How to use SmallWorld API: Difference between revisions
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===Example Request=== | ===Example Request=== | ||
Suppose you want to search for c1ccccc1 in the ZINC-Interesting-297K Database: There are two steps. The first step which involves /search/submit returns a stream of events that report the hit list id or hlid. This hlid is required to fetch results using the other options such as /search/view | Suppose you want to search for c1ccccc1 in the ZINC-Interesting-297K Database: There are two steps. The first step which involves /search/submit returns a stream of events that report the hit list id or hlid. This hlid is required to fetch results using the other options such as /search/view | ||
Change the smi to the SMILES for the molecule you want to query | |||
Change the db name to the database name from the list of publicly available databases below | |||
curl 'http://sw.docking.org//search/submit?smi=c1ccccc1&db=ZINC-Interesting-297K&dist=4&tdn=4&tup=4&rdn=4&rup=4&ldn=4&lup=4&maj=4&min=4&sub=4&scores=Atom%20Alignment,ECFP4,Daylight' | curl 'http://sw.docking.org//search/submit?smi=c1ccccc1&db=ZINC-Interesting-297K&dist=4&tdn=4&tup=4&rdn=4&rup=4&ldn=4&lup=4&maj=4&min=4&sub=4&scores=Atom%20Alignment,ECFP4,Daylight' |
Revision as of 21:47, 20 June 2019
Introduction
The Web Services API for SmallWorld Documentation is found in Section 8.3 of the SmallWorld version 4.0 manual starting from page 30 to 36. Copyright ©2012-2017 NextMove Software Limited. I copied the section here, and provided a list of publicly available databases for searching on sw.docking.org and some simple examples at the bottom.
8.3 Web Services API Important Entry Points
Unless stated otherwise all API entry points operate on HTTP GET/POST requests. A search on the server is first submitted (/search/submit), this returns a stream of events that report the hit list id (hlid). You can then use this hlid to fetch results either as JSON (/search/view) or TSV (/ search/export). An example Java client, SwHttpClient.java, shows how this works.
/search/submit
Start a new SmallWorld search with topological distance bounded by the provided upper bounds.
Parameter | Type | Description |
---|---|---|
smi | text | Query SMILES |
db | text | Reference database (see List of available maps) |
dist | int | Topological distance upper bound (default: 10) |
tdn | int | Topological terminal down distance upper bound (default: 10) |
tup | int | Topological terminal up distance upper bound (default: 10) |
rdn | int | Topological ring down distance upper bound (default: 10) |
rup | int | Topological ring up distance upper bound (default: 10) |
ldn | int | Topological linker down distance upper bound (default: 10) |
lup | int | Topological linker up distance upper bound (default: 10) |
scores | text | List of scoring functions (default : none) - see /search/config |
Example Request
Suppose you want to search for c1ccccc1 in the ZINC-Interesting-297K Database: There are two steps. The first step which involves /search/submit returns a stream of events that report the hit list id or hlid. This hlid is required to fetch results using the other options such as /search/view
Change the smi to the SMILES for the molecule you want to query Change the db name to the database name from the list of publicly available databases below
curl 'http://sw.docking.org//search/submit?smi=c1ccccc1&db=ZINC-Interesting-297K&dist=4&tdn=4&tup=4&rdn=4&rup=4&ldn=4&lup=4&maj=4&min=4&sub=4&scores=Atom%20Alignment,ECFP4,Daylight'
The API streams back JSON chunks. Possible status messages are FIRST, MORE, END, and ‘Ground Control to Major Tom’ (hangup ping). Each status contains the hit list id (hlid) which can be used with the export and view API entry points.
From this example:
data:{"status":"FIRST","hlid":5908,"elap":"0.0 s","numEdges":0,"numNodes":0,"numWaveFront":1,"numEdgesPerSec":"NaN"} data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"0.0 s","numEdges":0,"numNodes":0,"numWaveFront":0,"numEdgesPerSec":0.0} data:{"status":"MORE","hlid":5908,"elap":"0.0 s","numEdges":1,"numNodes":2,"numWaveFront":3,"numEdgesPerSec":47.783445425332395} data:{"status":"MORE","hlid":5908,"elap":"0.0 s","numEdges":7,"numNodes":8,"numWaveFront":14,"numEdgesPerSec":237.99311152737997} data:{"status":"MORE","hlid":5908,"elap":"0.1 s","numEdges":47,"numNodes":42,"numWaveFront":51,"numEdgesPerSec":583.5923096639136} data:{"status":"MORE","hlid":5908,"elap":"0.4 s","numEdges":363,"numNodes":216,"numWaveFront":221,"numEdgesPerSec":884.1124840482239} data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"0.5 s","numEdges":363,"numNodes":216,"numWaveFront":221,"numEdgesPerSec":700.4466134439543} data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"1.0 s","numEdges":441,"numNodes":253,"numWaveFront":224,"numEdgesPerSec":426.04845162109694} data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"1.6 s","numEdges":441,"numNodes":253,"numWaveFront":224,"numEdgesPerSec":284.05782226150757} data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"2.1 s","numEdges":458,"numNodes":263,"numWaveFront":278,"numEdgesPerSec":223.1371219908375} data:{"status":"END","hlid":5908,"elap":"2.2 s","numEdges":2417,"numNodes":981,"numWaveFront":885,"numEdgesPerSec":1104.50351038177}
Here the hlid for my request was 5908.
