ZINC15:Syntax: Difference between revisions
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The general form of a ZINC 15 api request is | The general form of a ZINC 15 api request is | ||
'''http[s]://host | '''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 resources in the table below. | ||
- | * format is one of the 12 formats in the formats table below. 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. | |||
= | = Resources = | ||
A resource is the type of object you are asking for. Each ZINC URL specifies only one of 15 available resources. Resources are always plurals, indicating that the result is always a selection from among the rows in that resource. The supported reference-tables are: | |||
{| class="wikitable" | {| class="wikitable" | ||
| Line 18: | Line 22: | ||
| substances || substance table || notes about substance table | | substances || substance table || notes about substance table | ||
|- | |- | ||
| | | catalogs || asdfasdf || sdfsdfdaf | ||
|- | |||
| genes || sdfasfd || sadfasdf | |||
|- | |- | ||
| catalogitems || lala || asdf | | catalogitems || lala || asdf | ||
|- | |- | ||
| protomers || qwer34 || seradsf | | protomers || qwer34 || seradsf | ||
|- | |- | ||
| targets || asdfasdf || asdfasdf sa | | targets || asdfasdf || asdfasdf sa | ||
|- | |- | ||
| activities || sadfasfsd || asdfasfd | | activities || sadfasfsd || asdfasfd | ||
|- | |||
| purchasability ||asdf asdf || asdfasfd sadf | |||
|- | |||
| representatives ||asdf asdf || asdfasfd sadf | |||
|- | |||
| clusters ||asdf asdf || asdfasfd sadf | |||
|- | |||
| bioactivities ||asdf asdf || asdfasfd sadf | |||
|- | |||
| majorclasses ||asdf asdf || asdfasfd sadf | |||
|- | |||
| targetclasses ||asdf asdf || asdfasfd sadf | |||
|- | |- | ||
| organisms ||asdf asdf || asdfasfd sadf | | organisms ||asdf asdf || asdfasfd sadf | ||
|- | |||
| modeltypes ||asdf asdf || asdfasfd sadf | |||
|- | |||
| structures ||asdf asdf || asdfasfd sadf | |||
|- | |||
| traits ||asdf asdf || asdfasfd sadf | |||
|- | |||
| tools ||asdf asdf || asdfasfd sadf | |||
|- | |||
| ecfp4s || lala || fingerprints | |||
|} | |} | ||
Revision as of 20:48, 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 resources in the table below.
- format is one of the 12 formats in the formats table below. 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.
Resources
A resource is the type of object you are asking for. Each ZINC URL specifies only one of 15 available resources. Resources are always plurals, indicating that the result is always a selection from among the rows in that resource. The supported reference-tables are:
| table name | Description | Notes/Links |
|---|---|---|
| substances | substance table | notes about substance table |
| catalogs | asdfasdf | sdfsdfdaf |
| genes | sdfasfd | sadfasdf |
| catalogitems | lala | asdf |
| protomers | qwer34 | seradsf |
| targets | asdfasdf | asdfasdf sa |
| activities | sadfasfsd | asdfasfd |
| purchasability | asdf asdf | asdfasfd sadf |
| representatives | asdf asdf | asdfasfd sadf |
| clusters | asdf asdf | asdfasfd sadf |
| bioactivities | asdf asdf | asdfasfd sadf |
| majorclasses | asdf asdf | asdfasfd sadf |
| targetclasses | asdf asdf | asdfasfd sadf |
| organisms | asdf asdf | asdfasfd sadf |
| modeltypes | asdf asdf | asdfasfd sadf |
| structures | asdf asdf | asdfasfd sadf |
| traits | asdf asdf | asdfasfd sadf |
| tools | asdf asdf | asdfasfd sadf |
| ecfp4s | lala | fingerprints |
Historical note: In ZINC 12, the reference-table was always substances, and thus the result of any query was always a set of molecules. A few reports such as vendor and target listings were available via the webpages, but were not supported by the API. This is a substantial change that appeared first in ZINC 15.
Format
We support the following formats
| format | Description | options/links |
|---|---|---|
| json | substance table | notes about substance table |
| txt | lala | lala |
| csv | lala | asdf |
| xls | asdfasdf | sdfsdfdaf |
| tsv | qwer34 | seradsf |
| xml | sdfasfd | sadfasdf |
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 |
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