[akutuva21]

💡 What:
Replaced highly expensive copy.deepcopy() calls with custom object .copy() methods and explicit list() constructions for primitive lists. Also used direct assignment for immutable string variables (like activeState).

🎯 Why:
Python's copy.deepcopy() is incredibly slow because it detects circular references, utilizes memoization maps, and performs dynamic dispatching for every object it traverses. Profiling Bionetgen indicates this is a frequent bottleneck when instantiating or modifying Atomizer structures in a tight loop.

📊 Impact:
Significantly reduces function overhead in hot loops throughout Species, Molecule, and Component methods. O(N) recursion calls and map lookups from deepcopy have been entirely eliminated.

🔬 Measurement:
Observe memory footprint and execution speed during large-scale network generation or parsing; time measurements of atomizer should show a measurable improvement. Tests pass via PYTHONPATH=python pytest tests/python -m "not needs_sbml".

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PR created automatically by Jules for task 12762357049537114973 started by @akutuva21

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