Skip to content


CHEESE Inference

The CLI tool supports running CHEESE inference on your custom database. You can just run the command cheese inference and you can check the available options by running cheese inference --help

 Usage: -c inference [OPTIONS]                                                                                         
 Run CHEESE Inference for an input file.'                                                                              
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *  --input_file                                         TEXT  The input file in CSV format. Please provide a CSV    │
│                                                               file in the following format : 'SMILES,ID             │
│                                                               [default: None]                                       │
│                                                               [required]                                            │
│    --dest                                               TEXT  Destination folder where to save the results. Will be │
│                                                               inside your source folder                             │
│                                                               [default: output]                                     │
│    --index_type                                         TEXT  Index type : clustered, in_memory, auto               │
│                                                               [default: auto]                                       │
│    --gpu_devices                                        TEXT  List of GPU devices on which to run computation : e.g │
│                                                               '0,3,2'                                               │
│                                                               [default: 0]                                          │
│    --validate_smiles        --no-validate_smiles              Whether to validate the SMILES of the input file      │
│                                                               [default: no-validate_smiles]                         │
│    --canonicalize_smiles    --no-canonicalize_smiles          Whether to canonicalize the SMILES of the input file  │
│                                                               [default: no-canonicalize_smiles]                     │
│    --help                                                     Show this message and exit.                           │

The input file should contain lines of molecules in SMILES format and their IDs in the following format : SMILES,ID. Here is an example of an input CSV file.


Please note that the index type is defined automatically by default. If the input file exceeds 1GB in size, the script will automatically run the clustered inference, otherwise it will run the in_memory inference.


cheese inference --input_file '/data/mydb.csv' --dest /path/to/my_output --index_type in_memory

Multiple GPUs inference speed benchmark