ZINC15:Syntax: Difference between revisions

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


Where items in \[ square brackets \] are optional.
Where items in [ square brackets ] are optional.


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Revision as of 20:55, 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 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.
  • 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.

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.


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.


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


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