ZINC15:Syntax
The general form of a ZINC 15 api request is
http[s]://host:port/reference-table/format:column1,column2,...columnN/query-specification
We take up each element in turn.
- We support both http and https protocols. - host name on request - port number on request
reference-table
There is one reference table per ZINC api request. Each row in the output corresponds to one row in the reference-table. Reference tables are always plurals, indicating that the result is always a selection from among the rows in the reference-table. The supported reference-tables are:
| 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 |
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 |
= Similarity and Substructure
.../substance.structure similarto c1ccccc1CCCOC within .7 using tanimoto
/substance/txt:zinc_id/substance isa metabolite
/substances/txt:zinc_id?sort=substance.structure+near+c1ccccc1CCNC+using+dice
Closest purchasable metabolite
select s.sub_id, s.smiles, tanimoto_sml(f.data, bfp_from_binary_text('\x804300004000200080400000800000008220800040000120008002002011000010040081010000002840400009d040048000020200001a404100000002000040')), short_name from fingerprints.ecfp4_data as f join fingerprints.ecfp4_id on ecfp4_id=f.ecfp4_fk join substance as s on s.ecfp4_fk=ecfp4_id join catalog_item on sub_id_fk=s.sub_id join catalog on cat_id_fk=cat_id where f.ecfp4_fk < 1000000 and purchasable > 30 order by bfp_from_binary_text('\x804300004000200080400000800000008220800040000120008002002011000010040081010000002840400009d040048000020200001a404100000002000040') <%> f.data limit 5;