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README.md
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## CHAFF processing
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Download bioassay datasets from PubChem using a single AID (Assay ID) and save them in CSV format.
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st2_run_download_pubchem.py
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Automate the download process for multiple AIDs by allowing you to input a list of AIDs, sequentially downloading each dataset.
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st3_extract_active_compounds.py
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Parse each dataset and filters rows labeled as "Active".
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st4_smiles_curation.py
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Purpose:
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Standardize and validate 'CanonicalSMILES' column. Apply sanitization, standardization, and fragment removal using RDKit and MolVS.
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st5_detergent_smiles_curation.py
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Special handling for AIDs 584, 585, 1476, 1478, 485294, 485341.
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Instead of a simple activity filter, these datasets are processed to remove overlapping compounds based on detergent-related assay pairs:
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## CHAFF processing
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# st1_download_pubchem.py
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Download bioassay datasets from PubChem using a single AID (Assay ID) and save them in CSV format.
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# st2_run_download_pubchem.py
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Automate the download process for multiple AIDs by allowing you to input a list of AIDs, sequentially downloading each dataset.
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# st3_extract_active_compounds.py
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Parse each dataset and filters rows labeled as "Active".
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# st4_smiles_curation.py
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Standardize and validate 'CanonicalSMILES' column. Apply sanitization, standardization, and fragment removal using RDKit and MolVS.
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# st5_detergent_smiles_curation.py
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Special handling for AIDs 584, 585, 1476, 1478, 485294, 485341.
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Instead of a simple activity filter, these datasets are processed to remove overlapping compounds based on detergent-related assay pairs:
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