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Prediction

Prediction#

To load a trained model and make predictions, run:

chemprop predict --test-path <test_path> --model-path <model_path>

where <test_path> is the path to the data to test on, and <model_path> is the path to the trained model. By default, predictions will be saved to the same directory as the test path. If desired, a different directory can be specified by using --preds-path <path>

For example:

chemprop predict --test-path tests/data/smis.csv \
    --model-path tests/data/example_model_v2_regression_mol.ckpt \
    --preds-path preds.csv

Specifying Data to Parse#

By default, Chemprop will assume that the the 0th column in the data .csv will have the data. To use a separate column, specify:

  • --smiles-columns Text label of the column that includes the SMILES strings

If atom-mapped reaction SMILES are used, specify:

  • --reaction-columns Text labels of the columns that include the reaction SMILES

If --reaction-mode was specified during training, those same flags must be specified for the prediction step.

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