Legacy CHEESE API
Migration-only documentation for the legacy hosted API.
Legacy API
This section documents the legacy 39-route service. New integrations should use the CHEESE API v2 quickstart. Do not copy legacy GET query strings, job helpers, or UI-shaped response contracts into a new client.
These pages remain available during the migration/support window for existing integrations.
API Base URL
Legacy host: https://api.cheese.deepmedchem.com/. Current v2 host:
https://api.deepmedchem.com/api/v2.
Two API surfaces
Endpoint reference
All 39 legacy routes generated from the pinned legacy OpenAPI contract — requests, responses, and schemas. Replaces the former web /api Scalar page.
Public API
For registered users of CHEESE Search. Includes molecular search and ADMET property prediction.
On-Premise API
Advanced features: embedding computation, similarity matrices, visualization, and custom database indexing.
Authentication
API calls require an API key. To obtain one:
- Go to cheese.deepmedchem.com and sign in
- Click "Generate API Key" in the top right corner
- Copy the API key and include it in request headers
X-API-Key: your_api_key_hereGetting started (Python)
Prerequisites: pip install requests numpy rdkit
import requests
import json
MY_URL = "https://api.cheese.deepmedchem.com"
API_KEY = "your_api_key_here"
headers = {"X-API-Key": API_KEY, "accept": "application/json"}Search types reference
| Code | Name | Description |
|---|---|---|
morgan | 2D Morgan Fingerprint | Structural fingerprints (Morgan/ECFP) with Tanimoto similarity. Fast and reliable for structural analogs. |
espsim_shape | 3D Shape Similarity | Based on 3D surface overlap of the best aligned pair of randomly generated conformers. |
espsim_electrostatic | 3D Electrostatic Similarity | Best overlap of electrostatic potential (ESP) between aligned conformer pairs. Preserves protein-ligand binding properties. |
active_pairs | Activity-Based Similarity | Similarity learned from known active compound pairs. |
Available databases
ZINC15, ENAMINE-REAL, MCULE-FULL, MCULE-IN-STOCK, SYNPLE,
ENAMINE-CARBOXYLIC, EXPLORE-ENUMERATED, EXPLORE-DIVERSE, CHEMRIYA