ZINC15:Syntax: Difference between revisions

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* resource is one of the 15 [[ZINC15:Resources]]
* resource is one of the 15 [[ZINC15:Resources]]
* format is one of the 12 [[ZINC15:Formats]].  If omitted, a web page is requested.
* format is one of the 12 [[ZINC15:Formats]].  If omitted, a web page is requested.
* columns is one or more of the columns in the columns table below. Not all columns make sense in all resource contexts.  Examples are provided. There are sensible defaults for each resource, so the column specification may be omitted.
* columns is one or more of the [[ZINC15:Columns]]. Not all columns make sense in all resource contexts.  Examples are provided. There are sensible defaults for each resource, so the column specification may be omitted.
* variant is optionally one or more of the variants in the variants table below
* variant is optionally one or more of the variants in the variants table below
* page-view-controls is optionally one or more of those listed in the page-view-controls table, below.
* page-view-controls is optionally one or more of those listed in the page-view-controls table, below.
* resource constraints is optionally one or more of those in the resource-constraints table, below.
* resource constraints is optionally one or more of those in the resource-constraints table, below.


= Columns =
The result contains the specified columns in the output.  If the column is in the reference-table, it is specified without a table specfification, otherwise, the column specification must be of the form table.item.
The following items are supported in each of the tables.
{| class="wikitable"
|-
! table name !! Description !! Notes/Links
|-
|  substances || substance table || notes about substance table
|-
| ecfp4s  || lala || lala
|-
| catalogitems || lala || asdf
|-
| catalogs || asdfasdf || sdfsdfdaf
|-
| protomers || qwer34 || seradsf
|-
| genes || sdfasfd || sadfasdf
|-
| targets || asdfasdf || asdfasdf sa
|-
| activities || sadfasfsd || asdfasfd
|-
| organisms ||asdf asdf || asdfasfd sadf
|}
Objects from among these may be specified as part of a query_specification.
{| class="wikitable"
|-
! table name !! Description !! Notes/Links
|-
|  substances || sub_id, structure, inchikey, up_date, logp, tpsa, hbd, hba || notes about substance table
|-
| structure  || mwt, logp, tpsa, hba, hbd, num_atoms, num_heavy_atoms, rotatable_bonds, num_hetero_atoms, num_rings, inchi || lala
|-
| protomers || prot_id, sub_id_fk, desolv_apol, desolv_pol, net_charge || asdf
|-
| catalogs || cat_id, name, short_name, purchasable, free, version, updated, bb, np, drug || sdfsdfdaf
|-
| catalogitems || sub_id_fk, cat_id_fk, supplier_code, depleted || seradsf
|-
| genes || short_name || sadfasdf
|-
| targets || swissprot, uniprot, target, gene, affinity || asdfasdf sa
|-
| activities || affinitynM, target, gene, organism || asdfasfd
|-
| organisms ||asdf asdf || asdfasfd sadf
|}




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| xml || sdfasfd || sadfasdf
| xml || sdfasfd || sadfasdf
|}
|}


= Format =
= Format =

Revision as of 20:58, 4 March 2015

The general form of a ZINC 15 api request is

http[s]://host/resource[.format[:columns][/variant][?page-view-controls | resource-constraints]

Where items in [ square brackets ] are optional.

  • host = zinc15.docking.org
  • resource is one of the 15 ZINC15:Resources
  • format is one of the 12 ZINC15:Formats. If omitted, a web page is requested.
  • columns is one or more of the ZINC15:Columns. Not all columns make sense in all resource contexts. Examples are provided. There are sensible defaults for each resource, so the column specification may be omitted.
  • variant is optionally one or more of the variants in the variants table below
  • page-view-controls is optionally one or more of those listed in the page-view-controls table, below.
  • resource constraints is optionally one or more of those in the resource-constraints table, below.


Variants

We support the following variants

format Description options/links
page=x substance table notes about substance table
perpage=y lala lala
count=all lala asdf
distinct asdfasdf sdfsdfdaf
sort-by qwer34 seradsf
xml sdfasfd sadfasdf

Format

We support the following resource constraints

format Description options/links
resource.attribute:operator substance table notes about substance table
blah lala lala
blah lala asdf
xls asdfasdf sdfsdfdaf
tsv qwer34 seradsf
xml sdfasfd sadfasdf


Query operators

operator Description synonyms
@> lala contains
<@ lala contained in
= equals eq
< less than lt
> greater than gt
<= less than or equal le
>= greater than or equal ge
between sadfasfsd asdfasfd
like, is, not , startswith, endswith, similar to asdf asdf asdfasfd sadf

NP, Drug and BB

quality values Notes/Links
NP 0=unknown, 1=biogenic, 2=metabolite, 3=endogenous human metabolite lala
Drug 0=unknown, 1=annotated catalog, 2=bioactive, 4=bioactive in vitro < 1uM, 5=bioactive in cells <1uM, 6=in man, 8=world drug, 10=fda approved lala
BB f=not bb, t=bb asdf

examples

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/catalog.purchasable%20gt%209&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5?count=all
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