ZINC15:Syntax: Difference between revisions
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* host = zinc15.docking.org | * host = zinc15.docking.org | ||
* resource is one of the 15 | * resource is one of the 15 [[ZINC15:Resources]] | ||
* format is one of the 12 formats in the formats table below. If omitted, a web page is requested. | * 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. | * 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. | ||
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* 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. | ||
= Format = | = Format = | ||
Revision as of 20:53, 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 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.
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 |
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