/search/export
Export a hit list (given by the id) to a tab-separated value table. The other parameters describe what columns, order, and filters are applied to the hit list. Like /search/view it uses the JQuery DataTables server-side processing parameters - https://www.datatables.net/manual/server-side.
Useful information about column names and values: 'hlid': hlid,
'columns[0][data]': 0, 'columns[0][name]': 'alignment', 'columns[0][searchable]': 'true', 'columns[0][orderable]': 'false', 'columns[0][search][value]': , 'columns[0][search][regex]': 'false',
'columns[1][data]': 1, 'columns[1][name]': 'dist', 'columns[1][searchable]': 'true', 'columns[1][orderable]': 'true', 'columns[1][search][value]': '0 - 10', 'columns[1][search][regex]': 'false',
'columns[2][data]': 2, 'columns[2][name]': 'ecfp4', 'columns[2][searchable]': 'true', 'columns[2][orderable]': 'true', 'columns[2][search][value]': , 'columns[2][search][regex]': 'false',
'columns[3][data]': 3, 'columns[3][name]': 'daylight', 'columns[3][searchable]': 'true', 'columns[3][orderable]': 'true', 'columns[3][search][value]': , 'columns[3][search][regex]': 'false',
'columns[4][data]': 4, 'columns[4][name]': 'topodist', 'columns[4][searchable]': 'true', 'columns[4][orderable]': 'true', 'columns[4][search][value]': '0 - 10', 'columns[4][search][regex]': 'false',
'columns[5][data]': 5, 'columns[5][name]': 'mces', 'columns[5][searchable]': 'true', 'columns[5][orderable]': 'true', 'columns[5][search][value]': , 'columns[5][search][regex]': 'false',
'columns[6][data]': 6, 'columns[6][name]': 'tdn', 'columns[6][searchable]': 'true', 'columns[6][orderable]': 'true', 'columns[6][search][value]': '0 - 0', 'columns[6][search][regex]': 'false',
'columns[7][data]': 7, 'columns[7][name]': 'tup', 'columns[7][searchable]': 'true', 'columns[7][orderable]': 'true', 'columns[7][search][value]': '0 - 10', 'columns[7][search][regex]': 'false',
'columns[8][data]': 8, 'columns[8][name]': 'rdn', 'columns[8][searchable]': 'true', 'columns[8][orderable]': 'true', 'columns[8][search][value]': '0 - 0', 'columns[8][search][regex]': 'false',
'columns[9][data]': 9, 'columns[9][name]': 'rup', 'columns[9][searchable]': 'true', 'columns[9][orderable]': 'true', 'columns[9][search][value]': '0 - 10', 'columns[9][search][regex]': 'false',
'columns[10][data]': 10, 'columns[10][name]': 'ldn', 'columns[10][searchable]': 'true', 'columns[10][orderable]':
Important! Once you run the /search/submit the most important value is the hlid
The columns in the resulting tab separated file are alignment dist ecfp4 daylight topodist mces tdn tup rdn rup ldn lup mut maj min hyb sub The results are sorted in starting with the highest ECFP4
curl 'http://sw.docking.org//search/export/?hlid=5908&draw=8&columns%5B0%5D%5Bdata%5D=0&columns%5B0%5D%5Bname%5D=alignment&columns%5B0%5D%5Bsearchable%5D=true&columns%5B0%5D%5Borderable%5D=false&columns%5B0%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B0%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B1%5D%5Bdata%5D=1&columns%5B1%5D%5Bname%5D=dist&columns%5B1%5D%5Bsearchable%5D=true&columns%5B1%5D%5Borderable%5D=true&columns%5B1%5D%5Bsearch%5D%5Bvalue%5D=0-10&columns%5B1%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B2%5D%5Bdata%5D=2&columns%5B2%5D%5Bname%5D=ecfp4&columns%5B2%5D%5Bsearchable%5D=true&columns%5B2%5D%5Borderable%5D=true&columns%5B2%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B2%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B3%5D%5Bdata%5D=3&columns%5B3%5D%5Bname%5D=daylight&columns%5B3%5D%5Bsearchable%5D=true&columns%5B3%5D%5Borderable%5D=true&columns%5B3%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B3%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B4%5D%5Bdata%5D=4&columns%5B4%5D%5Bname%5D=topodist&columns%5B4%5D%5Bsearchable%5D=true&columns%5B4%5D%5Borderable%5D=true&columns%5B4%