.name=:ChemBridge,Molport


e.g. target:5ht1a*      and      hdac*        and  DRD2_HUMAN    and Q2LFS1    ; are all supported
= ZINC ID =


6) Attempt to interpret as catalog name. To force this behavior, prefix with catalog:
zinc.id =


  e.g. ChemBridge    and catalog:Enamine  ;  are all supported
  e.g.http://zinc.docking.org/results?zinc.id=29323


6a) Attempt to interpret as vendor code, optionally prefixed with vendor name. Thus
= Annotation =
annotation.swiss_prot=Q9R297
annotation.uniprot=HRH1_HUMAN
annotation.term=:Q9R297,HRH1_HUMAN


  e.g. ChemBridge T12345    and Enamine 194394*    and    vendor 12345 ; are all supported. In the last case, any compound called 12345 by any vendor.
  e.g.http://zinc.docking.org/results?annotation.uniprot=HRH1_HUMAN


= Prediction =
prediction.swiss_prot=Q9R297
prediction.uniprot=HRH1_HUMAN


== Structure ==
  e.g.http://zinc.docking.org/results?prediction.swissprot=Q112345
structure[similarity]=n where 0<=n<=1
structure[smiles]=smiles
structure[smiles]=name


Example:
= Clustered Targets =
  http://zinc12.docking.org/search/results.php?structure[smiles]=cetirizine&structure[similarity]=1.0
  target.code=drd2-1-e


== Vendor ==
  e.g.http://zinc.docking.org/results?target.code=drd2-1-e
  catalog[purchasability][]=n where 0=not for sale, 1=0-2 week delivery, 2=6-10 week delivery, 4=expensive


== ZINC ID ==  
= Reports, Formats, Filters =
 
page.format=X where X = sdf, mol2, smi, Flexibase
filter.representation=X where X= usual, single, metal, all, ref, mid, hi, lo
filter.purchasability=X where X= in-stock, on-demand, purchasable, not-for-sale, all, ...
 
e.g. http://zinc.docking.org/results?annotation.name=DRD2_HUMAN&filter.purchasability=purchasable


== Annotation ==
annotation[swiss_prot]=Q9R297
annotation[uniprot]=HRH1_HUMAN


== Prediction ==  
== Complete list of supported purchasability types ==
  prediction[swiss_prot]=Q9R297
* purchasable
prediction[uniprot]=HRH1_HUMAN
* stock-demand = in stock OR make on demand
* in-stock
* on-demand
* boutique
* not-for-sale
* annotated
* modelsystems
* collabocules
* all
* jfk = boutique


= Reports, Formats, Filters = 
== Complete list of supported page/report formats ==
* list
* compact
* summary
* basic
* targets
* ratings
 
* properties
* purchasing-info
* sdf
* smiles
* mol2
* db
* zinc
* 800-lb-gorilla
 
and for completeness
 
* chimera
* pymol
* marvin
* ijchem
These last 4 don't really make sense in a wget/curl context, and are really there for future support and/or nonstandard browser support.


page[format]=X where X = sdf, mol2, smi, Flexibase
page[filter]=X where X= usual, single, metal, all, ref, mid, hi, lo


[[Category:ZINC]]
[[Category:ZINC]]
[[Category:API]]

Latest revision as of 21:34, 28 December 2018

You can control ZINC-12 remotely by hand writing URLs. This document is a guide to how to use them. A subset of these qualify as RESTful. There are more pages about controlling ZINC via various kinds of APIs we've experimented with at ZINC api.

URLs are generally of the form: http://zinc.docking.org/results?category.field=argument&category2.field2=argument2

Multiple queries and format instructions may be supplied in a single transaction.

Quick Search Bar

You can access all the functionality of the Quick Search Bar (QSB) using the /find/ command to form a valid RESTful query. 

e.g.  http://zinc.docking.org/find/12346+3432+3343    ; search for 3 ZINC IDs
e.g.  http://zinc.docking.org/find/drug:ibuprofen            ; interpreted as in the interactive Quick Search Bar

The commands supported in the QSB (before the :, no spaces) in the quick search bar are zinc, cas, smiles, drug, target, catalog and vendor. See the QSB article for examples.

Structure

The SMILES and SMARTS must be URL encoded. 

structure.similarity=n where 0<=n<=1
structure.smiles=<SMILES>
structure.substructure=<SMARTS>

e.g. http://zinc.docking.org/results.?structure.smiles=C1CCCCC1&structure.similarity=1.0   ; search for exactly cyclohexane

Catalog

catalog.purchasability={not-for-sale, in-stock, on-demand, boutique, agent, collabocules>
catalog.name=<name>

e.g. http://zinc.docking.org/results?catalog.purchasablity=in-stock
e.g. http://zinc.docking.org/results?catalog.name=:ChemBridge,Molport

ZINC ID

zinc.id =

e.g.http://zinc.docking.org/results?zinc.id=29323

Annotation

annotation.swiss_prot=Q9R297
annotation.uniprot=HRH1_HUMAN
annotation.term=:Q9R297,HRH1_HUMAN

e.g.http://zinc.docking.org/results?annotation.uniprot=HRH1_HUMAN

Prediction

prediction.swiss_prot=Q9R297
prediction.uniprot=HRH1_HUMAN

 e.g.http://zinc.docking.org/results?prediction.swissprot=Q112345

Clustered Targets

target.code=drd2-1-e

e.g.http://zinc.docking.org/results?target.code=drd2-1-e

Reports, Formats, Filters

page.format=X where X = sdf, mol2, smi, Flexibase
filter.representation=X where X= usual, single, metal, all, ref, mid, hi, lo
filter.purchasability=X where X= in-stock, on-demand, purchasable, not-for-sale, all, ...

e.g. http://zinc.docking.org/results?annotation.name=DRD2_HUMAN&filter.purchasability=purchasable


Complete list of supported purchasability types

  • purchasable
  • stock-demand = in stock OR make on demand
  • in-stock
  • on-demand
  • boutique
  • not-for-sale
  • annotated
  • modelsystems
  • collabocules
  • all
  • jfk = boutique

Complete list of supported page/report formats

  • list
  • compact
  • summary
  • basic
  • targets
  • ratings
  • properties
  • purchasing-info
  • sdf
  • smiles
  • mol2
  • db
  • zinc
  • 800-lb-gorilla

and for completeness

  • chimera
  • pymol
  • marvin
  • ijchem

These last 4 don't really make sense in a wget/curl context, and are really there for future support and/or nonstandard browser support.

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