workbench 0.8.172__py3-none-any.whl → 0.8.173__py3-none-any.whl

workbench/model_scripts/custom_models/chem_info/tautomerize.py

@@ -1,83 +0,0 @@
-# Model: tautomerization_processor
-#
-# Description: The tautomerization_processor model uses RDKit to perform tautomer enumeration
-#     and canonicalization of chemical compounds. Tautomerization is the chemical process where
-#     compounds can interconvert between structurally distinct forms, often affecting their
-#     chemical properties and reactivity. This model provides a robust approach to identifying
-#     and processing tautomers, crucial for improving molecular modeling and cheminformatics tasks
-#     like virtual screening, QSAR modeling, and property prediction.
-#
-import argparse
-import os
-import joblib
-from io import StringIO
-import pandas as pd
-import json
-
-# Local imports
-from local_utils import tautomerize_smiles
-
-
-# TRAINING SECTION
-#
-# This section (__main__) is where SageMaker will execute the job and save the model artifacts.
-#
-if __name__ == "__main__":
-    # Script arguments for input/output directories
-    parser = argparse.ArgumentParser()
-    parser.add_argument("--model-dir", type=str, default=os.environ.get("SM_MODEL_DIR", "/opt/ml/model"))
-    parser.add_argument("--train", type=str, default=os.environ.get("SM_CHANNEL_TRAIN", "/opt/ml/input/data/train"))
-    parser.add_argument(
-        "--output-data-dir", type=str, default=os.environ.get("SM_OUTPUT_DATA_DIR", "/opt/ml/output/data")
-    )
-    args = parser.parse_args()
-
-    # This model doesn't get trained; it's a feature processing 'model'
-
-    # Sagemaker expects a model artifact, so we'll save a placeholder
-    placeholder_model = {}
-    joblib.dump(placeholder_model, os.path.join(args.model_dir, "model.joblib"))
-
-
-# Model loading and prediction functions
-def model_fn(model_dir):
-    return joblib.load(os.path.join(model_dir, "model.joblib"))
-
-
-def input_fn(input_data, content_type):
-    """Parse input data and return a DataFrame."""
-    if not input_data:
-        raise ValueError("Empty input data is not supported!")
-
-    # Decode bytes to string if necessary
-    if isinstance(input_data, bytes):
-        input_data = input_data.decode("utf-8")
-
-    if "text/csv" in content_type:
-        return pd.read_csv(StringIO(input_data))
-    elif "application/json" in content_type:
-        return pd.DataFrame(json.loads(input_data))  # Assumes JSON array of records
-    else:
-        raise ValueError(f"{content_type} not supported!")
-
-
-def output_fn(output_df, accept_type):
-    """Supports both CSV and JSON output formats."""
-    use_explicit_na = False
-    if "text/csv" in accept_type:
-        if use_explicit_na:
-            csv_output = output_df.fillna("N/A").to_csv(index=False)  # CSV with N/A for missing values
-        else:
-            csv_output = output_df.to_csv(index=False)
-        return csv_output, "text/csv"
-    elif "application/json" in accept_type:
-        return output_df.to_json(orient="records"), "application/json"  # JSON array of records (NaNs -> null)
-    else:
-        raise RuntimeError(f"{accept_type} accept type is not supported by this script.")
-
-
-# Prediction function
-def predict_fn(df, model):
-    # Perform Tautomerization
-    df = tautomerize_smiles(df)
-    return df