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B4%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B5%5D%5Bdata%5D=5&columns%5B5%5D%5Bname%5D=mces&columns%5B5%5D%5Bsearchable%5D=true&columns%5B5%5D%5Borderable%5D=true&columns%5B5%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B5%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B6%5D%5Bdata%5D=6&columns%5B6%5D%5Bname%5D=tdn&columns%5B6%5D%5Bsearchable%5D=true&columns%5B6%5D%5Borderable%5D=true&columns%5B6%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B6%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B7%5D%5Bdata%5D=7&columns%5B7%5D%5Bname%5D=tup&columns%5B7%5D%5Bsearchable%5D=true&columns%5B7%5D%5Borderable%5D=true&columns%5B7%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B7%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B8%5D%5Bdata%5D=8&columns%5B8%5D%5Bname%5D=rdn&columns%5B8%5D%5Bsearchable%5D=true&columns%5B8%5D%5Borderable%5D=true&columns%5B8%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B8%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B9%5D%5Bdata%5D=9&columns%5B9%5D%5Bname%5D=rup&columns%5B9%5D%5Bsearchable%5D=true&columns%5B9%5D%5Borderable%5D=true&columns%5B9%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B9%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B10%5D%5Bdata%5D=10&columns%5B10%5D%5Bname%5D=ldn&columns%5B10%5D%5Bsearchable%5D=true&columns%5B10%5D%5Borderable%5D=true&columns%5B10%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B10%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B11%5D%5Bdata%5D=11&columns%5B11%5D%5Bname%5D=lup&columns%5B11%5D%5Bsearchable%5D=true&columns%5B11%5D%5Borderable%5D=true&columns%5B11%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B11%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B12%5D%5Bdata%5D=12&columns%5B12%5D%5Bname%5D=mut&columns%5B12%5D%5Bsearchable%5D=true&columns%5B12%5D%5Borderable%5D=true&columns%5B12%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B12%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B13%5D%5Bdata%5D=13&columns%5B13%5D%5Bname%5D=maj&columns%5B13%5D%5Bsearchable%5D=true&columns%5B13%5D%5Borderable%5D=true&columns%5B13%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B13%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B14%5D%5Bdata%5D=14&columns%5B14%5D%5Bname%5D=min&columns%5B14%5D%5Bsearchable%5D=true&columns%5B14%5D%5Borderable%5D=true&columns%5B14%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B14%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B15%5D%5Bdata%5D=15&columns%5B15%5D%5Bname%5D=hyb&columns%5B15%5D%5Bsearchable%5D=true&columns%5B15%5D%5Borderable%5D=true&columns%5B15%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B15%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B16%5D%5Bdata%5D=16&columns%5B16%5D%5Bname%5D=sub&columns%5B16%5D%5Bsearchable%5D=true&columns%5B16%5D%5Borderable%5D=true&columns%5B16%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B16%5D%5Bsearch%5D%5Bregex%5D=false&order%5B0%5D%5Bcolumn%5D=0&order%5B0%5D%5Bdir%5D=asc&start=0&length=18&search%5Bvalue%5D=&search%5Bregex%5D=false&_=1561063193443'
List of Publicly Available Maps
- ZINC-Interesting-297K
- BB-Stock-1.5M
- In-Stock-13.9M
- ZINC-All-For-Sale-1.2B
- ZINC-All-1.2B
- BB-all-for-sale-18M
- ZINC-On-Demand-1B
- GDB13-977M
- Wait-OK-1B
- WuXi-58.6M
The SmallWorld API provides the following additional entry points:
/search/maps
Lists all available dataset mapfiles. The response is a JSON detailing the map name, id prefix, resolve url
Example Request:
curl 'http://sw.docking.org/search/maps'
/search/config
Retrieves the public server configuration as JSON including the list of available score functions. The names of the scoring functions can be provided as a parameter to the /search/submit endpoint. Example Request:
curl 'http://sw.docking.org/search/config'