predict.py

"""
This files includes a predict function for the Tox21.
As an input it takes a list of SMILES and it outputs a nested dictionary with
SMILES and target names as keys.
"""

# ---------------------------------------------------------------------------------------
# Dependencies
from collections import defaultdict

import numpy as np

from src.model import Tox21XGBClassifier
from src.preprocess import create_descriptors

# ---------------------------------------------------------------------------------------


def predict(smiles_list: list[str]) -> dict[str, dict[str, float]]:
    """Applies the classifier to a list of SMILES strings. Returns prediction=0.0 for
    any molecule that could not be cleaned.

    Args:
        smiles_list (list[str]): list of SMILES strings

    Returns:
        dict: nested prediction dictionary, following {'<smiles>': {'<target>': <pred>}}
    """
    print(f"Received {len(smiles_list)} SMILES strings")
    # preprocessing pipeline
    features, mol_mask = create_descriptors(
        smiles_list,
    )
    print(f"Created {features.shape[1]} descriptors for the molecules.")
    print(f"{len(mol_mask) - sum(mol_mask)} molecules removed during cleaning. All predictions for these will be set to 0.0.")

    # setup model
    model = Tox21XGBClassifier(seed=42)
    model_dir = "assets/"
    model.load_model(model_dir)
    print(f"Loaded model and feature processors from {model_dir}")

    # make predictions
    predictions = defaultdict(dict)
    feat_indices = np.cumsum(mol_mask) - 1
    for target in model.tasks:
        feature_processors = model.feature_processors[target]
        task_features = feature_processors['selector'].transform(features)
        task_features = feature_processors['scaler'].transform(task_features)
        target_pred = model.predict(target, task_features)
        for smiles, is_clean, i in zip(smiles_list, mol_mask, feat_indices):
            predictions[smiles][target] = float(target_pred[i]) if is_clean else 0.0
    return predictions

if __name__ == "__main__":
    # simple test
    test_smiles = [
        "CCO",
        "CCN",
        "invalid_smiles",
    ]
    preds = predict(test_smiles)
    print(preds)