rdkit

Error Handling

Always check for None when parsing molecules:

mol = Chem.MolFromSmiles(smiles)
if mol is None:
    print(f"Failed to parse: {smiles}")
    continue

Performance Optimization

Use binary formats for storage:

import pickle
Pickle molecules for fast loading
with open('molecules.pkl', 'wb') as f:
    pickle.dump(mols, f)
Load pickled molecules (much faster than reparsing)
with open('molecules.pkl', 'rb') as f:
    mols = pickle.load(f)

Use bulk operations:

# Calculate fingerprints for all molecules at once
fps = [AllChem.GetMorganFingerprintAsBitVect(mol, 2) for mol in mols]
Use bulk similarity calculations
similarities = DataStructs.BulkTanimotoSimilarity(fps[0], fps[1:])

Thread Safety

RDKit operations are generally thread-safe for:

Not thread-safe: MolSuppliers when accessed concurrently.

Memory Management

For large datasets:

# Use ForwardSDMolSupplier to avoid loading entire file
with open('large.sdf') as f:
    suppl = Chem.ForwardSDMolSupplier(f)
    for mol in suppl:
        # Process one molecule at a time
        pass
Use MultithreadedSDMolSupplier for parallel processing
suppl = Chem.MultithreadedSDMolSupplier('large.sdf', numWriterThreads=4)