How to use SmallWorld API
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Introduction
The Web Services API for SmallWorld Documentation is found in Section 6.3 of the SmallWorld version 5.6.2 manual.
Here are some simple examples.
API Routes
/search/maps
List all available databases (map files).
curl "https://sw.docking.org/search/maps"
/search/view
View the results of a search.
Access the results of a search either using the a hit-list id or by using the query parameters to start a new search automatically.
Parameter | Type | Description |
---|---|---|
id | integer | Hit List id |
smi | array | Query SMILES/SMARTS strings |
db | string | Database name |
fmt | string | Format of results: tsv,csv |
scores | string | Scoring function(s) to use |
top | integer | Only collect this many (top) results, this option allows more resource efficient searches |
async | boolean | Start new searches asynchronously or not (returns right away) or wait until timeout for search to run (default) |
dist | string | Maximum Anonymous Distance |
sdist | string | Maximum Scored Distance |
tdn | string | Terminal Down Bounds |
tup | string | Terminal Up Bounds |
rdn | string | Ring Down Bounds |
rup | string | Ring Up Bounds |
ldn | string | Linker Down Bounds |
lup | string | Linker Up Bounds |
maj | string | Major Transmutation Bounds (Aligned Atom Scores only) |
min | string | Minor Transmutation Bounds (Aligned Atom Scores only) |
sub | string | Substitution Bounds (Aligned Atom Scores only) |
hyb | string | Hybridisation Bounds (Aligned Atom Scores only) |
ms | string | Interpret a single SMILES query with multiple components as a multi-source (ms) search. |
/search/submit
Start a new SmallWorld search with topological distance bounded by the provided upper bounds.
Parameter | Type | Description |
---|---|---|
smi | array | Query SMILES/SMARTS strings (Required) |
db | string | Database name (Required) |
top | integer | Only collect this many (top) results, this option allows more resource efficient searches |
dist | string | Maxmium Anonymous Distance |
sdist | string | Maxmium Scored Distance |
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) |
maj | string | Major Transmutation Bounds (Aligned Atom Scores only) |
min | string | Minor Transmutation Bounds (Aligned Atom Scores only) |
sub | string | Substitution Bounds (Aligned Atom Scores only) |
hyb | string | Hybridisation Bounds (Aligned Atom Scores only) |
Examples
/search/view
- Search of similar entries to benzene in ZINC-All-22Q2-1.6B
curl "https://sw.docking.org/search/view?smi=c1ccccc1&db=ZINC-All-22Q2-1.6B"
- Search of similar entries to pyridine in ZINC-All-22Q2-1.6B. Display in TSV. Show results from 0 to 50
curl "https://sw.docking.org/search/view?smi=c1ccccc1&db=ZINC-All-22Q2-1.6B&fmt=tsv&start=0&length=50"
- Search of similar entries to either benzene or the chlorobenzene in ZINC-All-22Q2-1.6B. Display in TSV. Only show top 20 results.
curl "https://sw.docking.org/search/view?smi=c1ccccc1&smi=Clc1ccccc1&db=ZINC-All-22Q2-1.6B&fmt=tsv&length=30&top=20"
- Search of similar entries to either benzene or the chlorobenzene in ZINC-All-22Q2-1.6B. Tagging which molecule the similarity is closest to. Display in TSV. Display 30 results
curl "https://sw.docking.org/search/view?smi=c1ccccc1%20benzene&smi=Clc1ccccc1%20chlorobenzene&db=ZINC-All-22Q2-1.6B&fmt=tsv&length=30"