On-Premise Endpoints
Embeddings, centroids, pairwise/matrix similarity, and visualization endpoints available exclusively with an on-premise CHEESE installation.
The following endpoints are available exclusively with an
on-premise CHEESE installation. Replace
YOUR_ONPREM_URL with your deployment's base URL.
GET /embeddings — Compute Embeddings
Compute CHEESE embeddings (256-dimensional vectors) for molecules.
params = {
"search_input": ["Fc1ccccc1", "Clc1ccccc1"],
"save_embs": False,
}
response = requests.get(MY_URL + "/embeddings",
params=params, headers=headers)
# Returns 256-dim vectors per molecule per search typeGET /centroid_embeddings — Centroid Embeddings
Retrieve cluster centroid embeddings for databases. Optionally include representative molecules for each cluster.
params = {
"db_name": "ZINC15",
"search_type": "espsim_shape",
"centroid_mols": False,
}
response = requests.get(MY_URL + "/centroid_embeddings",
params=params, headers=headers)GET /similarity — Pairwise Similarity
Compute pairwise similarity between two molecules using euclidean or cosine distance across all similarity metrics.
params = {
"smiles1": "Fc1ccccc1",
"smiles2": "Clc1ccccc1",
"similarity_metric": "all",
"distance_type": "cosine",
}
response = requests.get(MY_URL + "/similarity",
params=params, headers=headers)GET /similarity_matrix — Similarity Matrix
Compute a full pairwise similarity matrix for a list of molecules. Useful for clustering and network analysis.
params = {
"smiles": ["SMILES1", "SMILES2", "SMILES3"],
"similarity_metric": "espsim_shape",
"distance_type": "cosine",
}
response = requests.get(MY_URL + "/similarity_matrix",
params=params, headers=headers)GET /visualise — Visualization
Generate 2D coordinates for visualization using UMAP or PCA dimensionality reduction. Supports saving coordinates to disk.
params = {
"search_input": ["Fc1ccccc1", "Clc1ccccc1", "Brc1ccccc1"],
"search_type": "espsim_electrostatic",
"visualisation_method": "umap",
}
response = requests.get(MY_URL + "/visualise",
params=params, headers=headers)