Interfaces (CLI)

QSARmil ships a click-based command-line interface, installed as the qsarmil command, with a single subcommand: train_predict.

qsarmil train_predict \
    --train-path train.csv \
    --test-path test.csv \
    --task-type regression \
    --output-folder ./results \
    --num-conf 10 \
    --hopt True \
    --verbose

Both --train-path and --test-path point to CSV files: the first column is SMILES, and for the training file the second column is the target property. --task-type is either regression or classification.

Options

  • --train-path (required) — training CSV; first column SMILES, second column target.

  • --test-path (required) — test CSV; first column SMILES.

  • --task-type (required) — regression or classification.

  • --output-folder — where model files (train.csv/val.csv/ test.csv) are written. Defaults to a timestamped folder if omitted.

  • --num-conf (default 10) — conformers generated per molecule.

  • --hopt (default False) — enable hyperparameter optimization for each estimator (see Hyperparameter optimization).

  • --num-cpu (default: all available CPUs) — threads used for conformer generation.

  • --accelerator (default "cpu") — cpu or gpu.

  • --random-seed (default 42).

  • --verbose — print progress output as the pipeline runs.

Predictions are written to test.csv inside the output folder.