[akutuva21]

💡 What: Replaced the inner list comprehensions used for membership tests in bionetgen/atomizer/writer/bnglWriter.py with precomputed sets (pMolecule_component_names and rMolecule_component_names).

🎯 Why: The previous implementation evaluated [y.name for y in rMolecule.components] (and vice versa) for every element in the outer list comprehension. This resulted in unnecessary $O(N \times M)$ complexity and redundant memory allocations. Precomputing a set changes the membership check to $O(1)$ and brings the overall complexity down to $O(N + M)$.

📊 Measured Improvement:
Using a custom benchmark simulating molecules with 100 components, the optimization yielded a massive improvement:

• Baseline: 0.8192 seconds (per 1000 runs)
• Optimized: 0.0205 seconds (per 1000 runs)
• Improvement: ~97.5% reduction in execution time
• Speedup: ~40x

Linting (black, flake8) and relevant test suite (tests/test_bng_atomizer.py) passed successfully.

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PR created automatically by Jules for task 3773139331906415621 started by @akutuva21

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